@article {pmid39699520,
year = {2024},
author = {Vargas, LC and Faria, LC and Pereira, LT and Signori, CN},
title = {Water masses drive the spatial and temporal distribution of marine Archaea in the northern Antarctic Peninsula.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {96},
number = {suppl 2},
pages = {e20240585},
doi = {10.1590/0001-3765202420240585},
pmid = {39699520},
issn = {1678-2690},
mesh = {Antarctic Regions ; *Archaea/classification/genetics/isolation & purification ; *Seawater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Seasons ; Spatio-Temporal Analysis ; },
abstract = {The Southern Ocean influences the planet's biogeochemical cycles. Marine microorganisms are important in this scenario, being the main biological agents in the cycling of many elements. The Archaea domain is widely distributed in the oceans, and its presence in Antarctica is acknowledged. In this context, this work aimed to analyze the diversity and distribution of archaea according to environmental parameters in the waters surrounding the north of the Antarctic Peninsula. For environmental characterization studies, surface and bottom data were used for the ten monitoring stations of expeditions that took place in the summer of 2014 and 2015. The sequencing of the 16S rRNA gene was performed on the Illumina HiSeq platform, using the SILVA v138 database. The results revealed the presence of three main water bodies: Antarctic Surface Water, Shelf Waters, and modified Circumpolar Deep Water. Deep waters had higher diversity than surface waters, and the dominant groups were Nitrososphaeria and MGII. In the study region, the main factor responsible for the differences in the ecosystems was the presence of distinct water masses and the stratification of the water column. We argue that it is essential to consider water mass dynamics to study the microbial landscape of the Southern Ocean.},
}

Antarctic Regions
*Archaea/classification/genetics/isolation & purification
*Seawater/microbiology
*RNA, Ribosomal, 16S/genetics
*Biodiversity
Seasons
Spatio-Temporal Analysis

@article {pmid39688758,
year = {2024},
author = {Řezanka, P and Řezanka, M and Kyselová, L and Řezanka, T},
title = {Characterization of Archaea membrane lipids in radioactive springs using shotgun lipidomics.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39688758},
issn = {1874-9356},
support = {MZE-RO1923//Ministerstvo Zemědělství/ ; RVO61388971//Mikrobiologický Ústav, Akademie Věd České Republiky/ ; },
abstract = {Lipids from microorganisms, and especially lipids from Archaea, are used as taxonomic markers. Unfortunately, knowledge is very limited due to the uncultivability of most Archaea, which greatly reduces the importance of the diversity of lipids and their ecological role. One possible solution is to use lipidomic analysis. Six radioactive sources were investigated, two of which are surface (Wettinquelle and Radonka) and four deep from the Svornost mine (Agricola, Behounek, C1, and Curie). A total of 15 core lipids and 82 intact polar lipids were identified from the membranes of microorganisms in six radioactive springs. Using shotgun lipidomics, typical Archaea lipids were identified in spring water, namely dialkyl glycerol tetraethers, archaeol, hydroxyarchaeol and dihydroxyarchaeol. Diverse groups of polar heads were formed in archaeal IPLs, whose polar heads are formed mainly by hexose, deoxyhexose, and phosphoglycerol. The analysis was performed using shotgun lipidomics and the structure of all molecular species was confirmed by tandem mass spectrometry. After acid hydrolysis, a mixture of polar compounds was obtained from the polar head. Further analysis by GC-MS confirmed that the carbohydrates were glucose and rhamnose. Analysis by HPLC-MS of diastereoisomers of 2-(polyhydroxyalkyl)-3-(O-tolylthiocarbamoyl)thiazolidine-4(R)-carboxylates revealed that both L-rhamnose and D-glucose are present in spring samples only in varying amounts. The glycoside composition depends on the type of spring, that is, Wettinquelle and Radonka springs are basically shallow groundwater, while the samples from the Svornost mine are deep groundwater and do not contain glycosides with rhamnose. This method enables quick screening for characteristic Archaea lipids, allowing decisions on whether to pursue further analyses, such as metagenomic analysis, to directly confirm the presence of Archaea.},
}

@article {pmid39682435,
year = {2024},
author = {Dou, X and Zhang, G and Tang, H and Chen, X and Chen, B and Mei, Y and Jiao, H and Ren, M},
title = {Carotenoids from Halophilic Archaea: A Novel Approach to Improve Egg Quality and Cecal Microbiota in Laying Hens.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/ani14233470},
pmid = {39682435},
issn = {2076-2615},
support = {TDZKCX202413//the President's Fund of Tarim University/ ; 31900007//the National Natural Science Foundation of China/ ; 202410757009//Innovation and Entrepreneurship Training Program for College Students of Tarim University/ ; },
abstract = {Carotenoids from different sources have different structures and functions, and their dietary components benefit the health of various organisms. The effects of halophilic Archaea-derived C50 carotenoids on poultry egg quality and gut microbiota remain largely unexplored. In this study, we isolated a carotenoid-secreting strain of Halalkalicoccus paucihalophilus, TRM89021, from the Pamir Plateau. We characterized the carotenoid pigments produced by this strain; the major components were bacterioruberin and its derivatives. The effects of these carotenoids on the egg quality and cecal microbiota composition of hens were investigated. Compared to the basal diet group (BDG), supplementation with carotenoids in the carotenoids-supplemented diet group (CDG) resulted in significantly lower a* and b* scores at week 5 and lower b* scores and Haugh units at week 2, while egg strength and weight were higher. CDG also showed increased yolk antioxidant capacity, higher glutathione peroxidase levels, and significantly lower catalase levels (p < 0.05). Plasma analysis revealed elevated total bilirubin and aspartate aminotransferase levels, along with reduced inorganic phosphorus levels in the CDG (p < 0.05). No significant differences in cecal microbiota diversity were observed between the groups at any taxonomic level. This result suggests that halophilic archaea-derived carotenoids have the potential to be used as natural feed supplements to improve egg quality. Our study provides a theoretical basis for applying archaea-derived carotenoids in poultry diets.},
}

@article {pmid39663550,
year = {2024},
author = {Saranya, S and Prathiviraj, R and Chellapandi, P},
title = {Evolutionary Transitions of DNA Replication Origins Between Archaea and Bacteria.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400527},
doi = {10.1002/jobm.202400527},
pmid = {39663550},
issn = {1521-4028},
support = {//This work was funded by Science and Engineering Research Board, Ministry of Science and Technology, Government of India, Grant/Award Number EEQ/2020/000095 and Ministry of Education, India, Rashtriya Uchchatar Shiksha Abhiyan, Grant/Award Number 12/BDU/RUSA/TRP/BS./ ; },
abstract = {DNA replication origins play a crucial role in cellular division and are evolutionarily conserved across domains. This study investigated the evolutionary transitions of replication origins between archaea and bacteria by analyzing 2733 bacterial and 257 archaeal genomes. Our findings revealed that certain methanogens and bacteria share phylogenetic proximity, suggesting evolutionary interactions across diverse ecological systems. Evolutionary transitions in replication origins may have occurred between gut methanogens and bacteria, haloarchaea (Halogeometricum borinquense DSM 11551 and Halovivax ruber XH-70), halobacteria, and sulfur-reducing archaea. Methanosarcina barkeri (M. barkeri), Methanosaeta thermophila, and Methanococcoides burtonii (M. burtonii) were closely related to respiratory tract bacteria in humans. Methanohalobium evestigatum (M. evestigatum) is strongly linked to the animal gut pathogen Mycoplasma putrefaciens (M. putrefaciens). Several thermophilic hydrogenotrophic methanogens clustered with oral and fish pathogens. Pyrococcus furiosus (P. furiosus) was evolutionarily related to the replication origin of plant pathogens. This study sheds light on the ecological drivers of DNA replication origin evolution and their role in microbial speciation and adaptation. Our findings highlight the influence of mutualistic and parasitic relationships on these evolutionary transitions. It could have significant implications in biotechnology and medicine, such as developing novel antimicrobial strategies and understanding host-pathogen dynamics.},
}

@article {pmid39657077,
year = {2024},
author = {Najjari, A and Elmnasri, K and Cherif, H and Burleigh, S and Guesmi, A and Mahjoubi, M and Linares-Pastén, JA and Cherif, A and Ouzari, HI},
title = {Metataxonomic analysis of halophilic archaea community in two geothermal oases in the southern Tunisian Sahara.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae106},
pmid = {39657077},
issn = {1574-6968},
abstract = {This study assesses halophilic archaea's phylogenetic diversity in southern Tunisia's geothermal water. In the arid southern regions, limited surface freshwater resources make geothermal waters a vital source for oases and greenhouse irrigation. Three samples, including water, sediment, and halite-soil crust, were collected downstream of two geothermal springs of the Ksar Ghilane (KGH) and Zaouet Al Aness (ZAN) oases, Tunisia. The samples were subjected to 16S rRNA gene sequencing using the Illumina Miseq sequencing approach. Several haloarchaea were identified in the geothermal springs. The average taxonomic composition revealed that 20 out of 33 genera were shared between the two geothermal sources, with uneven distribution, where the Halogranum genus was the most represented genus with an abundance of 18.9% and 11.58% for ZAW and KGH, respectively. Several unique site-specific genera were observed: Halonotius, Halopelagius, Natronorubrum, and Haloarcula in ZAN, and Haloprofundus, Halomarina, Halovivax, Haloplanus, Natrinema, Halobium, Natronoarchaeum, and Haloterrigena in the KGH pool. Most genus members are typically found in low-salinity ecosystems. These findings suggest that haloarchaea can disperse downstream from geothermal sources and may survive temperature and chemical fluctuations in the runoff.},
}

@article {pmid39611976,
year = {2024},
author = {Riyaz, Z and Khan, ST},
title = {Nitrogen fixation by methanogenic Archaea, literature review and DNA database-based analysis; significance in face of climate change.},
journal = {Archives of microbiology},
volume = {207},
number = {1},
pages = {6},
pmid = {39611976},
issn = {1432-072X},
mesh = {*Nitrogen Fixation/genetics ; *Archaea/genetics/metabolism/classification ; *Climate Change ; *Soil Microbiology ; Phylogeny ; Databases, Nucleic Acid ; Methane/metabolism ; DNA, Archaeal/genetics ; },
abstract = {Archaea represents a significant population of up to 10% in soil microbial communities. The role of Archaea in soil is often overlooked mainly due to its unculturability. Among the three domains of life biological nitrogen fixation (BNF) is mainly a trait of Eubacteria and some Archaea. Archaea mediated processes like BNF may become even more important in the face of global Climate change. Although there are reports on nitrogen fixation by Archaea, to best of our knowledge there is no comprehensive report on BNF by Archaea under environmental stresses typical to climate change. Here we report a survey of literature and DNA database to study N2-fixation among Archaea. A total of 37 Archaea belonging to Methanogens of the phylum Euryarchaeota within the class Methanococcus, Methanomicrobia Methanobacteria, and Methanotrophic ANME2 lineages either contain genes for BNF or are known to fix atmospheric N2. Archaea were found to have their nif genes arranged as clusters of 6-8 genes in a single operon. The genes code for commonly found Mo-nitrogenase while in some archaea the genes for alternative metal nitrogenases like vnf were also found. The nifHDK gene similarity matrices show that Archaea shared the highest similarity with the nifHDK gene of anaerobic Clostridium beijerinckii. Although there are various theories about the origin of N2-fixation in Archaea, the most acceptable is the origin of N2-fixation first in bacteria and its subsequent transfer to Archaea. Since Archaea can survive under extreme environmental conditions their role in BNF should be studied especially in soil under environmental stress.},
}

*Nitrogen Fixation/genetics
*Archaea/genetics/metabolism/classification
*Climate Change
*Soil Microbiology
Phylogeny
Databases, Nucleic Acid
Methane/metabolism
DNA, Archaeal/genetics

@article {pmid39604363,
year = {2024},
author = {Ma, J and Yi, G and Ye, M and MacGregor-Chatwin, C and Sheng, Y and Lu, Y and Li, M and Li, Q and Wang, D and Gilbert, RJC and Zhang, P},
title = {Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10304},
pmid = {39604363},
issn = {2041-1723},
support = {206422/Z/17/Z//Wellcome Trust (Wellcome)/ ; BB/S003339/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 101021133//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; U54 AI170791-7522//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21 CA280467/CA/NCI NIH HHS/United States ; },
mesh = {*Cryoelectron Microscopy/methods ; *Streptavidin/chemistry/metabolism ; *Thermococcus/metabolism ; Archaeal Proteins/metabolism/chemistry/ultrastructure ; DNA/metabolism/chemistry ; Minichromosome Maintenance Proteins/metabolism/chemistry ; Biotinylation ; Models, Molecular ; DNA, Archaeal/metabolism/genetics/chemistry ; Saccharomyces cerevisiae/metabolism ; Adenosine Triphosphate/metabolism/chemistry ; },
abstract = {The cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging proteins and complexes, especially those with low abundance or with preferential orientation, remains a major hurdle. We developed an affinity-grid method employing monodispersed single particle streptavidin on a lipid monolayer to enhance particle absorption on the grid surface and alleviate sample exposure to the air-water interface. Using this approach, we successfully enriched the Thermococcus kodakarensis mini-chromosome maintenance complex 3 (MCM3) on cryoEM grids through biotinylation and resolved its structure. We further utilized this affinity method to tether the biotin-tagged dsDNA to selectively enrich a stable MCM3-ATP-dsDNA complex for cryoEM structure determination. Intriguingly, both MCM3 apo and dsDNA bound structures exhibit left-handed open spiral conformations, distinct from other reported MCM structures. The large open gate is sufficient to accommodate a dsDNA which could potentially be melted. The value of mspSA affinity method was further demonstrated by mitigating the issue of preferential angular distribution of HIV-1 capsid protein hexamer and RNA polymerase II elongation complex from Saccharomyces cerevisiae.},
}

*Cryoelectron Microscopy/methods
*Streptavidin/chemistry/metabolism
*Thermococcus/metabolism
Archaeal Proteins/metabolism/chemistry/ultrastructure
DNA/metabolism/chemistry
Minichromosome Maintenance Proteins/metabolism/chemistry
Biotinylation
Models, Molecular
DNA, Archaeal/metabolism/genetics/chemistry
Saccharomyces cerevisiae/metabolism
Adenosine Triphosphate/metabolism/chemistry

@article {pmid39577734,
year = {2024},
author = {Di Giulio, M},
title = {The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes.},
journal = {Bio Systems},
volume = {247},
number = {},
pages = {105375},
doi = {10.1016/j.biosystems.2024.105375},
pmid = {39577734},
issn = {1872-8324},
abstract = {The length of the deepest branches of the tree of life would tend to support the hypothesis that the distance of the branch that separates the sequences of archaea from those of bacteria, i.e. the interdomain one, is longer than the intradomain ones, i.e. those that separate the sequences of archaea and those of bacteria within them. Why should interdomain distance be larger than intradomain distances? The fact that the rate of amino acid substitutions was slowed as the domains of life appeared would seem to imply an evolutionary transition. The slowdown in the speed of evolution that occurred during the formation of the two domains of life would be the consequence of the progenote- > cell evolutionary transition. Indeed, the evolutionary stage of the progenote being characterized by an accelerated tempo and mode of evolution might explain the considerable interdomain distance because the accumulation of many amino acid substitutions on this branch would indicate the progenote stage that is also characterized by a high rate of amino acid substitutions. Furthermore, the fact that intradomain distances are smaller than interdomain distances would corroborate the hypothesis of the achievement of cellularity at the appearance of the main phyletic lineages. Indeed, the cell stage, unlike the progenotic one, definitively establishes the relationship between the genotype and phenotype, lowering the rate of evolution. Therefore, the arguments presented lead to the conclusion that LUCA was a progenote.},
}

@article {pmid39572458,
year = {2024},
author = {Tamang, M and Sikorski, J and van Bommel, M and Piecha, M and Urich, T and Ruess, L and Huber, K and Neumann-Schaal, M and Pester, M},
title = {Succession of Bacteria and Archaea Within the Soil Micro-Food Web Shifts Soil Respiration Dynamics.},
journal = {Environmental microbiology},
volume = {26},
number = {11},
pages = {e70007},
pmid = {39572458},
issn = {1462-2920},
support = {HU3067/1-1//German Research Foundation (SPP 2322)/ ; NE2192/4-1//German Research Foundation (SPP 2322)/ ; PE2147/6-1//German Research Foundation (SPP 2322)/ ; RU 780/22-1//German Research Foundation (SPP 2322)/ ; UR198/7-1//German Research Foundation (SPP 2322)/ ; },
mesh = {*Soil Microbiology ; *Archaea/genetics/classification ; *Bacteria/classification/genetics ; *Soil/chemistry ; *Food Chain ; *Microbiota ; Animals ; *Zea mays/microbiology ; *RNA, Ribosomal, 16S/genetics ; Nematoda/microbiology ; },
abstract = {Bacterivorous nematodes are important grazers in the soil micro-food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by maize litter amendment and their combination over 32 days. Maize litter amendment significantly increased soil respiration, while A. buetschlii addition caused an earlier peak in soil respiration. Underlying bacterial and archaeal population dynamics separated into five major response types, differentiating in their temporal abundance maxima and minima. In-depth analysis of these population dynamics identified a broad imprint of A. buetschlii grazing on dominant bacterial (Acidobacteriota, Bacteroidota, Gemmatimonadota, Pseudomonadota) and archaeal (Nitrososphaerota) ASVs. Combined bottom-up control by maize litter and top-down control by A. buetschlii grazing caused a succession of soil microbiota, driven by population changes first in the Bacteroidota, then in the Pseudomonadota and finally in the Acidobacteriota and Nitrososphaerota. Our results are an essential step forward in understanding trophic modulation of soil microbiota and its feedback on soil respiration.},
}

*Soil Microbiology
*Archaea/genetics/classification
*Bacteria/classification/genetics
*Soil/chemistry
*Food Chain
*Microbiota
Animals
*Zea mays/microbiology
*RNA, Ribosomal, 16S/genetics
Nematoda/microbiology

@article {pmid39568122,
year = {2024},
author = {Matarredona, L and Zafrilla, B and Camacho, M and Bonete, MJ and Esclapez, J},
title = {Understanding the tolerance of halophilic archaea to stress landscapes.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70039},
doi = {10.1111/1758-2229.70039},
pmid = {39568122},
issn = {1758-2229},
support = {VIGROB-016//Universidad de Alicante/ ; CIAICO/2022/047//Generalitat Valenciana/ ; },
mesh = {*Stress, Physiological ; Salinity ; Salt Tolerance ; Sodium Chloride/metabolism ; Archaea/metabolism/drug effects ; },
abstract = {Haloarchaea, known for their resilience to environmental fluctuations, require a minimum salt concentration of 10% (w/v) for growth and can survive up to 35% (w/v) salinity. In biotechnology, these halophiles have diverse industrial applications. This study investigates the tolerance responses of nine haloarchaea: Haloferax mediterranei, Haloferax volcanii, Haloferax gibbonsii, Halorubrum californiense, Halorubrum litoreum, Natrinema pellirubrum, Natrinema altunense, Haloterrigena thermotolerans and Haloarcula sinaiiensis, under various stressful conditions. All these archaea demonstrated the ability to thrive in the presence of toxic metals such as chromium, nickel, cobalt and arsenic, and their tolerance to significantly elevated lithium concentrations in the medium was remarkable. Among the studied haloarchaea, Hfx. mediterranei exhibited superior resilience, particularly against lithium, with an impressive minimum inhibitory concentration (MIC) of up to 4 M LiCl, even replacing NaCl entirely. Haloferax species showed specificity for conditions with maximal growth rates, while Htg. thermotolerans and Nnm. altunense displayed high resilience without losing growth throughout the ranges, although these were generally low. ICP-MS results highlighted the impressive intracellular lithium accumulation in Nnm. pellirubrum, emphasizing its potential significance in bioremediation. This research highlights a new characteristic of haloarchaea, their tolerance to high lithium concentrations and the potential for new applications in extreme industrial processes and bioremediation.},
}

*Stress, Physiological
Salinity
Salt Tolerance
Sodium Chloride/metabolism
Archaea/metabolism/drug effects

@article {pmid39567663,
year = {2024},
author = {Nobu, MK},
title = {Engineering history with Asgard archaea of the kingdom Promethearchaeati.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39567663},
issn = {2058-5276},
}

@article {pmid39562414,
year = {2024},
author = {Kemp, JA and Schultz, J and Modolon, F and Ribeiro-Alves, M and Rosado, AS and Mafra, D},
title = {Is there a correlation between TMAO plasma levels and archaea in the gut of patients undergoing hemodialysis?.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {39562414},
issn = {1573-2584},
abstract = {PURPOSE: Patients with chronic kidney disease (CKD) present high plasma levels of trimethylamine N-oxide (TMAO), a uremic toxin produced by gut microbiota associated with atherogenesis. Experimental studies have shown that certain methanogenic archaea members use trimethylamine (TMA), the TMAO precursor in the human gut, to produce methane, suggesting a potential strategy to reduce TMAO levels in patients with CKD. Hence, this study aimed to evaluate the association of Archaea in the gut microbiota and TMAO plasma levels in patients with CKD undergoing hemodialysis.

METHODS: Twenty-five patients were enrolled in the study (15 women, 53 (18) years, BMI, 25.8 (6.75) kg/m[2]). TMAO plasma levels were evaluated using the HPLC-EM/EM method. Fecal DNA was extracted using a commercial kit. Subsequently, we sequenced the V4 region of the 16S rRNA gene to characterize the microbial composition. NCT04600258 was retrospectively registered in September 2022.

RESULTS: According to the reference values in the European Uremic Toxins Work Group (EUTox) database, the patients exhibited high TMAO plasma levels, as expected. The most abundant Archaea members were assigned to the Euryarchaeota phylum, the Methanobacteriaceae family, and the genus Methanobrevibacter. A significant negative correlation between TMAO and Methanobrevibacter was observed.

CONCLUSIONS: To our knowledge, this study represents the first investigation into the correlation between TMAO levels and the prevalence of Archaea in patients with CKD. Our findings support the archaebiotic hypothesis, suggesting that specific members of the archaea community could play a crucial role in reducing TMA production in the human gut, potentially decreasing TMAO synthesis in CKD patients.},
}

@article {pmid39560730,
year = {2024},
author = {Liang, Y and Yan, Y and Shi, L and Wang, M and Yuan, X and Wang, S and Ye, L and Yan, Z},
title = {Molecular Basis of Thioredoxin-Dependent Arsenic Transformation in Methanogenic Archaea.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c06611},
pmid = {39560730},
issn = {1520-5851},
abstract = {Methanogenic archaea are known to play a crucial role in the biogeochemical cycling of arsenic (As); however, the molecular basis of As transformation mediated by methanogenic archaea remains poorly understood. Herein, the characterization of the redox transformation and methylation of As by Methanosarcina acetivorans, a model methanogenic archaeon, is reported. M. acetivorans was demonstrated to mediate As(V) reduction via a cytoplasmic As reductase (ArsC) in the exponential phase of methanogenic growth and to methylate As(III) via a cytoplasmic As(III) methyltransferase (ArsM) in the stationary phase. Characterization of the ArsC-catalyzed As(V) reduction and the ArsM-catalyzed As(III) methylation showed that a thioredoxin (Trx) encoded by MA4683 was preferentially utilized as a physiological electron donor for ArsC and ArsM, providing a redox link between methanogenesis and As transformation. The structures of ArsC and ArsM complexed with Trx were modeled using AlphaFold-Multimer. Site-directed mutagenesis of key cysteine residues at the interaction sites of the complexes indicated that the archaeal ArsC and ArsM employ evolutionarily distinct disulfide bonds for interacting with Trx compared to those used by bacterial ArsC or eukaryotic ArsM. The findings of this study present a major advance in our current understanding of the physiological roles and underlying mechanism of As transformation in methanogenic archaea.},
}

@article {pmid39545734,
year = {2024},
author = {Xu, T and Ni, Y and Li, H and Wu, S and Yan, S and Chen, L and Yu, Y and Wang, Y},
title = {Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0049224},
doi = {10.1128/spectrum.00492-24},
pmid = {39545734},
issn = {2165-0497},
abstract = {Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.},
}

@article {pmid39544964,
year = {2024},
author = {Abiola, C and Gwak, JH and Lee, UJ and Awala, SI and Jung, MY and Park, W and Rhee, SK},
title = {Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae129},
pmid = {39544964},
issn = {2730-6151},
abstract = {Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.},
}

@article {pmid39541851,
year = {2024},
author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J},
title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122773},
doi = {10.1016/j.watres.2024.122773},
pmid = {39541851},
issn = {1879-2448},
abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.},
}

@article {pmid39514410,
year = {2024},
author = {Dodsworth, JA and Prakash, O},
title = {International Committee on Systematics of Prokaryotes: subcommittee on the taxonomy of methanogenic archaea. Minutes of the closed, online meeting held 06 September 2023.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006569},
pmid = {39514410},
issn = {1466-5034},
}

@article {pmid39511174,
year = {2024},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9628},
pmid = {39511174},
issn = {2041-1723},
support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; },
abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.},
}

*Oxidation-Reduction
Anaerobiosis
*Archaea/metabolism/genetics
*Butanes/metabolism
*Carbon Dioxide/metabolism
Oxidoreductases/metabolism/genetics
Kinetics
Alkanes/metabolism
Thermodynamics

@article {pmid39530672,
year = {2024},
author = {Lee, U-J and Gwak, J-H and Choi, S and Jung, M-Y and Lee, TK and Ryu, H and Imisi Awala, S and Wanek, W and Wagner, M and Quan, Z-X and Rhee, S-K},
title = {"Ca. Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0082124},
doi = {10.1128/msphere.00821-24},
pmid = {39530672},
issn = {2379-5042},
abstract = {UNLABELLED: Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper (Capsicum anuum L.) and ginseng plants (Panax ginseng C.A. Mey.) compared to bulk soil not penetrated by roots. While the abundance of total AOA decreased in the rhizosphere soils, AOA related to "Candidatus Nitrosocosmicus," which harbor gene encoding manganese catalase (MnKat) in contrast to most other AOA, dominated the AOA community in the rhizosphere soils. For both plant species, the ratio of copy numbers of the AOA MnKat gene to the amoA gene (encoding the ammonia monooxygenase subunit A) was significantly higher in the rhizospheres than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. Due to their abundance, "Ca. Nitrosocosmicus" members can be considered important players mediating the nitrification process in rhizospheres. The dominance of this MnKat-containing AOA in rhizospheres of agriculturally important plants hints at a previously overlooked AOA-plant interaction.

IMPORTANCE: Ammonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the "Ca. Nitrosocosmicus" clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that "Ca. Nitrosocosmicus" may be an important clade of AOA with potential AOA-plant interaction.},
}

@article {pmid39529672,
year = {2024},
author = {Hernández-Magaña, E and Kraft, B},
title = {Corrigendum: Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1506979},
doi = {10.3389/fmicb.2024.1506979},
pmid = {39529672},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1410251.].},
}

@article {pmid39499858,
year = {2024},
author = {Takamiya, H and Kouduka, M and Kato, S and Suga, H and Oura, M and Yokoyama, T and Suzuki, M and Mori, M and Kanai, A and Suzuki, Y},
title = {Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae207},
pmid = {39499858},
issn = {1751-7370},
mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/metabolism/classification/isolation & purification ; *Genome, Archaeal ; Phylogeny ; Metagenomics ; Proteomics ; Ecosystem ; },
abstract = {Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.},
}

*Hydrothermal Vents/microbiology
*Archaea/genetics/metabolism/classification/isolation & purification
*Genome, Archaeal
Phylogeny
Metagenomics
Proteomics
Ecosystem

@article {pmid39499655,
year = {2024},
author = {Medvedeva, S and Borrel, G and Gribaldo, S},
title = {Sheaths are diverse and abundant cell surface layers in archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae225},
pmid = {39499655},
issn = {1751-7370},
abstract = {Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings. Here, we conducted a comprehensive survey of sheath-forming proteins (SH proteins) across archaeal genomes. Structural modeling reveals a rich diversity of SH proteins, indicating the presence of a sheath in members of the TACK superphylum (Thermoprotei), as well as in the methanotrophic ANME-1. SH proteins are present in up to 40 copies per genome and display diverse domain arrangements suggesting multifunctional roles within the sheath, and potential involvement in cell-cell interaction with syntrophic partners. We uncover a complex evolutionary dynamic, indicating active exchange of SH proteins in archaeal communities. We find that viruses infecting sheathed archaea encode a diversity of SH-like proteins and we use them as markers to identify 580 vOTUs potentially associated with sheathed archaea. Structural modeling suggests that viral SH proteins can form complexes with the host SH proteins. We propose a previously unreported egress strategy where the expression of viral SH-like proteins may disrupt the integrity of the host sheath and facilitate viral exit during lysis. Together, our results significantly expand knowledge of the diversity and evolution of the archaeal sheath, which has been largely understudied but might have an important role in shaping microbial communities.},
}

@article {pmid39495356,
year = {2024},
author = {Ma, X and Hu, Y and Hou, J and Zhou, YG and Cui, HL},
title = {Genome-Based Classification of 'Haloarcula aidinensis' and Description of Three Novel Halophilic Archaea Isolated from an Inland Saline Lake, Coastal Saline Soil, and a Marine Solar Saltern.},
journal = {Current microbiology},
volume = {81},
number = {12},
pages = {442},
pmid = {39495356},
issn = {1432-0991},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Haloarcula/genetics/classification ; *Genome, Archaeal ; China ; *Lakes/microbiology ; *Soil Microbiology ; DNA, Archaeal/genetics/chemistry ; RNA, Ribosomal, 16S/genetics ; Phospholipids/analysis ; Sequence Analysis, DNA ; },
abstract = {'Haloarcula aidinensis' was described by a pioneer Chinese scientist focused on halophilic archaea thirty years ago, and the type strain of 'Haloarcula aidinensis' was recently classified based on phylogenetic, phylogenomic, and comparative genomic analyses. Other three novel halophilic archaeal strains, CK38[T], DT43[T], and SYNS111[T], isolated from diverse saline environments in China, were simultaneously subjected to polyphasic classification. 'Haloarcula aidinensis' A5 was found to be related to Haloarcula amylolytica, while strains CK38[T], DT43[T], and SYNS111[T] represented three novel species of Haloarcula based on phylogenetic, phylogenomic, and comparative genomic analyses. These strains can be distinguished from other species within the genus Haloarcula based on multiple phenotypic characteristics. The major phospholipids, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate can be detected in these strains, while the glycolipid profiles of these strains are diverse. Strains A5 and DT43[T] contained glucosyl mannosyl glucosyl diether and a diglycosyl diether, while other strains CK38[T] and SYNS111[T] had sulfated mannosyl glucosyl diether and mannosyl glucosyl diether. Thus, strain A5 should be a reference strain of Har. amylolytica and three novel species of Haloarcula, Haloarcula sediminis sp. nov., Haloarcula brevis sp. nov., and Haloarcula regularis sp. nov. are proposed to accommodate strains CK38[T] (= CGMCC 1.62732[T] = JCM 36675[T]), DT43[T] (= CGMCC 1.18924[T] = JCM 36146[T]), and SYNS111[T] (= CGMCC 1.62601[T] = JCM 36149[T]).},
}

*Phylogeny
*Haloarcula/genetics/classification
*Genome, Archaeal
China
*Lakes/microbiology
*Soil Microbiology
DNA, Archaeal/genetics/chemistry
RNA, Ribosomal, 16S/genetics
Phospholipids/analysis
Sequence Analysis, DNA

@article {pmid39490771,
year = {2024},
author = {Li, T and Coker, OO and Sun, Y and Li, S and Liu, C and Lin, Y and Wong, SH and Miao, Y and Sung, JJ and Yu, J},
title = {Multi-cohort analysis reveals altered archaea in colorectal cancer fecal samples across populations.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2024.10.023},
pmid = {39490771},
issn = {1528-0012},
abstract = {BACKGROUND AND AIM: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts from 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls (HC)). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria and methanogenic functions were analyzed. Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HC, adenoma patients to CRC patients with Methanobacteriota phylum enriched while order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, while 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in CRC patients across multiple cohorts. Among them, M. stadmanae, Methanobrevibacter_A sp900314695 and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in CRC patients. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating CRC patients from healthy individuals with AUC ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, adenoma patients and CRC patients. Archaeal biomarkers, combined with bacterial features, have potential as non-invasive diagnostic biomarkers for CRC.},
}

@article {pmid39486247,
year = {2024},
author = {Ma, JY and Jiang, YQ and Liu, XY and Sun, XD and Jia, YN and Wang, Y and Tan, MM and Duan, JL and Yuan, XZ},
title = {Amplified selenite toxicity in methanogenic archaea mediated by cysteine.},
journal = {Ecotoxicology and environmental safety},
volume = {287},
number = {},
pages = {117263},
doi = {10.1016/j.ecoenv.2024.117263},
pmid = {39486247},
issn = {1090-2414},
abstract = {The challenge of understanding the interaction between trace elements and microbial life is critical for assessing environmental and ecological impacts. Nevertheless, cysteine (Cys), a low molecular weight thiol substance prevalent in the ecosystem, is able to influence the fate of certain trace elements, which increases the complexity of the interaction between trace elements and microorganisms. Therefore, we chose Cys, selenite and the model methanogenic archaeon Methanosarcina acetivorans C2A as research targets, and comprehensively explored the intricate role of Cys in modulating the biological effects of selenite on M. acetivorans C2A in terms of population growth, methane production and oxidative stress. Our results demonstrate that Cys significantly exacerbates the inhibitory effects of selenite on growth and methane production in M. acetivorans C2A. This increased toxicity is linked to heightened membrane permeability and oxidative stress, with a marked upregulation in reactive oxygen species and changes in NADPH levels. Transcriptomic analysis reveals alterations in genes associated with transmembrane transport and methanogenesis. Intriguingly, we also observed a potential interaction between selenite and phosphate transmembrane transporters, suggesting a novel pathway for selenite entry into cells. These findings highlight the complex interplay between trace elements and microbial processes, with significant implications for understanding environmental risks and developing remediation strategies.},
}

@article {pmid39466404,
year = {2024},
author = {Ortjohann, M and Schönheit, P},
title = {Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {48},
pmid = {39466404},
issn = {1433-4909},
mesh = {*Haloarcula/metabolism/genetics ; *Sorbitol/metabolism ; *Mannitol/metabolism ; Archaeal Proteins/metabolism/genetics ; Fructokinases/metabolism/genetics ; Fructose/metabolism ; ATP-Binding Cassette Transporters/metabolism/genetics ; },
abstract = {The halophilic archaeon Haloarcula hispanica utilizes the sugar alcohols mannitol and sorbitol as carbon and energy sources. Genes, enzymes, and transcriptional regulators involved in uptake and degradation of these sugar alcohols were identified by growth experiments with deletion mutants and enzyme characterization. It is shown that both mannitol and sorbitol are taken up via a single ABC transporter of the CUT1 transporter family. Then, mannitol and sorbitol are oxidized to fructose by two distinct dehydrogenases. Fructose is further phosphorylated to fructose-1-phosphate by a haloarchaeal ketohexokinase, providing the first evidence for a physiological function of ketohexokinase in prokaryotes. Finally, fructose-1-phosphate is phosphorylated via fructose-1-phosphate kinase to fructose-1,6-bisphosphate, which is cleaved to triosephosphates by a Class I fructose-1,6-bisphosphate aldolase. Two distinct transcriptional regulators, acting as activators, have been identified: an IclR-like regulator involved in activating genes for sugar alcohol uptake and oxidation to fructose, and a GfcR-like regulator that likely activates genes involved in the degradation of fructose to pyruvate. This is the first comprehensive analysis of a sugar alcohol degradation pathway in Archaea.},
}

*Haloarcula/metabolism/genetics
*Sorbitol/metabolism
*Mannitol/metabolism
Archaeal Proteins/metabolism/genetics
Fructokinases/metabolism/genetics
Fructose/metabolism
ATP-Binding Cassette Transporters/metabolism/genetics

@article {pmid39455151,
year = {2024},
author = {Pan, YC and Zhao, JW and Niu, HJ and Huang, YL and Wang, Y and Zhang, XX},
title = {[Effects of Vegetable Planting Ages on Community Structure of Ammonia-oxidizing Archaea and Ammonia-oxidizing Bacteria in Greenhouse Vegetable Fields].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {10},
pages = {6077-6085},
doi = {10.13227/j.hjkx.202310135},
pmid = {39455151},
issn = {0250-3301},
mesh = {*Archaea/metabolism/growth & development/classification ; *Ammonia/metabolism ; *Soil Microbiology ; *Bacteria/classification/growth & development/metabolism ; *Oxidation-Reduction ; *Vegetables/growth & development ; Soil/chemistry ; China ; Nitrous Oxide/metabolism/analysis ; Time Factors ; Agriculture/methods ; Nitrogen/metabolism ; },
abstract = {The ammonia oxidation process driven by microorganisms is a dominant source for nitrous oxide （N2O） emissions. Here, we examined the influence of greenhouse vegetable planting ages on soil ammonia-oxidizing archaea （AOA） and ammonia-oxidizing bacteria （AOB）, which is of great significance for assessing the soil quality status and greenhouse gas transformations. A field study was conducted at different times （1, 5, 10, and 20 a） in greenhouse vegetable soils of Gaoyi, Hebei Province. Chemical analysis and Illumina NovaSeq high-throughput sequencing were used to analyze the soil physicochemical properties and community structures and diversity of AOA and AOB. The variation in AOA and AOB communities and the driving factors in greenhouse soils at different ages were also investigated. The results showed that the contents of total nitrogen, organic matter, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium first increased and then decreased with the prolongation of growth. The contents of nitrate nitrogen, ammonium nitrogen, and electrical conductivity first decreased and then increased with the prolongation of growth. The pH value of soils decreased with the prolongation of growth. The abundance and diversity index of AOA and AOB first decreased and then increased with the prolongation of growth. Nitrososphaeria, unclassified Thaumarchaeota, and Candidatus Nitrosocaldus were the dominant species of AOA, while Betaproteobacteria and Nitrosospira were the dominant species of AOB. The composition of the soil AOA community varied greatly compared to that of AOB with the prolongation of growth. Correlation analysis showed that the changes in soil nutrient factors had a significant correlation with AOA and AOB communities. Redundancy analysis indicated that ammonium nitrogen, alkali-hydrolyzable nitrogen, and nitrate nitrogen were key factors of AOA communities, while electrical conductivity, available potassium, and nitrate nitrogen were key factors for AOB. In summary, long-term planting of greenhouse vegetables significantly affected the abundance and composition of soil AOA and AOB communities. Our results provide a theoretical basis for further studies on the greenhouse gas transformation and microbial mechanisms of the nitrogen cycle in greenhouse soils.},
}

*Archaea/metabolism/growth & development/classification
*Ammonia/metabolism
*Soil Microbiology
*Bacteria/classification/growth & development/metabolism
*Oxidation-Reduction
*Vegetables/growth & development
Soil/chemistry
China
Nitrous Oxide/metabolism/analysis
Time Factors
Agriculture/methods
Nitrogen/metabolism

@article {pmid39437693,
year = {2024},
author = {Zhang, L and Yang, J and Ge, AH and Xie, W and Yao, R and Wang, X},
title = {Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122977},
doi = {10.1016/j.jenvman.2024.122977},
pmid = {39437693},
issn = {1095-8630},
abstract = {Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km[2]. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.},
}

@article {pmid39436425,
year = {2024},
author = {Dong, XY and Mao, YL and Zhang, QK and Zhu, LR and Hou, J and Cui, HL},
title = {Genome‑based classification of the family Natrialbaceae and description of four novel halophilic archaea from three saline lakes and a saline-alkaline land.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {47},
pmid = {39436425},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Genome, Archaeal ; *Lakes/microbiology ; Halobacteriales/genetics/classification ; Salt Tolerance ; Salinity ; },
abstract = {The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amino acid identity (AAI) (≤ 76%) proposed to differentiate genera within the family Natrialbaceae, Halobiforma, and Natronoglomus should be merged with Natronobacterium and Halomontanus, respectively. Beyond these, four novel halophilic archaeal strains, CCL63[T], AD-5[T], CG52[T], and KLK7[T], isolated from three saline lakes and a saline-alkaline land in China, were simultaneously subjected to polyphasic classification. The phenotypic, phylogenetic, phylogenomic, and comparative genomic analyses indicated that strain CCL63[T] (= CGMCC 1.18663[T] = JCM 35096[T]) represents a novel genus of the family Natrialbaceae, strains AD-5[T] (= CGMCC 1.13783[T] = JCM 33734[T]) and CG52[T] (= CGMCC 1.17139[T] = JCM 34160[T]) represent two novel species of the genus Natronococcus, and strain KLK7[T] (= MCCC 4K00128[T] = KCTC 4307[T]) represents a novel species of Haloterrigena. Halovalidus salilacus gen. nov., sp. nov., Natronococcus wangiae sp. nov., Natronococcus zhouii sp. nov., and Haloterrigena salinisoli sp. nov. are further proposed based on these type strains accordingly.},
}

*Phylogeny
*Genome, Archaeal
*Lakes/microbiology
Halobacteriales/genetics/classification
Salt Tolerance
Salinity

@article {pmid39433727,
year = {2024},
author = {Lemaire, ON and Wegener, G and Wagner, T},
title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9065},
pmid = {39433727},
issn = {2041-1723},
support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs & derivatives ; },
abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.},
}

*Oxidation-Reduction
*Carbon Dioxide/metabolism
*Ethane/metabolism/chemistry
Archaea/metabolism/genetics
Aldehyde Oxidoreductases/metabolism/genetics/chemistry
Multienzyme Complexes/metabolism/genetics/chemistry
Crystallography, X-Ray
Archaeal Proteins/metabolism/genetics/chemistry
Anaerobiosis
Ferredoxins/metabolism
Riboflavin/analogs & derivatives

@article {pmid39413712,
year = {2024},
author = {Wang, M and Peñuelas, J and Sardans, J and Zeng, Q and Song, Z and Zhou, J and Xu, X and Zhou, X and Fang, Y and Vancov, T and Wang, W},
title = {Conversion of coastal marsh to aquaculture ponds decreased the potential of methane production by altering soil chemical properties and methanogenic archaea community structure.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122608},
doi = {10.1016/j.watres.2024.122608},
pmid = {39413712},
issn = {1879-2448},
abstract = {Coastal wetlands are among the most productive and dynamic ecosystems globally, contributing significantly to atmospheric methane (CH4) emissions. The widespread conversion of these wetlands into aquaculture ponds degrades these ecosystems, yet its effects on CH4 production and associated microbial mechanisms are not well understood. This study aimed to assess the impact of land conversion on CH4 production potential, total and active soil organic C (SOC) content, and microbial communities. We conducted a comparative study on three brackish marshes and adjacent aquaculture ponds in southeastern China. Compared to costal marshes, aquaculture ponds exhibited significantly (P < 0.05) lower CH4 production potential (0.05 vs. 0.02 μg kg[-1] h[-1]), SOC (17.64 vs. 6.97 g kg[-1]), total nitrogen (TN) content (1.62 vs. 1.24 g kg[-1]) and carbon/nitrogen (C/N) ratio (10.85 vs. 5.66). CH4 production potential in aquaculture ponds was influenced by both microbial and abiotic factors. Specifically, the relative abundance of Methanosarcina slightly decreased in aquaculture ponds, while the potential for CH4 production declined with lower SOC contents and C/N ratio. Overall, our findings demonstrate that converting natural coastal marshes into aquaculture ponds reduces CH4 production by altering key soil properties and the structure and diversity of methanogenic archaea communities. These results provide empirical evidence to enhance global carbon models, improving predictions of carbon feedback from wetland land conversion in the context of climate change.},
}

@article {pmid39406503,
year = {2024},
author = {Valentin-Alvarado, LE and Shi, LD and Appler, KE and Crits-Christoph, A and De Anda, V and Adler, BA and Cui, ML and Ly, L and Leão, P and Roberts, RJ and Sachdeva, R and Baker, BJ and Savage, DF and Banfield, JF},
title = {Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279480.124},
pmid = {39406503},
issn = {1549-5469},
abstract = {Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.},
}

@article {pmid39404452,
year = {2024},
author = {Villa, EA and Escalante-Semerena, JC},
title = {Corrinoid salvaging and cobamide remodeling in bacteria and archaea.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0028624},
doi = {10.1128/jb.00286-24},
pmid = {39404452},
issn = {1098-5530},
abstract = {Cobamides (Cbas) are cobalt-containing cyclic tetrapyrroles used by cells from all domains of life as co-catalyst of diverse reactions. There are several structural features that distinguish Cbas from one another. The most relevant of those features discussed in this review is the lower ligand, which is the nucleobase of a ribotide located in the lower face of the cyclic tetrapyrrole ring. The above-mentioned ribotide is known as the nucleotide loop, which is attached to the ring by a short linker. In Cbas, the nucleobase of the ribotide can be benzimidazole or derivatives of it, purine or derivatives of it, or phenolic compounds. Given the importance of Cbas in prokaryotic metabolism, it is not surprising that prokaryotes have evolved enzymes that cleave part or the entire nucleotide loop. This function is advantageous when Cbas contain nucleobases that somehow interfere with the function of Cba-dependent enzymes in the organism. After cleavage, Cbas are rebuilt via the nucleotide loop assembly (NLA) pathway, which includes enzymes that activate the nucleobase and the ring intermediate, followed by condensation of activated intermediates and a final dephosphorylation reaction. This exchange of nucleobases is known as Cba remodeling. The NLA pathway is used to salvage Cba precursors from the environment.},
}

@article {pmid39402493,
year = {2024},
author = {Bobbo, T and Biscarini, F and Yaddehige, SK and Alberghini, L and Rigoni, D and Bianchi, N and Taccioli, C},
title = {Machine learning classification of archaea and bacteria identifies novel predictive genomic features.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {955},
pmid = {39402493},
issn = {1471-2164},
mesh = {*Archaea/genetics/classification ; *Machine Learning ; *Bacteria/genetics/classification ; *Genomics/methods ; *Genome, Archaeal ; Genome, Bacterial ; RNA, Transfer/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Archaea and Bacteria are distinct domains of life that are adapted to a variety of ecological niches. Several genome-based methods have been developed for their accurate classification, yet many aspects of the specific genomic features that determine these differences are not fully understood. In this study, we used publicly available whole-genome sequences from bacteria (N = 2546) and archaea (N = 109). From these, a set of genomic features (nucleotide frequencies and proportions, coding sequences (CDS), non-coding, ribosomal and transfer RNA genes (ncRNA, rRNA, tRNA), Chargaff's, topological entropy and Shannon's entropy scores) was extracted and used as input data to develop machine learning models for the classification of archaea and bacteria.

RESULTS: The classification accuracy ranged from 0.993 (Random Forest) to 0.998 (Neural Networks). Over the four models, only 11 examples were misclassified, especially those belonging to the minority class (Archaea). From variable importance, tRNA topological and Shannon's entropy, nucleotide frequencies in tRNA, rRNA and ncRNA, CDS, tRNA and rRNA Chargaff's scores have emerged as the top discriminating factors. In particular, tRNA entropy (both topological and Shannon's) was the most important genomic feature for classification, pointing at the complex interactions between the genetic code, tRNAs and the translational machinery.

CONCLUSIONS: tRNA, rRNA and ncRNA genes emerged as the key genomic elements that underpin the classification of archaea and bacteria. In particular, higher nucleotide diversity was found in tRNA from bacteria compared to archaea. The analysis of the few classification errors reflects the complex phylogenetic relationships between bacteria, archaea and eukaryotes.},
}

*Archaea/genetics/classification
*Machine Learning
*Bacteria/genetics/classification
*Genomics/methods
*Genome, Archaeal
Genome, Bacterial
RNA, Transfer/genetics
Phylogeny

@article {pmid39390113,
year = {2024},
author = {Nagar, DN and Mani, K and Braganca, JM},
title = {Author Correction: Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcularubripromontorii BS2, Haloferaxlucentense BBK2 and Halogeometricumborinquense E3 isolated from the solar salterns of India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23750},
doi = {10.1038/s41598-024-74079-z},
pmid = {39390113},
issn = {2045-2322},
}

@article {pmid39383165,
year = {2024},
author = {, },
title = {Correction: A Versatile Medium for Cultivating Methanogenic Archaea.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0312093},
pmid = {39383165},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0061563.].},
}

@article {pmid39363002,
year = {2024},
author = {Mühling, L and Baur, T and Molitor, B},
title = {Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39363002},
issn = {0724-6145},
abstract = {Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.},
}

@article {pmid39360821,
year = {2024},
author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y},
title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0216924},
doi = {10.1128/mbio.02169-24},
pmid = {39360821},
issn = {2150-7511},
abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.

IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.},
}

@article {pmid39359677,
year = {2024},
author = {Pereira, O and Qin, W and Galand, PE and Debroas, D and Lami, R and Hochart, C and Zhou, Y and Zhou, J and Zhang, C},
title = {Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.},
journal = {mLife},
volume = {3},
number = {3},
pages = {417-429},
pmid = {39359677},
issn = {2770-100X},
abstract = {Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.},
}

@article {pmid39348174,
year = {2024},
author = {Lehtovirta-Morley, LE and Ge, C and Ross, J and Yao, H and Hazard, C and Gubry-Rangin, C and Prosser, JI and Nicol, GW},
title = {Nitrosotalea devaniterrae gen. nov., sp. nov. and Nitrosotalea sinensis sp. nov., two acidophilic ammonia oxidising archaea isolated from acidic soil, and proposal of the new order Nitrosotaleales ord. nov. within the class Nitrososphaeria of the phylum Nitrososphaerota.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006387},
pmid = {39348174},
issn = {1466-5034},
mesh = {*Soil Microbiology ; *Phylogeny ; *Base Composition ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ammonia/metabolism ; *DNA, Archaeal/genetics ; *Oxidation-Reduction ; China ; Archaea/classification/genetics/isolation & purification ; Hydrogen-Ion Concentration ; Nitrites/metabolism ; Chemoautotrophic Growth ; },
abstract = {Two obligately acidophilic, mesophilic and aerobic soil ammonia-oxidising archaea were isolated from a pH 4.5 arable sandy loam (UK) and pH 4.7 acidic sulphate paddy soil (PR China) and designated strains Nd1[T] and Nd2[T], respectively. The strains shared more than 99 % 16S rRNA gene sequence identity and their genomes were both less than 2 Mb in length, sharing 79 % average nucleotide identity, 81 % average amino acid identity and a DNA G+C content of approximately 37 mol%. Both strains were chemolithotrophs that fixed carbon dioxide and gained energy by oxidising ammonia to nitrite, with no evidence of mixotrophic growth. Neither strain was capable of using urea as a source of ammonia. Both strains were non-motile in culture, although Nd1[T] does possess genes encoding flagella components and therefore may be motile under certain conditions. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.2-5.6 and at 20-30 °C. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.0-6.1 and at 20-42 °C. Nd1[T] and Nd2[T] are distinct with respect to genomic and physiological features and are assigned as the type strains for the species Nitrosotalea devaniterrae sp. nov. (type strain, Nd1[T]=NCIMB 15248[T]=DSM 110862[T]) and Nitrosotalea sinensis sp. nov. (type strain, Nd2[T]=NCIMB 15249[T]=DSM 110863[T]), respectively, within the genus Nitrosotalea gen. nov. The family Nitrosotaleaceae fam. nov. and order Nitrosotaleales ord. nov. are also proposed officially.},
}

*Soil Microbiology
*Phylogeny
*Base Composition
*RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
*Ammonia/metabolism
*DNA, Archaeal/genetics
*Oxidation-Reduction
China
Archaea/classification/genetics/isolation & purification
Hydrogen-Ion Concentration
Nitrites/metabolism
Chemoautotrophic Growth

@article {pmid39304533,
year = {2024},
author = {Zhang, QK and Zhu, LR and Dong, XY and Yang, XY and Hou, J and Cui, HL},
title = {Salinirarus marinus gen. nov., sp. nov., Haloplanus salilacus sp. nov., Haloplanus pelagicus sp. nov., Haloplanus halophilus sp. nov., Haloplanus halobius sp. nov., halophilic archaea isolated from commercial coarse salts with potential as starter cultures for salt-fermented foods.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae075},
pmid = {39304533},
issn = {1574-6968},
abstract = {Five halophilic archaeal strains, XH8T, CK5-1T, GDY1T, HW8-1T, and XH21T, were isolated from commercial coarse salt produced in different regions of China. Their 16S rRNA and rpoB' gene sequences indicated that four of the strains (CK5-1T, GDY1T, HW8-1T, and XH21T) represent distinct species within the genus Haloplanus (family Haloferacaceae), while strain XH8T represents a novel genus within the same family. These assignments were supported by phylogenetic and phylogenomic analyses, which showed that strains CK5-1T, GDY1T, HW8-1T, and XH21T cluster with the current species of the genus Haloplanus, while strain XH8T forms a separate branch from the genus Haloplanus. The digital DNA-DNA hybridization and average amino acid identity (AAI) values among these four strains and the current members of the genus Haloplanus were 23.1-35.2% and 75.9-83.8%, respectively; and those values between strain XH8T and other genera in the family Haloferacaceae were 18.8-33.6% and 59.8-66.6%, respectively, much lower than the threshold values for species demarcation. Strain XH8T may represent a novel genus of the family Haloferacaceae according to the cut-off value of AAI (≤72.1%) proposed to differentiate genera within the family Haloferacaceae. These five strains could be distinguished from the related species according to differential phenotypic characteristics. Based on these results, it is proposed that strain XH8T represents a novel genus within the family Haloferacaceae, and strains CK5-1T, GDY1T, HW8-1T, and XH21T represent four novel species of the genus Haloplanus, respectively. Additionally, these five strains possess genes encoding enzymes critical for the fermentation process in salt-fermented foods, indicating their potential as starter cultures for these applications.},
}

@article {pmid39300577,
year = {2024},
author = {Lezcano, MÁ and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V},
title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {176},
pmid = {39300577},
issn = {2049-2618},
support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; },
mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.

RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.

CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.},
}

*Lakes/microbiology
*Archaea/genetics/metabolism/classification
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Genetic Variation
Chile
Phylogeny
Microbiota
Extremophiles/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics

@article {pmid39299940,
year = {2024},
author = {Obayori, OS and Salam, LB and Ashade, AO and Oseni, TD and Kalu, MD and Mustapha, FM},
title = {An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {10},
pages = {327},
pmid = {39299940},
issn = {1573-0972},
mesh = {*Metals, Heavy/analysis ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification/metabolism ; *Charcoal ; *Soil Pollutants/analysis ; *Soil/chemistry ; Nigeria ; High-Throughput Nucleotide Sequencing ; Animals ; Hydrocarbons/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.},
}

*Metals, Heavy/analysis
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification/metabolism
*Charcoal
*Soil Pollutants/analysis
*Soil/chemistry
Nigeria
High-Throughput Nucleotide Sequencing
Animals
Hydrocarbons/metabolism/analysis
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid39296579,
year = {2024},
author = {Vershinin, Z and Zaretsky, M and Eichler, J},
title = {N-glycosylation in Archaea - Expanding the process, components and roles of a universal post-translational modification.},
journal = {BBA advances},
volume = {6},
number = {},
pages = {100120},
pmid = {39296579},
issn = {2667-1603},
abstract = {While performed by all three domains of life, N-glycosylation in Archaea is less well described than are the parallel eukaryal and bacterial processes. Still, what is known of the archaeal version of this universal post-translational modification reveals numerous seemingly domain-specific traits. Specifically, the biosynthesis of archaeal N-linked glycans relies on distinct pathway steps and components, rare sugars and sugar modifications, as well as unique lipid carriers upon which N-linked glycans are assembled. At the same time, Archaea possess the apparently unique ability to simultaneously modify their glycoproteins with very different N-linked glycans. In addition to these biochemical aspects of archaeal N-glycosylation, such post-translational modification has been found to serve a wide range of roles possibly unique to Archaea, including allowing these microorganisms to not only cope with the harsh physical conditions of the niches they can inhabit but also providing the ability to adapt to transient changes in such environments.},
}

@article {pmid39296305,
year = {2024},
author = {Hernández-Magaña, E and Kraft, B},
title = {Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410251},
pmid = {39296305},
issn = {1664-302X},
abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures ([15]NO2 [-] pool +[44]N2O spike and [14]NO2 [-] pool +[46]N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.},
}

@article {pmid39287442,
year = {2024},
author = {Mattick, JSA and Bromley, RE and Watson, KJ and Adkins, RS and Holt, CI and Lebov, JF and Sparklin, BC and Tyson, TS and Rasko, DA and Dunning Hotopp, JC},
title = {Deciphering transcript architectural complexity in bacteria and archaea.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0235924},
pmid = {39287442},
issn = {2150-7511},
abstract = {RNA transcripts are potential therapeutic targets, yet bacterial transcripts have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict transcripts (mRNA and other RNAs) in Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria), Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria). From >5 million E. coli K12 and >3 million E. coli E2348/69 newly generated Oxford Nanopore Technologies direct RNA sequencing reads, 2,487 K12 mRNAs and 1,844 E2348/69 mRNAs were predicted, with the K12 mRNAs containing more than half of the predicted E. coli K12 proteins. While the number of predicted transcripts varied by strain based on the amount of sequence data used, across all strains examined, the predicted average size of the mRNAs was 1.6-1.7 kbp, while the median size of the 5'- and 3'-untranslated regions (UTRs) were 30-90 bp. Given the lack of bacterial and archaeal transcript annotation, most predictions were of novel transcripts, but we also predicted many previously characterized mRNAs and ncRNAs, including post-transcriptionally generated transcripts and small RNAs associated with pathogenesis in the E. coli E2348/69 LEE pathogenicity islands. We predicted small transcripts in the 100-200 bp range as well as >10 kbp transcripts for all strains, with the longest transcript for two of the seven strains being the nuo operon transcript, and for another two strains it was a phage/prophage transcript. This quick, easy, and reproducible method will facilitate the presentation of transcripts, and UTR predictions alongside coding sequences and protein predictions in bacterial genome annotation as important resources for the research community.IMPORTANCEOur understanding of bacterial and archaeal genes and genomes is largely focused on proteins since there have only been limited efforts to describe bacterial/archaeal RNA diversity. This contrasts with studies on the human genome, where transcripts were sequenced prior to the release of the human genome over two decades ago. We developed software for the quick, easy, and reproducible prediction of bacterial and archaeal transcripts from Oxford Nanopore Technologies direct RNA sequencing data. These predictions are urgently needed for more accurate studies examining bacterial/archaeal gene regulation, including regulation of virulence factors, and for the development of novel RNA-based therapeutics and diagnostics to combat bacterial pathogens, like those with extreme antimicrobial resistance.},
}

@article {pmid39281633,
year = {2024},
author = {Ben Hamad Bouhamed, S and Chaari, M and Baati, H and Zouari, S and Ammar, E},
title = {Extreme halophilic Archaea: Halobacterium salinarum carotenoids characterization and antioxidant properties.},
journal = {Heliyon},
volume = {10},
number = {17},
pages = {e36832},
pmid = {39281633},
issn = {2405-8440},
abstract = {Important marine microorganisms are resources of renewable energy that may face global population growth and needs. The application of biomass metabolites, such as carotenoids and their derivatives, may solve some agro-food health problems. Herein, a new halophilic Archaea Halobacterium salinarum producing carotenoid was screened from a Tunisian solar Saltworks (Sfax). The identification of the carotenoid pigments was carried out using HPLC-MS/MS. The predominant pigments produced by this Halobacterium were bacterioruberin and its derivatives and the carotenoids production was found to be of 21.51 mg/mL. Moreover, the data revealed that the carotenoids extract exhibited a high antioxidant activity across four oxidizing assays. The present results suggested that carotenoids extracted from halophilic Archaea are interesting sources of natural antioxidants for future innovative applications in agro-food, cosmetic and health fields.},
}

@article {pmid39215524,
year = {2024},
author = {Chatziargyri, AG and Stasi, EA and Tsirigos, KI and Litou, ZI and Iconomidou, VA and Bagos, PG},
title = {CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea.},
journal = {Journal of bioinformatics and computational biology},
volume = {22},
number = {4},
pages = {2450021},
doi = {10.1142/S0219720024500215},
pmid = {39215524},
issn = {1757-6334},
mesh = {*Protein Sorting Signals ; *Bacterial Proteins/metabolism/chemistry/genetics ; *Archaeal Proteins/metabolism/chemistry/genetics ; Archaea/metabolism/genetics ; Computational Biology/methods ; Cell Wall/metabolism/chemistry ; Markov Chains ; Amino Acid Motifs ; Software ; Bacteria/metabolism/genetics ; Algorithms ; },
abstract = {Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.},
}

*Protein Sorting Signals
*Bacterial Proteins/metabolism/chemistry/genetics
*Archaeal Proteins/metabolism/chemistry/genetics
Archaea/metabolism/genetics
Computational Biology/methods
Cell Wall/metabolism/chemistry
Markov Chains
Amino Acid Motifs
Software
Bacteria/metabolism/genetics
Algorithms

@article {pmid39215388,
year = {2024},
author = {Tejedor-Sanz, S and Song, YE and Sundstrom, ER},
title = {Utilization of formic acid by extremely thermoacidophilic archaea species.},
journal = {Microbial biotechnology},
volume = {17},
number = {9},
pages = {e70003},
pmid = {39215388},
issn = {1751-7915},
support = {CW367480//Energy Biosciences Institute/ ; },
mesh = {*Formates/metabolism ; Sulfolobales/metabolism/genetics ; },
abstract = {The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.},
}

*Formates/metabolism
Sulfolobales/metabolism/genetics

@article {pmid39215047,
year = {2024},
author = {Nagar, DN and Mani, K and Braganca, JM},
title = {Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20214},
pmid = {39215047},
issn = {2045-2322},
support = {(Level III) BT/INF/22/SP2543/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; 2023-24//DSTE&WM, Government of Goa/ ; },
mesh = {*Carotenoids/metabolism ; India ; *Phylogeny ; *Haloferax/genetics/metabolism ; *Haloarcula/genetics/metabolism ; Genome, Archaeal ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Halobacteriaceae/genetics/metabolism/isolation & purification/classification ; Genomics/methods ; Base Composition ; },
abstract = {Haloarchaeal cultures were isolated from solar salterns of Goa and Tamil Nadu and designated as BS2, BBK2 and E3. These isolates grew with a characteristic bright orange to pink pigmentation and were capable of growing in media containing upto 25% (w/vol) NaCl. Whole genome sequencing (WGS) of the three haloarchaeal strains BS2, BBK2 and E3 indicated an assembled genomic size of 4.1 Mb, 3.8 Mb and 4 Mb with G + C content of 61.8, 65.6 and 59.8% respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the archaeal isolates belong to Haloarcula, Haloferax and Halogeometricum genera. Haloarcula rubripromontorii BS2 was predicted to have 4292 genes with 4242 CDS regions, 46 tRNAs, 6 rRNAs and 3 misc_RNAs. In case of Haloferax lucentense BBK2,, 3840 genes with 3780 CDS regions were detected along with 52 tRNAs, 5 rRNAs and 3 misc_RNAs. Halogeometricum borinquense E3 contained 4101 genes, 4043 CDS regions, 52 tRNAs, 4 rRNAs, and 2 misc_RNAs. The functional annotation and curation of the haloarchaeal genome, revealed C50 carotenoid biosynthetic genes like phytoene desaturase/carotenoid 3' -4' desaturase (crtI), lycopene elongase (ubiA/lyeJ) and carotenoid biosynthesis membrane protein (cruF) in the three isolates. Whereas crtD (C-3',4' desaturase), crtY (lycopene cyclase) and brp/blh (β-carotene dioxygenase) genes were identified only in BS2.},
}

*Carotenoids/metabolism
India
*Phylogeny
*Haloferax/genetics/metabolism
*Haloarcula/genetics/metabolism
Genome, Archaeal
Whole Genome Sequencing
RNA, Ribosomal, 16S/genetics
Halobacteriaceae/genetics/metabolism/isolation & purification/classification
Genomics/methods
Base Composition

@article {pmid39210225,
year = {2024},
author = {da Costa Soares, S and Vezzani, FM and Favaretto, N and Auler, AC and da Silva Coelho, I and de Sousa Pires, A and Cruz, LM and de Souza, EM and Barth, G},
title = {Effect of long-term liquid dairy manure application on activity and structure of bacteria and archaea in no-till soils depends on plant in development.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {42},
pages = {54713-54728},
pmid = {39210225},
issn = {1614-7499},
mesh = {*Soil Microbiology ; *Manure/microbiology ; *Archaea ; *Bacteria ; *Soil/chemistry ; RNA, Ribosomal, 16S ; Brazil ; Agriculture/methods ; Dairying ; },
abstract = {This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m[3] ha[-1] year[-1], installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0-10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m[3] ha[-1] year[-1] doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant.},
}

*Soil Microbiology
*Manure/microbiology
*Archaea
*Bacteria
*Soil/chemistry
RNA, Ribosomal, 16S
Brazil
Agriculture/methods
Dairying

@article {pmid39207169,
year = {2024},
author = {Baker, BJ and Sarno, N},
title = {Small archaea may form intimate partnerships to maximize their metabolic potential.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0034724},
pmid = {39207169},
issn = {2150-7511},
abstract = {DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.},
}

@article {pmid39203380,
year = {2024},
author = {Bai, C and Wang, Q and Xu, J and Zhang, H and Huang, Y and Cai, L and Zheng, X and Yang, M},
title = {Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203380},
issn = {2076-2607},
support = {2022YFC3102003//the National Key Research and Development Program of China/ ; 2022ZD01//the Fund of Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, MNR)/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 41976127//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; },
abstract = {Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.},
}

@article {pmid39194224,
year = {2024},
author = {Nakagawa, S and Sakai, HD and Shimamura, S and Takamatsu, Y and Kato, S and Yagi, H and Yanaka, S and Yagi-Utsumi, M and Kurosawa, N and Ohkuma, M and Kato, K and Takai, K},
title = {N-linked protein glycosylation in Nanobdellati (formerly DPANN) archaea and their hosts.},
journal = {Journal of bacteriology},
volume = {206},
number = {9},
pages = {e0020524},
pmid = {39194224},
issn = {1098-5530},
support = {JP 20H03322//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP 23K20307//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //MEXT | National Institutes of Natural Sciences (NINS)/ ; 22EXC601//MEXT | NINS | Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences (ExCELLS)/ ; },
mesh = {Glycosylation ; *Archaeal Proteins/metabolism/genetics/chemistry ; Nanoarchaeota/metabolism/genetics ; Glycoproteins/metabolism/genetics/chemistry ; Archaea/metabolism/genetics ; Polysaccharides/metabolism ; Membrane Glycoproteins ; },
abstract = {Members of the kingdom Nanobdellati, previously known as DPANN archaea, are characterized by ultrasmall cell sizes and reduced genomes. They primarily thrive through ectosymbiotic interactions with specific hosts in diverse environments. Recent successful cultivations have emphasized the importance of adhesion to host cells for understanding the ecophysiology of Nanobdellati. Cell adhesion is often mediated by cell surface carbohydrates, and in archaea, this may be facilitated by the glycosylated S-layer protein that typically coats their cell surface. In this study, we conducted glycoproteomic analyses on two co-cultures of Nanobdellati with their host archaea, as well as on pure cultures of both host and non-host archaea. Nanobdellati exhibited various glycoproteins, including archaellins and hypothetical proteins, with glycans that were structurally distinct from those of their hosts. This indicated that Nanobdellati autonomously synthesize their glycans for protein modifications probably using host-derived substrates, despite the high energy cost. Glycan modifications on Nanobdellati proteins consistently occurred on asparagine residues within the N-X-S/T sequon, consistent with patterns observed across archaea, bacteria, and eukaryotes. In both host and non-host archaea, S-layer proteins were commonly modified with hexose, N-acetylhexosamine, and sulfonated deoxyhexose. However, the N-glycan structures of host archaea, characterized by distinct sugars such as deoxyhexose, nonulosonate sugar, and pentose at the nonreducing ends, were implicated in enabling Nanobdellati to differentiate between host and non-host cells. Interestingly, the specific sugar, xylose, was eliminated from the N-glycan in a host archaeon when co-cultured with Nanobdella. These findings enhance our understanding of the role of protein glycosylation in archaeal interactions.IMPORTANCENanobdellati archaea, formerly known as DPANN, are phylogenetically diverse, widely distributed, and obligately ectosymbiotic. The molecular mechanisms by which Nanobdellati recognize and adhere to their specific hosts remain largely unexplored. Protein glycosylation, a fundamental biological mechanism observed across all domains of life, is often crucial for various cell-cell interactions. This study provides the first insights into the glycoproteome of Nanobdellati and their host and non-host archaea. We discovered that Nanobdellati autonomously synthesize glycans for protein modifications, probably utilizing substrates derived from their hosts. Additionally, we identified distinctive glycosylation patterns that suggest mechanisms through which Nanobdellati differentiate between host and non-host cells. This research significantly advances our understanding of the molecular basis of microbial interactions in extreme environments.},
}

Glycosylation
*Archaeal Proteins/metabolism/genetics/chemistry
Nanoarchaeota/metabolism/genetics
Glycoproteins/metabolism/genetics/chemistry
Archaea/metabolism/genetics
Polysaccharides/metabolism
Membrane Glycoproteins

@article {pmid39134651,
year = {2024},
author = {Gutiérrez-Preciado, A and Dede, B and Baker, BA and Eme, L and Moreira, D and López-García, P},
title = {Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines.},
journal = {Nature ecology & evolution},
volume = {8},
number = {10},
pages = {1856-1869},
pmid = {39134651},
issn = {2397-334X},
support = {doi.org/10.37807/GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Proteome ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; Lakes/microbiology ; Metagenome ; Salinity ; Archaeal Proteins/genetics/metabolism ; Genome, Archaeal ; Hot Springs/microbiology ; },
abstract = {Few described archaeal, and fewer bacterial, lineages thrive under salt-saturating conditions, such as solar saltern crystallizers (salinity above 30% w/v). They accumulate molar K[+] cytoplasmic concentrations to maintain osmotic balance ('salt-in' strategy) and have proteins adaptively enriched in negatively charged acidic amino acids. Here we analysed metagenomes and metagenome-assembled genomes from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near-life-limiting conditions of the Western-Canyon Lakes. Danakil metagenome- and metagenome-assembled-genome-inferred proteomes, compared with those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that Western-Canyon Lake archaea encode the most acidic proteomes ever observed (median protein isoelectric points ≤4.4). We identified previously undescribed haloarchaeal families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shapes microbial diversity in these ecosystems near life limits.},
}

*Proteome
*Archaea/genetics/metabolism
*Bacteria/metabolism/genetics/classification
Lakes/microbiology
Metagenome
Salinity
Archaeal Proteins/genetics/metabolism
Genome, Archaeal
Hot Springs/microbiology

@article {pmid39128722,
year = {2024},
author = {Carilo, I and Senju, Y and Yokoyama, T and Robinson, RC},
title = {Intercompatibility of eukaryotic and Asgard archaea ribosome-translocon machineries.},
journal = {The Journal of biological chemistry},
volume = {300},
number = {9},
pages = {107673},
pmid = {39128722},
issn = {1083-351X},
mesh = {*Ribosomes/metabolism ; *Endoplasmic Reticulum/metabolism ; *Archaeal Proteins/metabolism/genetics ; Membrane Proteins/metabolism/genetics ; Archaea/metabolism/genetics ; Protein Transport ; Eukaryota/metabolism/genetics ; Phylogeny ; Protein Sorting Signals/physiology ; Eukaryotic Cells/metabolism ; },
abstract = {In all domains of life, the ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. Phylogenetic analyses indicate the inheritance of eukaryotic Sec61/oligosaccharyltransferase/translocon-associated protein translocon subunits from an Asgard archaea ancestor. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show compatibility between the eukaryotic ribosome-translocon complex and Asgard signal peptides and transmembrane proteins. We find that Asgard translocon proteins from Candidatus Prometheoarchaeum syntrophicum strain Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Furthermore, we show that the cytoplasmic domain of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 oligosaccharyltransferase 1 (ribophorin I) can interact with eukaryotic ribosomes. Our data indicate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet-to-be-translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have contributed to propagating the new translocon location, leading to their loss from the cell membrane.},
}

*Ribosomes/metabolism
*Endoplasmic Reticulum/metabolism
*Archaeal Proteins/metabolism/genetics
Membrane Proteins/metabolism/genetics
Archaea/metabolism/genetics
Protein Transport
Eukaryota/metabolism/genetics
Phylogeny
Protein Sorting Signals/physiology
Eukaryotic Cells/metabolism

@article {pmid39115222,
year = {2024},
author = {Zhao, Z and Qin, W and Li, L and Zhao, H and Ju, F},
title = {Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers.},
journal = {Environmental science & technology},
volume = {58},
number = {36},
pages = {16040-16054},
doi = {10.1021/acs.est.4c02321},
pmid = {39115222},
issn = {1520-5851},
mesh = {*Ammonia/metabolism ; *Archaea/metabolism/genetics ; Phylogeny ; Oxidation-Reduction ; },
abstract = {Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.},
}

*Ammonia/metabolism
*Archaea/metabolism/genetics
Phylogeny
Oxidation-Reduction

@article {pmid39097239,
year = {2024},
author = {Manesh, MJH and Willard, DJ and John, KM and Kelly, RM},
title = {Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation.},
journal = {Bioresource technology},
volume = {408},
number = {},
pages = {131198},
pmid = {39097239},
issn = {1873-2976},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Copper/metabolism ; *Iron/metabolism ; Archaea/metabolism ; Hydrogen-Ion Concentration ; Temperature ; Sulfolobales/metabolism ; },
abstract = {Factors that contribute to optimal chalcopyrite bioleaching by extremely thermoacidophilic archaea were examined for ten species belonging to the order Sulfolobales from the genera Acidianus (A. brierleyi), Metallosphaera (M. hakonensis, M. sedula, M. prunae), Sulfuracidifex (S. metallicus, S. tepriarius), Sulfolobus (S. acidocaldarius), Saccharlobus (S. solfataricus) and Sulfurisphaera (S. ohwakuensis, S. tokodaii). Only A. brierleyi, M. sedula, S. metallicus, S. tepriarius, S. ohwakuensis, and S. tokodai exhibited significant amounts of bioleaching and were investigated further. At 70-75 °C, Chalcopyrite loadings of 10 g/l were leached for 21 days during which pH, redox potential, planktonic cell density, iron concentrations and sulfate levels were monitored, in addition to copper mobilization. S. ohwakuensis proved to be the most prolific bioleacher. This was attributed to balanced iron and sulfur oxidation, thereby reducing by-product (e.g., jarosites) formation and minimizing surface passivation. Comparative genomics suggest markers for bioleaching potential, but the results here point to the need for experimental verification.},
}

*Sulfur/metabolism
*Oxidation-Reduction
*Copper/metabolism
*Iron/metabolism
Archaea/metabolism
Hydrogen-Ion Concentration
Temperature
Sulfolobales/metabolism

@article {pmid39096085,
year = {2024},
author = {Blombach, F and Werner, F},
title = {Chromatin and gene regulation in archaea.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15302},
pmid = {39096085},
issn = {1365-2958},
support = {207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The chromatinisation of DNA by nucleoid-associated proteins (NAPs) in archaea 'formats' the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP-specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re-analysis of genome-wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin-free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin-like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide-ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher-order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome-wide chromatin landscapes.},
}

@article {pmid39085212,
year = {2024},
author = {Leão, P and Little, ME and Appler, KE and Sahaya, D and Aguilar-Pine, E and Currie, K and Finkelstein, IJ and De Anda, V and Baker, BJ},
title = {Asgard archaea defense systems and their roles in the origin of eukaryotic immunity.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6386},
pmid = {39085212},
issn = {2041-1723},
support = {73592LPI//Simons Foundation/ ; F-1808//Welch Foundation/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/immunology/virology ; *Archaeal Proteins/metabolism/genetics ; Argonaute Proteins/metabolism/genetics ; Eukaryota/genetics/immunology ; Bacteriophages/genetics/physiology ; Evolution, Molecular ; },
abstract = {Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.},
}

*Phylogeny
*Archaea/genetics/immunology/virology
*Archaeal Proteins/metabolism/genetics
Argonaute Proteins/metabolism/genetics
Eukaryota/genetics/immunology
Bacteriophages/genetics/physiology
Evolution, Molecular

@article {pmid39085194,
year = {2024},
author = {Valentin-Alvarado, LE and Appler, KE and De Anda, V and Schoelmerich, MC and West-Roberts, J and Kivenson, V and Crits-Christoph, A and Ly, L and Sachdeva, R and Greening, C and Savage, DF and Baker, BJ and Banfield, JF},
title = {Asgard archaea modulate potential methanogenesis substrates in wetland soil.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6384},
pmid = {39085194},
issn = {2041-1723},
support = {INV-037174/GATES/Bill & Melinda Gates Foundation/United States ; LI-SIAME-00002001//Simons Foundation/ ; },
mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Archaea/genetics/metabolism ; *Carbon Cycle ; *Soil/chemistry ; Phylogeny ; Genome, Archaeal ; Oxidation-Reduction ; },
abstract = {The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.},
}

*Wetlands
*Methane/metabolism
*Soil Microbiology
*Archaea/genetics/metabolism
*Carbon Cycle
*Soil/chemistry
Phylogeny
Genome, Archaeal
Oxidation-Reduction

@article {pmid39085041,
year = {2024},
author = {Hayashi, M and Wada, Y and Yamamura, A and Inoue, H and Yamashita, N and Ichimura, S and Iida, Y},
title = {Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {88},
number = {10},
pages = {1155-1163},
doi = {10.1093/bbb/zbae106},
pmid = {39085041},
issn = {1347-6947},
mesh = {*Metals/pharmacology/metabolism ; DNA-Cytosine Methylases/metabolism ; DNA/metabolism ; Archaea/enzymology/genetics ; Copper/metabolism/pharmacology ; Archaeal Proteins/metabolism/genetics ; },
abstract = {We previously identified M.ApeKI from Aeropyum pernix K1 as a highly thermostable DNA (cytosine-5)-methyltransferase. M.ApeKI uses the type II restriction-modification system (R-M system), among the best-studied R-M systems. Although endonucleases generally utilize Mg (II) as a cofactor, several reports have shown that MTases exhibit different reactions in the presence of metal ions. This study aim was to evaluate the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. We evaluated the influence of metal ions on the catalytic activity and DNA binding of M.ApeKI. The catalytic activity was inhibited by Cu (II), Mg (II), Mn (II), and Zn (II), each at 5 m m. DNA binding was more strongly inhibited by 5 m m Cu (II) and 10 m m Zn (II). To our knowledge, this is the first report showing that DNA binding of type II MTase is inhibited by metal ions.},
}

*Metals/pharmacology/metabolism
DNA-Cytosine Methylases/metabolism
DNA/metabolism
Archaea/enzymology/genetics
Copper/metabolism/pharmacology
Archaeal Proteins/metabolism/genetics

@article {pmid39081362,
year = {2024},
author = {Kaneko, M and Omori, T and Igai, K and Mabuchi, T and Sakai-Tazawa, M and Nishihara, A and Kihara, K and Yoshimura, T and Ohkuma, M and Hongoh, Y},
title = {Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae097},
pmid = {39081362},
issn = {2730-6151},
abstract = {Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts' fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here "Candidatus Methanobrevibacter cononymphae", is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, "Ca. Methanobrevibacter cononymphae" is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of "Ca. Methanobrevibacter cononymphae" showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.},
}

@article {pmid39077992,
year = {2024},
author = {Rasmussen, AN and Francis, CA},
title = {Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39077992},
issn = {1751-7370},
support = {DE-AC02-05CH11231//Department of Energy/ ; //Stanford Data Science Scholars Program/ ; },
mesh = {*Ammonia/metabolism ; San Francisco ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Bays/microbiology ; *Oxidation-Reduction ; *Nitrification ; Metagenome ; Seasons ; Metagenomics ; },
abstract = {Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.},
}

*Ammonia/metabolism
San Francisco
*Archaea/genetics/classification/metabolism/isolation & purification
*Bays/microbiology
*Oxidation-Reduction
*Nitrification
Metagenome
Seasons
Metagenomics

@article {pmid39077943,
year = {2024},
author = {Lin, MG and Yen, CY and Shen, YY and Huang, YS and Ng, IW and Barillà, D and Sun, YJ and Hsiao, CD},
title = {Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea.},
journal = {Nucleic acids research},
volume = {52},
number = {16},
pages = {9966-9977},
pmid = {39077943},
issn = {1362-4962},
support = {NSTC 111-2311-B-001-001//National Science and Technology Council/ ; RPG-245//Leverhulme Trust/ ; BB/X00645X/1//BBSRC/ ; },
mesh = {*Chromosome Segregation ; *Archaeal Proteins/chemistry/metabolism/genetics ; *Models, Molecular ; Protein Binding ; Crystallography, X-Ray ; Adenosine Diphosphate/metabolism/chemistry ; Binding Sites ; DNA, Archaeal/metabolism/chemistry/genetics ; DNA-Binding Proteins/chemistry/metabolism/genetics/ultrastructure ; },
abstract = {Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5-15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.},
}

*Chromosome Segregation
*Archaeal Proteins/chemistry/metabolism/genetics
*Models, Molecular
Protein Binding
Crystallography, X-Ray
Adenosine Diphosphate/metabolism/chemistry
Binding Sites
DNA, Archaeal/metabolism/chemistry/genetics
DNA-Binding Proteins/chemistry/metabolism/genetics/ultrastructure

@article {pmid39071849,
year = {2024},
author = {Sakoula, D and Schatteman, A and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lehtovirta-Morley, L and Lücker, S},
title = {Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae092},
pmid = {39071849},
issn = {2730-6151},
abstract = {Recently, an activity-based labelling protocol for the in vivo detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of an activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this novel activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.},
}

@article {pmid39060562,
year = {2024},
author = {Harada, M and Endo, A and Wada, S and Watanabe, T and Epron, D and Asakawa, S},
title = {Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {107},
pmid = {39060562},
issn = {1572-9699},
support = {24K01797//Japan Society for the Promotion of Science/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Forests ; *Methane/metabolism ; *Phylogeny ; Trees/microbiology ; Archaea/classification/genetics/metabolism/isolation & purification ; Wood/microbiology ; DNA, Archaeal/genetics ; },
abstract = {Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 10[7] copies g[-1] dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 10[5] and 10[4] copies g[-1] dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 10[6] cells g[-1] dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.},
}

*RNA, Ribosomal, 16S/genetics
*Forests
*Methane/metabolism
*Phylogeny
Trees/microbiology
Archaea/classification/genetics/metabolism/isolation & purification
Wood/microbiology
DNA, Archaeal/genetics

@article {pmid39053544,
year = {2024},
author = {Yan, A and Pan, Z and Liang, Y and Mo, X and Guo, T and Li, J},
title = {Archaea communities in aerobic granular sludge: A mini-review.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174974},
doi = {10.1016/j.scitotenv.2024.174974},
pmid = {39053544},
issn = {1879-1026},
mesh = {*Sewage/microbiology ; *Archaea/physiology ; Aerobiosis ; Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; },
abstract = {Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.},
}

*Sewage/microbiology
*Archaea/physiology
Aerobiosis
Waste Disposal, Fluid/methods
Bioreactors/microbiology

@article {pmid39052173,
year = {2024},
author = {Tenorio-Salgado, S and Villalpando-Aguilar, JL and Hernandez-Guerrero, R and Poot-Hernández, AC and Perez-Rueda, E},
title = {Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39052173},
issn = {1678-4405},
abstract = {The evolution, survival, and adaptation of microbes are consequences of gene duplication, acquisition, and divergence in response to environmental challenges. In this context, enzymes play a central role in the evolution of organisms, because they are fundamental in cell metabolism. Here, we analyzed the enzymatic repertoire in 6,467 microbial genomes, including their abundances, and their associations with metabolic maps. We found that the enzymes follow a power-law distribution, in relation to the genome sizes. Therefore, we evaluated the total proportion enzymatic classes in relation to the genomes, identifying a descending-order proportion: transferases (EC:2.-), hydrolases (EC:3.-), oxidoreductases (EC:1.-), ligases (EC:6.-), lyases (EC:4.-), isomerases (EC:5.-), and translocases (EC:7-.). In addition, we identified a preferential use of enzymatic classes in metabolism pathways for xenobiotics, cofactors and vitamins, carbohydrates, amino acids, glycans, and energy. Therefore, this analysis provides clues about the functional constraints associated with the enzymatic repertoire of functions in Bacteria and Archaea.},
}

@article {pmid39043438,
year = {2024},
author = {Gemler, BT and Warner, BR and Bundschuh, R and Fredrick, K},
title = {Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea.},
journal = {RNA (New York, N.Y.)},
volume = {30},
number = {10},
pages = {1264-1276},
pmid = {39043438},
issn = {1469-9001},
support = {R01 GM072528/GM/NIGMS NIH HHS/United States ; },
mesh = {*Nucleic Acid Conformation ; *RNA, Archaeal/genetics/chemistry/metabolism ; *Archaea/genetics ; *RNA, Bacterial/genetics/chemistry/metabolism ; RNA, Ribosomal/genetics/chemistry/metabolism ; Bacteria/genetics ; RNA Precursors/genetics/metabolism/chemistry ; RNA, Ribosomal, 23S/genetics/chemistry/metabolism ; Base Sequence ; RNA, Ribosomal, 16S/genetics/chemistry ; Base Pairing ; },
abstract = {Ribosomal RNAs are transcribed as part of larger precursor molecules. In Escherichia coli, complementary RNA segments flank each rRNA and form long leader-trailer (LT) helices, which are crucial for subunit biogenesis in the cell. A previous study of 15 representative species suggested that most but not all prokaryotes contain LT helices. Here, we use a combination of in silico folding and covariation methods to identify and characterize LT helices in 4464 bacterial and 260 archaeal organisms. Our results suggest that LT helices are present in all phyla, including Deinococcota, which had previously been suspected to lack LT helices. In very few organisms, our pipeline failed to detect LT helices for both 16S and 23S rRNA. However, a closer case-by-case look revealed that LT helices are indeed present but escaped initial detection. Over 3600 secondary structure models, many well supported by nucleotide covariation, were generated. These structures show a high degree of diversity. Yet, all exhibit extensive base-pairing between the leader and trailer strands, in line with a common and essential function.},
}

*Nucleic Acid Conformation
*RNA, Archaeal/genetics/chemistry/metabolism
*Archaea/genetics
*RNA, Bacterial/genetics/chemistry/metabolism
RNA, Ribosomal/genetics/chemistry/metabolism
Bacteria/genetics
RNA Precursors/genetics/metabolism/chemistry
RNA, Ribosomal, 23S/genetics/chemistry/metabolism
Base Sequence
RNA, Ribosomal, 16S/genetics/chemistry
Base Pairing

@article {pmid39043386,
year = {2024},
author = {Duller, S and Moissl-Eichinger, C},
title = {Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease.},
journal = {Emerging infectious diseases},
volume = {30},
number = {8},
pages = {1505-1513},
pmid = {39043386},
issn = {1080-6059},
mesh = {Humans ; *Archaea/genetics ; *Microbiota ; Communicable Diseases/microbiology ; },
abstract = {Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.},
}

Humans
*Archaea/genetics
*Microbiota
Communicable Diseases/microbiology

@article {pmid39030685,
year = {2024},
author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and McIlroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU},
title = {Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39030685},
issn = {1751-7370},
support = {VI.Vidi.223.012//NWO-VIDI/ ; FT190100211//Australian Research Council/ ; 854088//ERC/ ; 024.002.002//NWO/ ; },
mesh = {*Methane/metabolism ; *Fresh Water/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics/classification ; *Salt Stress ; *Phylogeny ; *Osmoregulation ; Oxidation-Reduction ; },
abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.},
}

*Methane/metabolism
*Fresh Water/microbiology
Anaerobiosis
*Archaea/metabolism/genetics/classification
*Salt Stress
*Phylogeny
*Osmoregulation
Oxidation-Reduction

@article {pmid38967634,
year = {2024},
author = {Imachi, H and Nobu, MK and Kato, S and Takaki, Y and Miyazaki, M and Miyata, M and Ogawara, M and Saito, Y and Sakai, S and Tahara, YO and Takano, Y and Tasumi, E and Uematsu, K and Yoshimura, T and Itoh, T and Ohkuma, M and Takai, K},
title = {Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {7},
pages = {},
pmid = {38967634},
issn = {1466-5034},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Base Composition ; *Sequence Analysis, DNA ; *DNA, Archaeal/genetics ; Geologic Sediments/microbiology ; Anaerobiosis ; Seawater/microbiology ; Vitamin K 2/analogs & derivatives ; },
abstract = {An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1[T], was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1[T] and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1[T] grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1[T] showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×10[6] 16S rRNA gene copies ml[-1]. MK-D1[T] had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LT[T] (76.09 %) and Methanothermobacter tenebrarum RMAS[T] (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1[T] (JCM 39240[T] and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.},
}

*Phylogeny
*RNA, Ribosomal, 16S/genetics
*Base Composition
*Sequence Analysis, DNA
*DNA, Archaeal/genetics
Geologic Sediments/microbiology
Anaerobiosis
Seawater/microbiology
Vitamin K 2/analogs & derivatives

@article {pmid38953360,
year = {2024},
author = {Willard, DJ and H Manesh, MJ and Bing, RG and Alexander, BH and Kelly, RM},
title = {Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae.},
journal = {mBio},
volume = {15},
number = {8},
pages = {e0103324},
pmid = {38953360},
issn = {2150-7511},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; CBET-1802939//National Science Foundation (NSF)/ ; T32 GM008776-16//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; FA9550-20-1-0216//US Air Force Office of Sponsored Projects/ ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Sulfolobaceae/metabolism/genetics ; Phenotype ; Phylogeny ; Gene Expression Profiling ; Genome, Archaeal ; },
abstract = {Certain members of the family Sulfolobaceae represent the only archaea known to oxidize elemental sulfur, and their evolutionary history provides a framework to understand the development of chemolithotrophic growth by sulfur oxidation. Here, we evaluate the sulfur oxidation phenotype of Sulfolobaceae species and leverage comparative genomic and transcriptomic analysis to identify the key genes linked to sulfur oxidation. Metabolic engineering of the obligate heterotroph Sulfolobus acidocaldarius revealed that the known cytoplasmic components of sulfur oxidation alone are not sufficient to drive prolific sulfur oxidation. Imaging analysis showed that Sulfolobaceae species maintain proximity to the sulfur surface but do not necessarily contact the substrate directly. This indicates that a soluble form of sulfur must be transported to initiate cytoplasmic sulfur oxidation. Conservation patterns and transcriptomic response implicate an extracellular tetrathionate hydrolase and putative thiosulfate transporter in a newly proposed mechanism of sulfur acquisition in the Sulfolobaceae.IMPORTANCESulfur is one of the most abundant elements on earth (2.9% by mass), so it makes sense that the earliest biology found a way to use sulfur to create and sustain life. However, beyond evolutionary significance, sulfur and the molecules it comprises have important technological significance, not only in chemicals such as sulfuric acid and in pyritic ores containing critical metals but also as a waste product from oil and gas production. The thermoacidophilic Sulfolobaceae are unique among the archaea as sulfur oxidizers. The trajectory for how sulfur biooxidation arose and evolved can be traced using experimental and bioinformatic analyses of the available genomic data set. Such analysis can also inform the process by which extracellular sulfur is acquired and transported by thermoacidophilic archaea, a phenomenon that is critical to these microorganisms but has yet to be elucidated.},
}

*Sulfur/metabolism
*Oxidation-Reduction
*Sulfolobaceae/metabolism/genetics
Phenotype
Phylogeny
Gene Expression Profiling
Genome, Archaeal

@article {pmid38951176,
year = {2024},
author = {Martínez-Espinosa, RM},
title = {Halophilic archaea as tools for bioremediation technologies.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {401},
pmid = {38951176},
issn = {1432-0614},
support = {VIGROB-309//Universidad de Alicante/ ; PROMETEO/2021/055//Conselleria de Cultura, Educación y Ciencia, Generalitat Valenciana/ ; },
mesh = {*Biodegradation, Environmental ; Archaea/metabolism ; Halobacteriaceae/metabolism/genetics ; Metals, Heavy/metabolism ; Soil Pollutants/metabolism ; Soil Microbiology ; },
abstract = {Haloarchaea are extremophilic microorganisms belonging to the Archaea domain that require high salt concentrations to be alive, thus inhabiting ecosystems like salty ponds, salty marshes, or extremely salty lagoons. They are more abundantly and widely distributed worldwide than initially expected. Most of them are grouped into two families: Halobacteriaceae and Haloferacaceae. The extreme conditions under which haloarchaea survive contribute to their metabolic and molecular adaptations, thus making them good candidates for the design of bioremediation strategies to treat brines, salty water, and saline soils contaminated with toxic compounds such as nitrate, nitrite, oxychlorates such as perchlorate and chlorate, heavy metals, hydrocarbons, and aromatic compounds. New advances in understanding haloarchaea physiology, metabolism, biochemistry, and molecular biology suggest that biochemical pathways related to nitrogen and carbon, metals, hydrocarbons, or aromatic compounds can be used for bioremediation proposals. This review analyses the novelty of the most recent results showing the capability of some haloarchaeal species to assimilate, modify, or degrade toxic compounds for most living beings. Several examples of the role of these microorganisms in the treatment of polluted brine or salty soils are also discussed in connection with circular economy-based processes. KEY POINTS: • Haloarchaea are extremophilic microorganisms showing genuine metabolism • Haloarchaea can metabolise compounds that are highly toxic to most living beings • These metabolic capabilities are useful for designing soil and water bioremediation strategies.},
}

*Biodegradation, Environmental
Archaea/metabolism
Halobacteriaceae/metabolism/genetics
Metals, Heavy/metabolism
Soil Pollutants/metabolism
Soil Microbiology

@article {pmid38926353,
year = {2024},
author = {Schoelmerich, MC and Ly, L and West-Roberts, J and Shi, LD and Shen, C and Malvankar, NS and Taib, N and Gribaldo, S and Woodcroft, BJ and Schadt, CW and Al-Shayeb, B and Dai, X and Mozsary, C and Hickey, S and He, C and Beaulaurier, J and Juul, S and Sachdeva, R and Banfield, JF},
title = {Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5414},
pmid = {38926353},
issn = {2041-1723},
support = {INV-037174/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {*Genome, Archaeal ; *Methane/metabolism ; *Phylogeny ; Oxidation-Reduction ; Archaea/genetics/metabolism ; Nanopore Sequencing/methods ; DNA Methylation ; Soil Microbiology ; },
abstract = {Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming "Candidatus Methanoperedens" archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.},
}

*Genome, Archaeal
*Methane/metabolism
*Phylogeny
Oxidation-Reduction
Archaea/genetics/metabolism
Nanopore Sequencing/methods
DNA Methylation
Soil Microbiology

@article {pmid38922750,
year = {2024},
author = {Lawruk-Desjardins, C and Storck, V and Ponton, DE and Amyot, M and Walsh, DA},
title = {A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16669},
doi = {10.1111/1462-2920.16669},
pmid = {38922750},
issn = {1462-2920},
support = {ALLRP 560330 - 20//Natural Sciences and Engineering Research Council of Canada/ ; RDCPJ493474-15//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; *Archaea/genetics/metabolism/classification ; *Bacteria/genetics/classification/metabolism ; *Mercury/metabolism ; *Methylmercury Compounds/metabolism ; Metagenomics ; Humans ; Genome, Bacterial ; Genome, Archaeal ; Ecosystem ; Microbiota ; },
abstract = {Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.},
}

*Geologic Sediments/microbiology
*Rivers/microbiology
*Archaea/genetics/metabolism/classification
*Bacteria/genetics/classification/metabolism
*Mercury/metabolism
*Methylmercury Compounds/metabolism
Metagenomics
Humans
Genome, Bacterial
Genome, Archaeal
Ecosystem
Microbiota

@article {pmid38918468,
year = {2024},
author = {Shi, LD and West-Roberts, J and Schoelmerich, MC and Penev, PI and Chen, L and Amano, Y and Lei, S and Sachdeva, R and Banfield, JF},
title = {Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2422-2433},
pmid = {38918468},
issn = {2058-5276},
support = {INV-037174/GATES/Bill & Melinda Gates Foundation/United States ; INV-037174/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {*Methane/metabolism ; *Phylogeny ; Genome, Archaeal ; DNA Transposable Elements/genetics ; Euryarchaeota/genetics/metabolism ; Genetic Variation ; },
abstract = {Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report small enigmatic linear ECEs, circular viruses and unclassified ECEs that are predicted to replicate within Methanoperedens. Linear ECEs have inverted terminal repeats, tandem repeats and coding patterns that are strongly reminiscent of Borgs, but they are only 52-145 kb in length. As they share proteins with Borgs and Methanoperedens, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and can be assigned to at least five family-level groups. We identify eight families of Methanoperedens viruses, some of which encode multi-haem cytochromes, and circular ECEs encoding transposon-associated TnpB genes with proximal population-heterogeneous CRISPR arrays. These ECEs exchange genetic information with each other and with Methanoperedens, probably impacting their archaeal host activity and evolution.},
}

*Methane/metabolism
*Phylogeny
Genome, Archaeal
DNA Transposable Elements/genetics
Euryarchaeota/genetics/metabolism
Genetic Variation

@article {pmid38918384,
year = {2024},
author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, Å and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH},
title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5361},
pmid = {38918384},
issn = {2041-1723},
support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; },
mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; },
abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.},
}

*Archaea/genetics/classification/metabolism
*RNA, Ribosomal, 16S/genetics
Anaerobiosis
*Bacteria/genetics/classification/metabolism
*Microbiota/genetics
*Biodiversity
*Phylogeny
Wastewater/microbiology
Bioreactors/microbiology
Methane/metabolism
Sequence Analysis, DNA

@article {pmid38900790,
year = {2024},
author = {Murali, R and Pace, LA and Sanford, RA and Ward, LM and Lynes, MM and Hatzenpichler, R and Lingappa, UF and Fischer, WW and Gennis, RB and Hemp, J},
title = {Diversity and evolution of nitric oxide reduction in bacteria and archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {26},
pages = {e2316422121},
pmid = {38900790},
issn = {1091-6490},
support = {U12AB123456//National Institute of Health (NIH)/ ; 503546//Joint Genome Institute (JGI)/ ; DE-AC02-05CH11231//Joint Genome Institute (JGI)/ ; DE-AC05-76RL01830//DOE | SC | PNNL | Environmental Molecular Sciences Laboratory (EMSL)/ ; },
mesh = {*Nitric Oxide/metabolism ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; *Oxidation-Reduction ; Archaea/metabolism/genetics ; Rhodothermus/metabolism/enzymology/genetics ; Evolution, Molecular ; Bacteria/metabolism/genetics ; Bacterial Proteins/metabolism/genetics/chemistry ; },
abstract = {Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.},
}

*Nitric Oxide/metabolism
*Oxidoreductases/metabolism/genetics
*Phylogeny
*Oxidation-Reduction
Archaea/metabolism/genetics
Rhodothermus/metabolism/enzymology/genetics
Evolution, Molecular
Bacteria/metabolism/genetics
Bacterial Proteins/metabolism/genetics/chemistry

@article {pmid38898040,
year = {2024},
author = {Li, Y and Yu, T and Feng, X and Zhao, B and Chen, H and Yang, H and Chen, X and Zhang, XH and Anderson, HR and Burns, NZ and Zeng, F and Tao, L and Zeng, Z},
title = {Biosynthesis of GMGT lipids by a radical SAM enzyme associated with anaerobic archaea and oxygen-deficient environments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5256},
pmid = {38898040},
issn = {2041-1723},
support = {92351301//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
mesh = {*S-Adenosylmethionine/metabolism ; *Archaea/genetics/metabolism/enzymology ; *Oxygen/metabolism ; Anaerobiosis ; Archaeal Proteins/metabolism/genetics ; Glycerol/metabolism ; Metagenome ; Phylogeny ; },
abstract = {Archaea possess characteristic membrane-spanning lipids that are thought to contribute to the adaptation to extreme environments. However, the biosynthesis of these lipids is poorly understood. Here, we identify a radical S-adenosyl-L-methionine (SAM) enzyme that synthesizes glycerol monoalkyl glycerol tetraethers (GMGTs). The enzyme, which we name GMGT synthase (Gms), catalyzes the formation of a C(sp[3])-C(sp[3]) linkage between the two isoprenoid chains of glycerol dialkyl glycerol tetraethers (GDGTs). This conclusion is supported by heterologous expression of gene gms from a GMGT-producing species in a methanogen, as well as demonstration of in vitro activity using purified Gms enzyme. Additionally, we show that genes encoding putative Gms homologs are present in obligate anaerobic archaea and in metagenomes obtained from oxygen-deficient environments, and appear to be absent in metagenomes from oxic settings.},
}

*S-Adenosylmethionine/metabolism
*Archaea/genetics/metabolism/enzymology
*Oxygen/metabolism
Anaerobiosis
Archaeal Proteins/metabolism/genetics
Glycerol/metabolism
Metagenome
Phylogeny

@article {pmid38896033,
year = {2024},
author = {Huang, B and Xiao, Y and Zhang, Y},
title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38896033},
issn = {1751-7370},
support = {32270680//National Natural Science Foundation of China/ ; 2023SHIBS0003//Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; },
mesh = {*Selenocysteine/metabolism/genetics ; *Archaea/genetics/metabolism/classification ; *Selenoproteins/genetics/metabolism ; *Eukaryota/genetics/classification/metabolism ; Genome, Archaeal ; Proteome ; Codon, Terminator/genetics ; Archaeal Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.},
}

*Selenocysteine/metabolism/genetics
*Archaea/genetics/metabolism/classification
*Selenoproteins/genetics/metabolism
*Eukaryota/genetics/classification/metabolism
Genome, Archaeal
Proteome
Codon, Terminator/genetics
Archaeal Proteins/genetics/metabolism
Evolution, Molecular
Gene Transfer, Horizontal
Phylogeny

@article {pmid38890479,
year = {2024},
author = {Du Toit, A},
title = {Gassy archaea.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {8},
pages = {456},
pmid = {38890479},
issn = {1740-1534},
mesh = {*Archaea/genetics ; Genome, Archaeal ; Phylogeny ; },
}

*Archaea/genetics
Genome, Archaeal
Phylogeny

@article {pmid38890178,
year = {2024},
author = {Cui, L and Hu, Y and Li, XX and Ma, X and Cheng, M and Tan, S and Hou, J and Cui, HL},
title = {Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., Halobellus salinisoli sp. nov., halophilic archaea isolated from a saline lake and inland saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {2},
pages = {28},
pmid = {38890178},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Phylogeny ; Soil Microbiology ; Halobacterium/genetics/isolation & purification ; Genome, Archaeal ; Halobacteriaceae/genetics/isolation & purification/classification ; },
abstract = {Four halophilic archaeal strains YCN1[T], YCN58[T], LT38[T], and LT62[T] were isolated from Yuncheng Salt Lake (Shanxi, China) and Tarim Basin (Xinjiang, China), respectively. Phylogenetic and phylogenomic analyses showed that these four strains tightly cluster with related species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The AAI, ANI, and dDDH values between these four strains and their related species of respective genera were lower than the proposed threshold values for species delineation. Strains YCN1[T], YCN58[T], LT38[T], and LT62[T] could be differentiated from the current species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively, based on the comparison of diverse phenotypic characteristics. The polar lipid profiles of these four strains were closely similar to those of respective relatives within the genera Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The phenotypic, phylogenetic, and genome-based analyses indicated that strains YCN1[T], YCN58[T], LT38[T], and LT62[T] represent respective novel species within the genera Halobacterium, Natronomonas, Halorentalis, and Halobellus, for which the names Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., and Halobellus salinisoli sp. nov. are proposed, respectively.},
}

*Lakes/microbiology
*Phylogeny
Soil Microbiology
Halobacterium/genetics/isolation & purification
Genome, Archaeal
Halobacteriaceae/genetics/isolation & purification/classification

@article {pmid38887712,
year = {2024},
author = {Rekadwad, BN and Gonzalez, JM and Li, WJ},
title = {Editorial: Last universal common ancestor and origin of life: what uncultivated Bacteria, Archaea, and extremophiles can tell us.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1412625},
pmid = {38887712},
issn = {1664-302X},
}

@article {pmid38885730,
year = {2024},
author = {Lv, PL and Jia, C and Wei, CH and Zhao, HP and Chen, R},
title = {Biochar modulates intracellular electron transfer for nitrate reduction in denitrifying anaerobic methane oxidizing archaea.},
journal = {Bioresource technology},
volume = {406},
number = {},
pages = {130998},
doi = {10.1016/j.biortech.2024.130998},
pmid = {38885730},
issn = {1873-2976},
mesh = {*Methane/metabolism ; *Archaea/metabolism ; *Charcoal/metabolism ; *Nitrates/metabolism ; Electron Transport ; *Oxidation-Reduction ; Anaerobiosis ; *Denitrification/physiology ; Biofilms ; Extracellular Polymeric Substance Matrix/metabolism ; },
abstract = {Denitrifying anaerobic methane oxidizing (DAMO) archaea plays a significant role in simultaneously nitrogen removal and methane mitigation, yet its limited metabolic activity hinders engineering applications. This study employed biochar to explore its potential for enhancing the metabolic activity and nitrate reduction capacity of DAMO microorganisms. Sawdust biochar (7 g/L) was found to increase the nitrate reduction rate by 2.85 times, although it did not affect the nitrite reduction rate individually. Scanning electron microscopy (SEM) and fluorescence excitation-emission matrix (EEM) analyses revealed that biochar promoted microbial aggregation, and stimulated the secretion of extracellular polymeric substances (EPS). Moreover, biochar bolstered the redox capacity and conductivity of the biofilm, notably enhancing the activity of the electron transfer system by 1.65 times. Key genes involved in intracellular electron transport (Hdr, MHC, Rnf) and membrane transport proteins (BBP, ABC, NDH) of archaea were significantly up-regulated. These findings suggest that biochar regulates electrons generated by reverse methanogenesis to the membrane for nitrate reduction.},
}

*Methane/metabolism
*Archaea/metabolism
*Charcoal/metabolism
*Nitrates/metabolism
Electron Transport
*Oxidation-Reduction
Anaerobiosis
*Denitrification/physiology
Biofilms
Extracellular Polymeric Substance Matrix/metabolism

@article {pmid38884810,
year = {2024},
author = {Hu, Y and Ma, X and Tan, S and Li, XX and Cheng, M and Hou, J and Cui, HL},
title = {Correction: Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {90},
doi = {10.1007/s10482-024-01983-9},
pmid = {38884810},
issn = {1572-9699},
}

@article {pmid38866018,
year = {2024},
author = {Greening, C and Cabotaje, PR and Valentin Alvarado, LE and Leung, PM and Land, H and Rodrigues-Oliveira, T and Ponce-Toledo, RI and Senger, M and Klamke, MA and Milton, M and Lappan, R and Mullen, S and West-Roberts, J and Mao, J and Song, J and Schoelmerich, M and Stairs, CW and Schleper, C and Grinter, R and Spang, A and Banfield, JF and Berggren, G},
title = {Minimal and hybrid hydrogenases are active from archaea.},
journal = {Cell},
volume = {187},
number = {13},
pages = {3357-3372.e19},
pmid = {38866018},
issn = {1097-4172},
mesh = {*Archaea/genetics/enzymology ; Archaeal Proteins/metabolism/chemistry/genetics ; Genome, Archaeal ; *Hydrogen/metabolism ; *Hydrogenase/metabolism/genetics/chemistry ; Iron-Sulfur Proteins/metabolism/genetics/chemistry ; Models, Molecular ; *Phylogeny ; Protein Structure, Tertiary ; },
abstract = {Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.},
}

*Archaea/genetics/enzymology
Archaeal Proteins/metabolism/chemistry/genetics
Genome, Archaeal
*Hydrogen/metabolism
*Hydrogenase/metabolism/genetics/chemistry
Iron-Sulfur Proteins/metabolism/genetics/chemistry
Models, Molecular
*Phylogeny
Protein Structure, Tertiary

@article {pmid38852635,
year = {2024},
author = {Kong, L and Wang, Y and Cui, D and He, W and Zhang, C and Zheng, C},
title = {Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142500},
doi = {10.1016/j.chemosphere.2024.142500},
pmid = {38852635},
issn = {1879-1298},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Archaea/genetics/drug effects/metabolism ; Ammonia/metabolism ; Microbial Sensitivity Tests ; Oxidation-Reduction ; Single-Cell Analysis ; Spectrum Analysis, Raman ; Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.},
}

*Anti-Bacterial Agents/pharmacology
*Archaea/genetics/drug effects/metabolism
Ammonia/metabolism
Microbial Sensitivity Tests
Oxidation-Reduction
Single-Cell Analysis
Spectrum Analysis, Raman
Drug Resistance, Microbial/genetics

@article {pmid38829054,
year = {2024},
author = {Ma, Y and Sun, Z and Yang, H and Xie, W and Song, M and Zhang, B and Sui, L},
title = {The biosynthesis mechanism of bacterioruberin in halophilic archaea revealed by genome and transcriptome analysis.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0054024},
pmid = {38829054},
issn = {1098-5336},
support = {42306106//MOST | National Natural Science Foundation of China (NSFC)/ ; EMTUST-21-01//Key laboratory of Marine Resource Chemistry and Food Technology, Ministry of Education/ ; 2019KJ220//Tianjin Municipal Education Commission/ ; },
mesh = {*Genome, Archaeal ; *Carotenoids/metabolism ; *Gene Expression Profiling ; Halorubrum/genetics/metabolism/growth & development ; Transcriptome ; Archaeal Proteins/genetics/metabolism ; },
abstract = {UNLABELLED: Halophilic archaea are promising microbial cell factories for bacterioruberin (BR) production. BR is a natural product with multi-bioactivities, allowing potential application in many fields. In the previous work, a haloarchaeon Halorubrum sp. HRM-150 with a high proportion of BR (about 85%) was isolated, but the low yield impeded its large-scale production. This work figured out BR synthesis characteristics and mechanisms, and proposed strategies for yield improvement. First, glucose (10 g/L) and tryptone (15 g/L) were tested to be better sources for BR production. Besides, the combination of glucose and starch achieved the diauxic growth, and the biomass and BR productivity increased by 85% and 54% than using glucose. Additionally, this work first proposed the BR synthesis pattern, which differs from that of other carotenoids. As a structural component of cell membranes, the BR synthesis is highly coupled with growth, which was most active in the logarithm phase. Meanwhile, the osmotic down shock at the logarithm phase could increase the BR productivity without sacrificing the biomass. Moreover, the de-novo pathway for BR synthesis with a key gene of lyeJ, and its competitive pathways (notably tetraether lipids and retinal) were revealed through genome, transcriptome, and osmotic down shock. Therefore, the BR yield is expected to be improved through mutant construction, such as the overexpression of key gene lyeJ and the knockout of competitive genes, which need to be further explored. The findings will contribute to a better understanding of the metabolism mechanism in haloarchaea and the development of haloarchaea as microbial cell factories.

IMPORTANCE: Recent studies have revealed that halophilic microorganism is a promising microbial factory for the next-generation industrialization. Among them, halophilic archaea are advantageous as microbial factories due to their low contamination risk and low freshwater consumption. The halophilic archaea usually accumulate long chain C50 carotenoids, which are barely found in other organisms. Bacterioruberin (BR), the major C50 carotenoid, has multi-bioactivities, allowing potential application in food, cosmetic, and biomedical industries. However, the low yield impedes its large-scale application. This work figured out the BR synthesis characteristics and mechanism, and proposed several strategies for BR yield improvement, encouraging halophilic archaea to function as microbial factories for BR production. Meanwhile, the archaea have special evolutionary status and unique characteristics in taxonomy, the revelation of BR biosynthesis mechanism is beneficial for a better understanding of archaea.},
}

*Genome, Archaeal
*Carotenoids/metabolism
*Gene Expression Profiling
Halorubrum/genetics/metabolism/growth & development
Transcriptome
Archaeal Proteins/genetics/metabolism

@article {pmid38825783,
year = {2024},
author = {Orgler, E and Baumgartner, M and Duller, S and Kumptisch, C and Hausmann, B and Moser, D and Khare, V and Lang, M and Köcher, T and Frick, A and Muttenthaler, M and Makristathis, A and Moissl-Eichinger, C and Gasche, C},
title = {Archaea influence composition of endoscopically visible ileocolonic biofilms.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2359500},
pmid = {38825783},
issn = {1949-0984},
mesh = {Humans ; *Biofilms/growth & development ; *Gastrointestinal Microbiome ; *Archaea/classification/metabolism/genetics/isolation & purification ; Adult ; Middle Aged ; Female ; Male ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Feces/microbiology ; Colon/microbiology ; Methanobrevibacter/metabolism/genetics/growth & development/isolation & purification ; Colitis, Ulcerative/microbiology/metabolism ; Irritable Bowel Syndrome/microbiology/metabolism ; Aged ; Intestinal Mucosa/microbiology/metabolism ; Ileum/microbiology ; Fatty Acids, Volatile/metabolism ; Young Adult ; Bile Acids and Salts/metabolism ; },
abstract = {The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically Methanobrevibacter, correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of Methanobrevibacter correlated with Oscillospiraceae and epithelial short chain fatty acid metabolism and decreased levels of Ruminococcus gnavus. Absence of fecal Methanobrevibacter may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and Ruminococcus gnavus could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.},
}

Humans
*Biofilms/growth & development
*Gastrointestinal Microbiome
*Archaea/classification/metabolism/genetics/isolation & purification
Adult
Middle Aged
Female
Male
*Bacteria/classification/genetics/metabolism/isolation & purification
*Feces/microbiology
Colon/microbiology
Methanobrevibacter/metabolism/genetics/growth & development/isolation & purification
Colitis, Ulcerative/microbiology/metabolism
Irritable Bowel Syndrome/microbiology/metabolism
Aged
Intestinal Mucosa/microbiology/metabolism
Ileum/microbiology
Fatty Acids, Volatile/metabolism
Young Adult
Bile Acids and Salts/metabolism

@article {pmid38814265,
year = {2024},
author = {Rahn, HP and Sun, J and Li, Z and Waymouth, RM and Levy, R and Wender, PA},
title = {Isoprenoid CARTs: In Vitro and In Vivo mRNA Delivery by Charge-Altering Releasable Transporters Functionalized with Archaea-inspired Branched Lipids.},
journal = {Biomacromolecules},
volume = {25},
number = {7},
pages = {4305-4316},
doi = {10.1021/acs.biomac.4c00373},
pmid = {38814265},
issn = {1526-4602},
mesh = {Animals ; Mice ; *RNA, Messenger/genetics ; *Lipids/chemistry ; Humans ; Terpenes/chemistry ; Archaea/genetics/chemistry ; Nanoparticles/chemistry ; },
abstract = {The delivery of oligonucleotides across biological barriers is a challenge of unsurpassed significance at the interface of materials science and medicine, with emerging clinical utility in prophylactic and therapeutic vaccinations, immunotherapies, genome editing, and cell rejuvenation. Here, we address the role of readily available branched lipids in the design, synthesis, and evaluation of isoprenoid charge-altering releasable transporters (CARTs), a pH-responsive oligomeric nanoparticle delivery system for RNA. Systematic variation of the lipid block reveals an emergent relationship between the lipid block and the neutralization kinetics of the polycationic block. Unexpectedly, iA21A11, a CART with the smallest lipid side chain, isoamyl-, was identified as the lead isoprenoid CART for the in vitro transfection of immortalized lymphoblastic cell lines. When administered intramuscularly in a murine model, iA21A11-mRNA complexes induce higher protein expression levels than our previous lead CART, ONA. Isoprenoid CARTs represent a new delivery platform for RNA vaccines and other polyanion-based therapeutics.},
}

Animals
Mice
*RNA, Messenger/genetics
*Lipids/chemistry
Humans
Terpenes/chemistry
Archaea/genetics/chemistry
Nanoparticles/chemistry

@article {pmid38811725,
year = {2024},
author = {von Kügelgen, A and Cassidy, CK and van Dorst, S and Pagani, LL and Batters, C and Ford, Z and Löwe, J and Alva, V and Stansfeld, PJ and Bharat, TAM},
title = {Membraneless channels sieve cations in ammonia-oxidizing marine archaea.},
journal = {Nature},
volume = {630},
number = {8015},
pages = {230-236},
pmid = {38811725},
issn = {1476-4687},
mesh = {*Ammonia/chemistry/metabolism ; *Aquatic Organisms/chemistry/metabolism/ultrastructure ; *Archaea/chemistry/metabolism/ultrastructure ; Cations/chemistry/metabolism ; *Cell Membrane ; Cryoelectron Microscopy ; Models, Molecular ; Oxidation-Reduction ; Polysaccharides/metabolism/chemistry ; },
abstract = {Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle[1,2]. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.},
}

*Ammonia/chemistry/metabolism
*Aquatic Organisms/chemistry/metabolism/ultrastructure
*Archaea/chemistry/metabolism/ultrastructure
Cations/chemistry/metabolism
*Cell Membrane
Cryoelectron Microscopy
Models, Molecular
Oxidation-Reduction
Polysaccharides/metabolism/chemistry

@article {pmid38806737,
year = {2024},
author = {Cheng, M and Li, XX and Hou, J and Cui, HL},
title = {Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov., Halophilic Archaea Isolated from Coastal and Inland Saline Soil.},
journal = {Current microbiology},
volume = {81},
number = {7},
pages = {194},
pmid = {38806737},
issn = {1432-0991},
support = {32070003//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *DNA, Archaeal/genetics/chemistry ; Halobacteriaceae/classification/genetics/isolation & purification ; Base Composition ; Phospholipids/analysis ; Sequence Analysis, DNA ; },
abstract = {Four halophilic archaeal strains, BCD28[T], BND7[T], PSR21[T], and PSRA2[T], were isolated from coastal and inland saline soil, respectively. The 16S rRNA and rpoB' gene sequence similarities among these four strains and current species of Halomarina were 95.9-96.6% and 86.9-90.3%, respectively. Phylogenetic and phylogenomic analyses revealed that these four strains tightly cluster with the current species of the genus Halomarina. The AAI, ANI, and dDDH values among these four strains and current species of Halomarina were 65.3-68.4%, 75.8-77.7%, and 20.3-22.0%, respectively, clearly below the threshold values for species demarcation. Strains BCD28[T], BND7[T], PSR21[T], and PSRA2[T] could be differentiated from the current species of Halomarina based on the comparison of diverse phenotypic characteristics. The major polar lipids of these four strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and four to five glycolipids. Phosphatidylglycerol sulfate (PGS) was only detected in strain BND7[T]. The phenotypic, phylogenetic, and genome-based analyses suggested that strains BCD28[T] (= CGMCC 1.18776[T] = JCM 34908[T]), BND7[T] (= CGMCC 1.18778[T] = JCM 34910[T]), PSR21[T] (= CGMCC 1.17027[T] = JCM 34147[T]), and PSRA2[T] (= CGMCC 1.17214[T] = JCM 34148[T]) represent four novel species of the genus Halomarina, for which the names Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov. are proposed.},
}

*Phylogeny
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
*DNA, Archaeal/genetics/chemistry
Halobacteriaceae/classification/genetics/isolation & purification
Base Composition
Phospholipids/analysis
Sequence Analysis, DNA

@article {pmid38799924,
year = {2024},
author = {},
title = {Expression of Concern: Haloferax massiliensis sp. nov., the first human-associated halophilic archaea.},
journal = {New microbes and new infections},
volume = {59},
number = {},
pages = {101323},
pmid = {38799924},
issn = {2052-2975},
}

@article {pmid38765610,
year = {2024},
author = {Basu, S and Kurgan, L},
title = {Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1968-1977},
pmid = {38765610},
issn = {2001-0370},
abstract = {Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.},
}

@article {pmid38753237,
year = {2024},
author = {Zhang, Y and Xiang, Y and Yang, Z and Xu, R},
title = {Co-occurrence of dominant bacteria and methanogenic archaea and their metabolic traits in a thermophilic anaerobic digester.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {25},
pages = {36716-36727},
pmid = {38753237},
issn = {1614-7499},
support = {42007357//National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics ; Anaerobiosis ; *Methane/metabolism ; Phylogeny ; Bioreactors/microbiology ; },
abstract = {Thermophilic anaerobic digestion (TAD) represents a promising biotechnology for both methane energy production and waste stream treatment. However, numerous critical microorganisms and their metabolic characteristics involved in this process remain unidentified due to the limitations of culturable isolates. This study investigated the phylogenetic composition and potential metabolic traits of bacteria and methanogenic archaea in a TAD system using culture-independent metagenomics. Predominant microorganisms identified in the stable phase of TAD included hydrogenotrophic methanogens (Methanothermobacter and Methanosarcina) and hydrogen-producing bacteria (Coprothermobacter, Acetomicrobium, and Defluviitoga). Nine major metagenome-assembled genomes (MAGs) associated with the dominant genera were selected to infer their metabolic potentials. Genes related to thermal resistance were widely found in all nine major MAGs, such as the molecular chaperone genes, Clp protease gene, and RNA polymerase genes, which may contribute to their predominance under thermophilic condition. Thermophilic temperatures may increase the hydrogen partial pressure of Coprothermobacter, Acetomicrobium, and Defluviitoga, subsequently altering the primary methanogenesis pathway from acetoclastic pathway to hydrogenotrophic pathway in the TAD. Consequently, genes encoding the hydrogenotrophic methanogenesis pathway were the most abundant in the recovered archaeal MAGs. The potential interaction between hydrogen-producing bacteria and hydrogenotrophic methanogens may play critical roles in TAD processes.},
}

*Archaea/genetics/metabolism
*Bacteria/metabolism/genetics
Anaerobiosis
*Methane/metabolism
Phylogeny
Bioreactors/microbiology

@article {pmid38744628,
year = {2024},
author = {Liu, X and Su, D and Huan, H and Zhang, J and Zhen, H and Jia, Q and Zhao, M},
title = {Corrigendum to "Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China" [Sci. Total Environ. 927 (2024): 171642].},
journal = {The Science of the total environment},
volume = {933},
number = {},
pages = {172946},
doi = {10.1016/j.scitotenv.2024.172946},
pmid = {38744628},
issn = {1879-1026},
}

@article {pmid38733792,
year = {2024},
author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N},
title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102486},
doi = {10.1016/j.mib.2024.102486},
pmid = {38733792},
issn = {1879-0364},
mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; },
abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.},
}

*Alkanes/metabolism
*Archaea/enzymology/genetics/metabolism
*Oxidation-Reduction
*Oxidoreductases/metabolism/genetics
*Phylogeny
Electron Transport
Archaeal Proteins/metabolism/genetics/chemistry
Gene Transfer, Horizontal
Bacteria/enzymology/genetics/metabolism/classification

@article {pmid38700364,
year = {2024},
author = {Padalko, A and Nair, G and Sousa, FL},
title = {Fusion/fission protein family identification in Archaea.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0094823},
pmid = {38700364},
issn = {2379-5077},
support = {VRG15-007//Wien Wissenschafts- Forschungs- und TechnologieFonds/ ; },
mesh = {*Archaea/genetics ; *Archaeal Proteins/genetics/chemistry/metabolism ; *Genome, Archaeal/genetics ; *Phylogeny ; },
abstract = {The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.},
}

*Archaea/genetics
*Archaeal Proteins/genetics/chemistry/metabolism
*Genome, Archaeal/genetics
*Phylogeny