@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 = {},
number = {},
pages = {},
doi = {10.1261/rna.080091.124},
pmid = {39043438},
issn = {1469-9001},
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 4,464 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. 3,618 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.},
}

@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 = {},
doi = {10.3201/eid3008.240181},
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 Mcllroy, 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 = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae137},
pmid = {39030685},
issn = {1751-7370},
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.},
}

@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 = {},
doi = {10.1099/ijsem.0.006435},
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 = {},
number = {},
pages = {e0103324},
doi = {10.1128/mbio.01033-24},
pmid = {38953360},
issn = {2150-7511},
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.},
}

@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 = {},
number = {},
pages = {},
pmid = {38918468},
issn = {2058-5276},
support = {INV-037174/GATES/Bill & Melinda Gates Foundation/United States ; INV-037174/GATES/Bill & Melinda Gates Foundation/United States ; },
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.},
}

@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},
doi = {10.1073/pnas.2316422121},
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 = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae111},
pmid = {38896033},
issn = {1751-7370},
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 Sec insertion sequence (SECIS) element. Although archaea and eukaryotes adopt a similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed more than 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.},
}

@article {pmid38890479,
year = {2024},
author = {Du Toit, A},
title = {Gassy archaea.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38890479},
issn = {1740-1534},
}

@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},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.05.032},
pmid = {38866018},
issn = {1097-4172},
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.},
}

@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 = {},
number = {},
pages = {142500},
doi = {10.1016/j.chemosphere.2024.142500},
pmid = {38852635},
issn = {1879-1298},
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.},
}

@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 = {},
number = {},
pages = {e0054024},
doi = {10.1128/aem.00540-24},
pmid = {38829054},
issn = {1098-5336},
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.},
}

@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},
doi = {10.1080/19490976.2024.2359500},
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 {pmid38818484,
year = {2022},
author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M},
title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.},
journal = {mLife},
volume = {1},
number = {4},
pages = {374-381},
pmid = {38818484},
issn = {2770-100X},
abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1021/acs.biomac.4c00373},
pmid = {38814265},
issn = {1526-4602},
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.},
}

@article {pmid38817676,
year = {2022},
author = {Liu, Y and Li, M},
title = {The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea.},
journal = {mLife},
volume = {1},
number = {2},
pages = {218-222},
pmid = {38817676},
issn = {2770-100X},
abstract = {The applications of marker gene concatenation have been advanced to resolve the key questions in the Tree of Life. However, the interphylum evolutionary relationship between Korarchaeota of TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) and Asgard archaea remains uncertain. We applied a marker gene ranking procedure to examine their evolutionary history. Our updated trees showed confident placements of (1) Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea; (2) Njordarchaeota at basal branch to Korarchaeota instead of within Asgard archaea. They highlight the importance of evaluating marker genes for phylogeny inference of the Archaea domain.},
}

@article {pmid38818328,
year = {2022},
author = {Wang, Y and Xie, R and Hou, J and Lv, Z and Li, L and Hu, Y and Huang, H and Wang, F},
title = {The late Archaean to early Proterozoic origin and evolution of anaerobic methane-oxidizing archaea.},
journal = {mLife},
volume = {1},
number = {1},
pages = {96-100},
pmid = {38818328},
issn = {2770-100X},
abstract = {Microorganisms, called anaerobic methane-oxidizing archaea (ANME), can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth. We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating. Our results show that ANMEs originated in the late Archaean to early Proterozoic eon. During this period of time, our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation, a dramatic drop in the Earth's surface temperature. This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time, which is an unappreciated potential cause that led to the Huronian Glaciation.},
}

@article {pmid38818326,
year = {2022},
author = {Da Cunha, V and Gaïa, M and Forterre, P},
title = {The expanding Asgard archaea and their elusive relationships with Eukarya.},
journal = {mLife},
volume = {1},
number = {1},
pages = {3-12},
pmid = {38818326},
issn = {2770-100X},
abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.},
}

@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 = {},
number = {},
pages = {},
pmid = {38811725},
issn = {1476-4687},
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.},
}

@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 = {},
number = {},
pages = {},
pmid = {38753237},
issn = {1614-7499},
support = {42007357//National Natural Science Foundation of China/ ; },
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.},
}

@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 = {},
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},
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.},
}

@article {pmid38716123,
year = {2022},
author = {Kanno, N and Kato, S and Itoh, T and Ohkuma, M and Shigeto, S},
title = {Resonance Raman analysis of intracellular vitamin B12 analogs in methanogenic archaea.},
journal = {Analytical science advances},
volume = {3},
number = {5-6},
pages = {165-173},
pmid = {38716123},
issn = {2628-5452},
abstract = {Methanogenic archaea (methanogens) are microorganisms that can synthesize methane. They are found in diverse environments ranging from paddy fields to animal digestive tracts to deep-sea hydrothermal vents. Investigating their distribution and physiological activity is crucial for the detailed analysis of the dynamics of greenhouse gas generation and the search for the environmental limits of life. In methanogens, cobamide cofactors (vitamin B12 analogs) play a key role in methane synthesis and carbon fixation, thus serving as a marker compound that metabolically characterizes them. Here, we report on resonance Raman detection of cobamides in methanogenic cells without destroying cells and provide structural insights into those cobamides. We succeeded in detecting cobamides in four representative methanogens Methanosarcina mazei, Methanosarcina barkeri, Methanopyrus kandleri, and Methanocaldococcus jannaschii. The former two are mesophilic, cytochrome-containing methanogens, whereas the latter two are hyperthermophilic, non-cytochrome-containing methanogens. The 532 nm-excited Raman spectra of single or multiple cells of the four species all showed resonance Raman bands of cobamides arising mainly from the corrin ring, with the most intense one at ∼1500 cm[-1]. We envision that resonance Raman microspectroscopy could be useful for in situ, nondestructive identification of methanogenic cells that produce high levels of cobamides.},
}

@article {pmid38700364,
year = {2024},
author = {Padalko, A and Nair, G and Sousa, FL},
title = {Fusion/fission protein family identification in Archaea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0094823},
doi = {10.1128/msystems.00948-23},
pmid = {38700364},
issn = {2379-5077},
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.},
}

@article {pmid38673759,
year = {2024},
author = {Dobryakova, NV and Dumina, MV and Zhgun, AA and Pokrovskaya, MV and Aleksandrova, SS and Zhdanov, DD and Kudryashova, EV},
title = {L-Asparaginase Conjugates from the Hyperthermophilic Archaea Thermococcus sibiricus with Improved Biocatalytic Properties.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
pmid = {38673759},
issn = {1422-0067},
support = {project No. 22-74-10100//Russian Science Foundation/ ; },
mesh = {*Asparaginase/chemistry/metabolism ; *Thermococcus/enzymology ; Hydrogen-Ion Concentration ; *Enzyme Stability ; *Biocatalysis ; Polyethylene Glycols/chemistry ; Temperature ; Archaeal Proteins/chemistry/metabolism ; },
abstract = {This study investigated the effect of polycationic and uncharged polymers (and oligomers) on the catalytic parameters and thermostability of L-asparaginase from Thermococcus sibiricus (TsA). This enzyme has potential applications in the food industry to decrease the formation of carcinogenic acrylamide during the processing of carbohydrate-containing products. Conjugation with the polyamines polyethylenimine and spermine (PEI and Spm) or polyethylene glycol (PEG) did not significantly affect the secondary structure of the enzyme. PEG contributes to the stabilization of the dimeric form of TsA, as shown by HPLC. Furthermore, neither polyamines nor PEG significantly affected the binding of the L-Asn substrate to TsA. The conjugates showed greater maximum activity at pH 7.5 and 85 °C, 10-50% more than for native TsA. The pH optima for both TsA-PEI and TsA-Spm conjugates were shifted to lower pH ranges from pH 10 (for the native enzyme) to pH 8.0. Additionally, the TsA-Spm conjugate exhibited the highest activity at pH 6.5-9.0 among all the samples. Furthermore, the temperature optimum for activity at pH 7.5 shifted from 90-95 °C to 80-85 °C for the conjugates. The thermal inactivation mechanism of TsA-PEG appeared to change, and no aggregation was observed in contrast to that of the native enzyme. This was visually confirmed and supported by the analysis of the CD spectra, which remained almost unchanged after heating the conjugate solution. These results suggest that TsA-PEG may be a more stable form of TsA, making it a potentially more suitable option for industrial use.},
}

*Asparaginase/chemistry/metabolism
*Thermococcus/enzymology
Hydrogen-Ion Concentration
*Enzyme Stability
*Biocatalysis
Polyethylene Glycols/chemistry
Temperature
Archaeal Proteins/chemistry/metabolism

@article {pmid38664262,
year = {2024},
author = {Mukherjee, D and Selvi, VA and Ganguly, J and Masto, RE},
title = {New insights into the coal-associated methane architect: the ancient archaebacteria.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {234},
pmid = {38664262},
issn = {1432-072X},
mesh = {*Methane/metabolism ; *Coal ; *Archaea/metabolism/genetics ; Ecosystem ; Phylogeny ; },
abstract = {Exploration and marketable exploitation of coalbed methane (CBM) as cleaner fuel has been started globally. In addition, incidence of methane in coal basins is an imperative fraction of global carbon cycle. Significantly, subsurface coal ecosystem contains methane forming archaea. There is a rising attention in optimizing microbial coal gasification to exploit the abundant or inexpensive coal reserves worldwide. Therefore, it is essential to understand the coalbeds in geo-microbial perspective. Current review provides an in-depth analysis of recent advances in our understanding of how methanoarchaea are distributed in coal deposits globally. Specially, we highlight the findings on coal-associated methanoarchaeal existence, abundance, diversity, metabolic activity, and biogeography in diverse coal basins worldwide. Growing evidences indicates that we have arrived an exciting era of archaeal research. Moreover, gasification of coal into methane by utilizing microbial methanogenesis is a considerable way to mitigate the energy crisis for the rising world population.},
}

*Methane/metabolism
*Coal
*Archaea/metabolism/genetics
Ecosystem
Phylogeny

@article {pmid38659982,
year = {2024},
author = {Li, Q and Cheng, X and Liu, X and Gao, P and Wang, H and Su, C and Huang, Q},
title = {Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1377721},
pmid = {38659982},
issn = {1664-302X},
abstract = {Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4[+], and Cl[-] played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.},
}

@article {pmid38655083,
year = {2024},
author = {van Wolferen, M and Ithurbide, S and Santiago-Martínez, MG and Charles-Orszag, A},
title = {Editorial: Molecular Biology of Archaea - 2022.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1393932},
pmid = {38655083},
issn = {1664-302X},
}

@article {pmid38644887,
year = {2024},
author = {Gulati, P and Singh, A and Patra, S and Bhat, S and Verma, A},
title = {Restriction modification systems in archaea: A panoramic outlook.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e27382},
pmid = {38644887},
issn = {2405-8440},
abstract = {Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.},
}

@article {pmid38640671,
year = {2024},
author = {Wang, Q and Zheng, G and Ni, L and Wang, H and Li, W and Guo, P and Wang, Y and Zheng, D and Wu, J and Zhang, D},
title = {Colonization characteristics and dynamic transition of archaea communities on polyethylene and polypropylene microplastics in the sediments of mangrove ecosystems.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134343},
doi = {10.1016/j.jhazmat.2024.134343},
pmid = {38640671},
issn = {1873-3336},
abstract = {Microplastics are a growing concern in mangrove ecosystems; however, their effects on archaeal communities and related ecological processes remain unclear. We conducted in situ biofilm-enrichment experiments to investigate the ecological influence of polyethylene (PE) and polypropylene microplastics on archaeal communities in the sediments of mangrove ecosystems. The archaeal community present on microplastics was distinct from that of the surrounding sediments at an early stage but became increasingly similar over time. Bathyarchaeota, Thaumarchaeota, Euryarchaeota, and Asgardaeota were the most abundant phyla. Methanolobus, an archaeal biomarker, was enriched in PE biofilms, and significantly controlled by homogeneous selection in the plastisphere, indicating an increased potential risk of methane emission. The dominant archaeal assembly process in the sediments was deterministic (58.85%-70.47%), while that of the PE biofilm changed from stochastic to deterministic during the experiment. The network of PE plastispheres showed less complexity and competitive links, and higher modularity and stability than that of sediments. Functional prediction showed an increase in aerobic ammonia oxidation during the experiment, whereas methanogenesis and chemoheterotrophy were significantly higher in the plastisphere. This study provides novel insights into the impact of microplastic pollution on archaeal communities and their mediating ecological functions in mangrove ecosystems.},
}

@article {pmid38593165,
year = {2024},
author = {Price, MN and Arkin, AP},
title = {A fast comparative genome browser for diverse bacteria and archaea.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301871},
pmid = {38593165},
issn = {1932-6203},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genomics ; Proteins/genetics ; Chromosome Mapping ; },
abstract = {Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.},
}

*Archaea/genetics
*Bacteria/genetics
Genomics
Proteins/genetics
Chromosome Mapping

@article {pmid38593075,
year = {2024},
author = {Michimori, Y and Izaki, R and Su, Y and Fukuyama, Y and Shimamura, S and Nishimura, K and Miwa, Y and Hamakita, S and Shimosaka, T and Makino, Y and Takeno, R and Sato, T and Beppu, H and Cann, I and Kanai, T and Nunoura, T and Atomi, H},
title = {Removal of phosphoglycolate in hyperthermophilic archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {16},
pages = {e2311390121},
doi = {10.1073/pnas.2311390121},
pmid = {38593075},
issn = {1091-6490},
support = {JP19H05679//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19H05684//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPNP22010//New Energy and Industrial Technology Development Organization (NEDO)/ ; },
abstract = {Many organisms that utilize the Calvin-Benson-Bassham (CBB) cycle for autotrophic growth harbor metabolic pathways to remove and/or salvage 2-phosphoglycolate, the product of the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). It has been presumed that the occurrence of 2-phosphoglycolate salvage is linked to the CBB cycle, and in particular, the C2 pathway to the CBB cycle and oxygenic photosynthesis. Here, we examined 2-phosphoglycolate salvage in the hyperthermophilic archaeon Thermococcus kodakarensis, an obligate anaerobe that harbors a Rubisco that functions in the pentose bisphosphate pathway. T. kodakarensis harbors enzymes that have the potential to convert 2-phosphoglycolate to glycine and serine, and their genes were identified by biochemical and/or genetic analyses. 2-phosphoglycolate phosphatase activity increased 1.6-fold when cells were grown under microaerobic conditions compared to anaerobic conditions. Among two candidates, TK1734 encoded a phosphatase specific for 2-phosphoglycolate, and the enzyme was responsible for 80% of the 2-phosphoglycolate phosphatase activity in T. kodakarensis cells. The TK1734 disruption strain displayed growth impairment under microaerobic conditions, which was relieved upon addition of sodium sulfide. In addition, glycolate was detected in the medium when T. kodakarensis was grown under microaerobic conditions. The results suggest that T. kodakarensis removes 2-phosphoglycolate via a phosphatase reaction followed by secretion of glycolate to the medium. As the Rubisco in T. kodakarensis functions in the pentose bisphosphate pathway and not in the CBB cycle, mechanisms to remove 2-phosphoglycolate in this archaeon emerged independent of the CBB cycle.},
}

@article {pmid38592380,
year = {2024},
author = {Gao, X and Wang, S and Kong, W and Li, G and Zhang, L and Yin, X},
title = {Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {5},
pages = {167},
pmid = {38592380},
issn = {1573-2983},
support = {2022YSKY-41//Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China/ ; },
abstract = {Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.},
}

@article {pmid38570877,
year = {2024},
author = {Yin, X and Zhou, G and Cai, M and Richter-Heitmann, T and Zhu, QZ and Maeke, M and Kulkarni, AC and Nimzyk, R and Elvert, M and Friedrich, MW},
title = {Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {68},
pmid = {38570877},
issn = {2049-2618},
support = {49926684//Cluster of Excellence EXC 309/ ; 49926684//Cluster of Excellence EXC 309/ ; 390741601//Cluster of Excellence EXC 2077/ ; 390741601//Cluster of Excellence EXC 2077/ ; },
mesh = {*Archaea/genetics ; Isotope Labeling ; Oxidation-Reduction ; *Methane/metabolism ; Carbon/metabolism ; DNA ; Anaerobiosis ; Geologic Sediments ; Phylogeny ; },
abstract = {BACKGROUND: The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8).

RESULTS: To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and [13]C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated [13]C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated [13]C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility.

CONCLUSION: We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and Bathy-8 archaea in the environment. Video Abstract.},
}

*Archaea/genetics
Isotope Labeling
Oxidation-Reduction
*Methane/metabolism
Carbon/metabolism
DNA
Anaerobiosis
Geologic Sediments
Phylogeny

@article {pmid38530473,
year = {2024},
author = {Fry, M},
title = {The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree.},
journal = {History and philosophy of the life sciences},
volume = {46},
number = {2},
pages = {16},
pmid = {38530473},
issn = {1742-6316},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Phylogeny ; *Archaea/genetics ; Biological Evolution ; *Biological Science Disciplines ; },
abstract = {Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.},
}

Phylogeny
*Archaea/genetics
Biological Evolution
*Biological Science Disciplines

@article {pmid38519541,
year = {2024},
author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, Á and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38519541},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.},
}

@article {pmid38500564,
year = {2024},
author = {Batista, M and Langendijk-Genevaux, P and Kwapisz, M and Canal, I and Phung, DK and Plassart, L and Capeyrou, R and Moalic, Y and Jebbar, M and Flament, D and Fichant, G and Bouvier, M and Clouet-d'Orval, B},
title = {Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {1},
pages = {lqae026},
pmid = {38500564},
issn = {2631-9268},
abstract = {RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5'-3' aRNase J exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3'-5' polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ΔASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.},
}

@article {pmid38499200,
year = {2024},
author = {Guo, K and Li, D and Hao, T and Teng, L and Li, S and Zeng, H and Zhang, J},
title = {Potential directions for future development of mainstream partial nitrification-anammox processes: Ammonia-oxidizing archaea as novel functional microorganisms providing nitrite.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130605},
doi = {10.1016/j.biortech.2024.130605},
pmid = {38499200},
issn = {1873-2976},
abstract = {The application of ammonia-oxidizing archaea (AOA)-based partial nitrification-anammox (PN-A) for mainstream wastewater treatment has attracted research interest because AOA can maintain higher activity in low-temperature environments and they have higher affinity for oxygen and ammonia-nitrogen compared with ammonia-oxidizing bacteria (AOB), thus facilitating stabilized nitrite production, deep removal of low-ammonia, and nitrite-oxidizing bacteria suppression. Moreover, the low affinity of AOA for ammonia makes them more tolerant to N-shock loading and more efficiently integrated with anaerobic ammonium oxidation (anammox). Based on the limitations of the AOB-based PN-A process, this review comprehensively summarizes the potential and significance of AOA for nitrite supply, then gives strategies and influencing factors for replacing AOB with AOA. Additionally, the methods and key influences on the coupling of AOA and anammox are explored. Finally, this review proposes four AOA-based oxygen- or ammonia-limited autotrophic nitritation/denitrification processes to address the low effluent quality and instability of mainstream PN-A processes.},
}

@article {pmid38486239,
year = {2024},
author = {Alghamrawy, BT and Hegazy, GE and Sabry, SA and Ghozlan, H},
title = {Production, characterization and biomedical potential of biosurfactants produced by haloalkaliphilic archaea from Wadi El-Natrun, Egypt.},
journal = {Microbial cell factories},
volume = {23},
number = {1},
pages = {84},
pmid = {38486239},
issn = {1475-2859},
mesh = {*Sodium Chloride/pharmacology/metabolism ; Egypt ; Antioxidants/metabolism ; *Halobacteriaceae/metabolism ; Anti-Inflammatory Agents/metabolism ; },
abstract = {Extreme halophilic archaea that can live in high saline environments can offer potential applications in different biotechnological fields. This study delves into the fascinating field of halophilic archaea and their ability to produce biosurfactants. Some strains of haloarchaea were isolated from Wadi El-Natrun and were screened for biosurfactants production in a standard basal medium using emulsification index assay. Two strains were chosen as the potential strains for surface tension reduction. They were identified as Natrialba sp. BG1 and N3. The biosurfactants production was optimized and the produced emulsifiers were partially purified and identified using FTIR and NMR. Sequential statistical optimization, Plackett-Burman (PB) and Box-Behnken Designs (BBD) were carried out using 5 factors: oil, NaCl, casamino acids, pH, and inoculum size. The most significant factors were used for the next Response Surface Methodology experiment. The final optimal conditions for biosurfactants production were the inoculum size 2% pH 11 and NaCl 250 g/L, for Natrialba sp. BG1 and inoculum size 2.2%, pH 10 and NaCl 100 g/L for Natrialba sp. N3. The produced biosurfactants were tested for wound healing and the results indicated that Natrialba sp. BG1 biosurfactants is more efficient than Natrialba sp. N3 biosurfactants. Biosurfactants extracts were tested for their cytotoxic effects on normal cell line as well as on different cancer cells using MTT assay. The findings demonstrated that varying concentrations of the biosurfactants (31.25, 62.5, 125, 250, 500 and 1000 µg/mL) exhibited cytotoxic effects on the cell lines being tested. Additionally, the outcomes unveiled the presence of anti-inflammatory and antioxidant properties for both biosurfactants. Consequently, they could potentially serve as natural, safe, and efficient novel agents for combating cancer, promoting wound healing, and providing anti-inflammatory and antioxidant benefits.},
}

*Sodium Chloride/pharmacology/metabolism
Egypt
Antioxidants/metabolism
*Halobacteriaceae/metabolism
Anti-Inflammatory Agents/metabolism

@article {pmid38479518,
year = {2024},
author = {Liu, X and Sun, D and Huang, H and Zhang, J and Zheng, H and Jia, Q and Zhao, M},
title = {Rice-fish coculture improves paddy soil nitrogen availability in subtropical regions of South China by regulating ammonia-oxidizing bacteria and archaea without phosphorus addition.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171642},
doi = {10.1016/j.scitotenv.2024.171642},
pmid = {38479518},
issn = {1879-1026},
abstract = {Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions with phosphorus (P) deficiency limiting agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are responsible for ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition to improve soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of the inorganic P (0 and 50 mg P kg[-1] as KH2PO4) addition combined without and with fish on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content and urease activity without P addition compared with P addition. RFC significantly increased urease activity and shannon diversity of AOA, and reduced NAG activity and shannon diversity of AOB without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced by the introduction of fish and/or P availability, of which AOB is linked to N availability and indirectly influenced by the regulation of N-related enzymes. Overall, RFC could improve paddy soil N availability in subtropical region without P addition, which provides a scientific basis for promoting the practices that RFC reduce N fertilizer application in South China.},
}

@article {pmid38476944,
year = {2024},
author = {von Hoyningen-Huene, AJE and Bang, C and Rausch, P and Rühlemann, M and Fokt, H and He, J and Jensen, N and Knop, M and Petersen, C and Schmittmann, L and Zimmer, T and Baines, JF and Bosch, TCG and Hentschel, U and Reusch, TBH and Roeder, T and Franke, A and Schulenburg, H and Stukenbrock, E and Schmitz, RA},
title = {The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1347422},
pmid = {38476944},
issn = {1664-302X},
abstract = {Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.},
}

@article {pmid38472444,
year = {2024},
author = {Hu, Y and Ma, X and Tan, S and Li, XX and Cheng, M and Hou, J and Cui, HL},
title = {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 = {51},
pmid = {38472444},
issn = {1572-9699},
support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 32070003//National Natural Science Foundation of China/ ; },
abstract = {The current species of Halosegnis and Salella within the class Halobacteria are closely related based on phylogenetic, phylogenomic, and comparative genomic analyses. The Halosegnis species showed 99.8-100.0% 16S rRNA and 96.6-99.6% rpoB' gene similarities to the Salella species, respectively. Phylogenetic and phylogenomic analyses showed that Salella cibi CBA1133[T], the sole species of Salella, formed a single tight cluster with Halosegnis longus F12-1[T], then with Halosegnis rubeus F17-44[T]. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133[T] and Halosegnis longus F12-1[T] were 99.2, 94.2, and 98.6%, respectively, much higher than the thresholds for species demarcation. This genome-based classification revealed that the genus Salella should be merged with Halosegnis, and Salella cibi should be a later heterotypic synonym of Halosegnis longus. Halophilic archaeal strains DT72[T], DT80[T], DT85[T], and DT116[T], isolated from the saline soil of a tidal flat in China, were subjected to polyphasic taxonomic characterization. The phenotypic, chemotaxonomic, phylogenetic, and phylogenomic features indicated that strains DT72[T] (= CGMCC 1.18925[T] = JCM 35418[T]), DT80[T] (= CGMCC 1.18926[T] = JCM 35419[T]), DT85[T] (= CGMCC 1.19049[T] = JCM 35605[T]), and DT116[T] (= CGMCC 1.19045[T] = JCM 35606[T]) represent four novel species of the genera Halorussus, Halosegnis and Haloglomus, respectively, for which the names, Halorussus caseinilyticus sp. nov., Halorussus lipolyticus sp. nov., Halosegnis marinus sp. nov., and Haloglomus litoreum sp. nov., are proposed.},
}

@article {pmid38472392,
year = {2024},
author = {Tran, LT and Akıl, C and Senju, Y and Robinson, RC},
title = {The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {273},
pmid = {38472392},
issn = {2399-3642},
support = {JPMJCR19S5//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP20H00476//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19K23727//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K05718//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04423//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; GBMF9743//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9743//Simons Foundation/ ; },
abstract = {Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.},
}

@article {pmid38471592,
year = {2024},
author = {Chisholm, C and Di, H and Cameron, K and Podolyan, A and Shen, J and Zhang, L and Sirisena, K and Godsoe, W},
title = {Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171627},
doi = {10.1016/j.scitotenv.2024.171627},
pmid = {38471592},
issn = {1879-1026},
abstract = {This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.},
}

@article {pmid38466496,
year = {2024},
author = {Huda, N and Rana, MR and Huq, MA and Al-Mamun, A and Rahman, ST and Alam, MK and Rahman, MM},
title = {Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {4},
pages = {355},
pmid = {38466496},
issn = {1573-2959},
abstract = {Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu[2+], Fe[2+], Pb[2+], Cd[2+], and Zn[2+]) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe[2+], total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.},
}

@article {pmid38458444,
year = {2024},
author = {Peng, L and Jia, M and Li, S and Wang, X and Liang, C and Xu, Y},
title = {Developing antibiotics-based strategies to efficiently enrich ammonia-oxidizing archaea from wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {923},
number = {},
pages = {171479},
doi = {10.1016/j.scitotenv.2024.171479},
pmid = {38458444},
issn = {1879-1026},
abstract = {The effects of five antibiotics (i.e., ampicillin, streptomycin, carbenicillin, kanamycin and tetracycline) on ammonia-oxidizing archaea (AOA) enrichment from anoxic activated sludge were investigated. The combined use of five antibiotics during 90-day cultivation could selectively inhibit nitrite-oxidizing bacteria (NOB) and ammonia-oxidizing bacteria (AOB) with AOA unaffected, as evidenced by the nitrite accumulation ratio of 100 % and the proportion of AOA in ammonia-oxidizing microbes over 91 %. The alternative use of five antibiotics was the optimal approach to screening for AOA during 348-day cultivation, which inhibited AOB growth at a level equivalent to the combined use of five antibiotics (the AOB-amoA gene decreased by over 99.90 %), further promoted AOA abundance (the much higher AOA-amoA to AOB-amoA gene copy number ratio (1453.30) than that in the groups with the combined use of five antibiotics (192.94)), eliminated bacterial adaptation to antibiotics and reduced antibiotic-resistant bacteria to form Nitrocosmicus-dominant community (42.35 % in abundance).},
}

@article {pmid38444950,
year = {2024},
author = {Sun, D and Rozmoš, M and Kotianová, M and Hršelová, H and Jansa, J},
title = {Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils.},
journal = {Heliyon},
volume = {10},
number = {4},
pages = {e26485},
pmid = {38444950},
issn = {2405-8440},
abstract = {Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.},
}

@article {pmid38436843,
year = {2024},
author = {Wang, J and Wen, X and Fang, Z and Gao, P and Wu, P and Li, X and Zeng, G},
title = {Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38436843},
issn = {1614-7499},
support = {52000019//National Natural Science Foundation of China/ ; KJQN202101526//Chongqing Municipal Education Commission/ ; YS2021089//Chongqing Bayu Scholars Young Scholars Project/ ; },
abstract = {Studies published recently proposed that ammonia-oxidizing archaea (AOA) may be beneficial for hypersaline (salinity > 50 g NaCl L[-1]) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L[-1] in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance to the challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.},
}

@article {pmid38435527,
year = {2024},
author = {Liu, Y and Qian, Y and Fu, L and Zhu, C and Li, X and Wang, Q and Ling, H and Du, H and Zhou, S and Kong, XY and Jiang, L and Wen, L},
title = {Archaea-Inspired Switchable Nanochannels for On-Demand Lithium Detection by pH Activation.},
journal = {ACS central science},
volume = {10},
number = {2},
pages = {469-476},
pmid = {38435527},
issn = {2374-7943},
abstract = {With the rapid development of the lithium ion battery industry, emerging lithium (Li) enrichment in nature has attracted ever-growing attention due to the biotoxicity of high Li levels. To date, fast lithium ion (Li[+]) detection remains urgent but is limited by the selectivity, sensitivity, and stability of conventional technologies based on passive response processes. In nature, archaeal plasma membrane ion exchangers (NCLX_Mj) exhibit Li[+]-gated multi/monovalent ion transport behavior, activated by different stimuli. Inspired by NCLX_Mj, we design a pH-controlled biomimetic Li[+]-responsive solid-state nanochannel system for on-demand Li[+] detection using 2-(2-hydroxyphenyl)benzoxazole (HPBO) units as Li[+] recognition groups. Pristine HPBO is not reactive to Li[+], whereas negatively charged HPBO enables specific Li[+] coordination under alkaline conditions to decrease the ion exchange capacity of nanochannels. On-demand Li[+] detection is achieved by monitoring the decline in currents, thereby ensuring precise and stable Li[+] recognition (>0.1 mM) in the toxic range of Li[+] concentration (>1.5 mM) for human beings. This work provides a new approach to constructing Li[+] detection nanodevices and has potential for applications of Li-related industries and medical services.},
}

@article {pmid38428597,
year = {2024},
author = {Lee, KC and Archer, SDJ and Kansour, MK and Al-Mailem, DM},
title = {Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171279},
doi = {10.1016/j.scitotenv.2024.171279},
pmid = {38428597},
issn = {1879-1026},
abstract = {Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx10[4] g[-1] after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.},
}

@article {pmid38422909,
year = {2024},
author = {Cena, JA and Belmok, A and Kyaw, CM and Dame-Teixeira, N},
title = {The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry.},
journal = {Archives of oral biology},
volume = {161},
number = {},
pages = {105936},
doi = {10.1016/j.archoralbio.2024.105936},
pmid = {38422909},
issn = {1879-1506},
abstract = {OBJECTIVE: The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.

DESIGN: This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.

RESULTS: Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.

CONCLUSIONS: Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.},
}

@article {pmid38392629,
year = {2024},
author = {Cisek, AA and Szymańska, E and Aleksandrzak-Piekarczyk, T and Cukrowska, B},
title = {The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review.},
journal = {Journal of personalized medicine},
volume = {14},
number = {2},
pages = {},
pmid = {38392629},
issn = {2075-4426},
abstract = {Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.},
}

@article {pmid38380943,
year = {2024},
author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR},
title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential.},
journal = {mBio},
volume = {},
number = {},
pages = {e0291823},
doi = {10.1128/mbio.02918-23},
pmid = {38380943},
issn = {2150-7511},
abstract = {Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.IMPORTANCEArchaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.},
}

@article {pmid38368447,
year = {2024},
author = {Ouboter, HT and Mesman, R and Sleutels, T and Postma, J and Wissink, M and Jetten, MSM and Ter Heijne, A and Berben, T and Welte, CU},
title = {Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1477},
pmid = {38368447},
issn = {2041-1723},
support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 854088//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Archaea/genetics/metabolism ; Electron Transport ; *Bacteria/metabolism ; Anaerobiosis ; Electrons ; Oxidation-Reduction ; Methane/metabolism ; },
abstract = {Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea ('Ca. Methanoperedens') in bioelectrochemical systems and observe strong methane-dependent current (91-93% of total current) associated with high enrichment of 'Ca. Methanoperedens' on the anode (up to 82% of the community), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.},
}

*Archaea/genetics/metabolism
Electron Transport
*Bacteria/metabolism
Anaerobiosis
Electrons
Oxidation-Reduction
Methane/metabolism

@article {pmid38366050,
year = {2024},
author = {Baquero, DP and Bignon, EA and Krupovic, M},
title = {Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae008},
pmid = {38366050},
issn = {1751-7370},
abstract = {Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, "Thalassapleoviridae", for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.},
}

@article {pmid38365232,
year = {2024},
author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W},
title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrad002},
pmid = {38365232},
issn = {1751-7370},
support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.},
}

@article {pmid38358888,
year = {2024},
author = {Lu, Z and Zhang, S and Liu, Y and Xia, R and Li, M},
title = {Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea.},
journal = {Cell reports},
volume = {43},
number = {2},
pages = {113781},
doi = {10.1016/j.celrep.2024.113781},
pmid = {38358888},
issn = {2211-1247},
abstract = {Functional interplay between the endosomal sorting complexes required for transport (ESCRT) and the ubiquitin system underlies the ubiquitin-dependent cargo-sorting pathway of the eukaryotic endomembrane system, yet its evolutionary origin remains unclear. Here, we show that a UEV-Vps23 protein family, which contains UEV and Vps23 domains, mediates an ancient ESCRT and ubiquitin system interplay in Asgard archaea. The UEV binds ubiquitin with high affinity, making the UEV-Vps23 a sensor for sorting ubiquitinated cargo. A steadiness box in the Vps23 domain undergoes ubiquitination through an Asgard E1, E2, and RING E3 cascade. The UEV-Vps23 switches between autoinhibited and active forms, regulating the ESCRT and ubiquitin system interplay. Furthermore, the shared sequence and structural homology among the UEV-Vps23, eukaryotic Vps23, and archaeal CdvA suggest a common evolutionary origin. Together, this work expands our understanding of the ancient ESCRT and ubiquitin system interplay that likely arose antedating divergent evolution between Asgard archaea and eukaryotes.},
}

@article {pmid38354884,
year = {2024},
author = {Ju, H and Zhang, J and Zou, Y and Xie, F and Tang, X and Zhang, S and Li, J},
title = {Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118469},
doi = {10.1016/j.envres.2024.118469},
pmid = {38354884},
issn = {1096-0953},
abstract = {Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.},
}

@article {pmid38349190,
year = {2024},
author = {Ghimire-Kafle, S and Weaver, ME and Kimbrel, MP and Bollmann, A},
title = {Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0169823},
doi = {10.1128/aem.01698-23},
pmid = {38349190},
issn = {1098-5336},
abstract = {Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak.IMPORTANCENitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.},
}

@article {pmid38323857,
year = {2024},
author = {Kuroda, K and Nakajima, M and Nakai, R and Hirakata, Y and Kagemasa, S and Kubota, K and Noguchi, TQP and Yamamoto, K and Satoh, H and Nobu, MK and Narihiro, T},
title = {Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems.},
journal = {mBio},
volume = {},
number = {},
pages = {e0310223},
doi = {10.1128/mbio.03102-23},
pmid = {38323857},
issn = {2150-7511},
abstract = {To verify whether members of the phylum Candidatus Patescibacteria parasitize archaea, we applied cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses on the Patescibacteria-enriched cultures derived from a methanogenic bioreactor. Amendment of cultures with exogenous methanogenic archaea, acetate, amino acids, and nucleoside monophosphates increased the relative abundance of Ca. Patescibacteria. The predominant Ca. Patescibacteria were families Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, and the former showed positive linear relationships (r[2] ≥ 0.70) Methanothrix in their relative abundances, suggesting related growth patterns. Methanothrix and Methanospirillum cells with attached Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, respectively, had significantly lower cellular activity than those of the methanogens without Ca. Patescibacteria, as extrapolated from fluorescence in situ hybridization-based fluorescence. We also observed that parasitized methanogens often had cell surface deformations. Some Methanothrix-like filamentous cells were dented where the submicron cells were attached. Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae highly expressed extracellular enzymes, and based on structural predictions, some contained peptidoglycan-binding domains with potential involvement in host cell attachment. Collectively, we propose that the interactions of Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae with methanogenic archaea are parasitisms.IMPORTANCECulture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, Ca. Patescibacteria (also known as candidate phyla radiation), is widely distributed in natural and engineered ecosystems and has been thought to be dependent on host bacteria due to the lack of several biosynthetic pathways and small cell/genome size. Although bacteria-parasitizing or bacteria-preying Ca. Patescibacteria have been described, our recent studies revealed that some lineages can specifically interact with archaea. In this study, we provide strong evidence that the relationship is parasitic, shedding light on overlooked roles of Ca. Patescibacteria in anaerobic habitats.},
}

@article {pmid38314098,
year = {2023},
author = {Tirumalai, MR and Sivaraman, RV and Kutty, LA and Song, EL and Fox, GE},
title = {Ribosomal Protein Cluster Organization in Asgard Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2023},
number = {},
pages = {5512414},
pmid = {38314098},
issn = {1472-3654},
mesh = {*Archaea/genetics/metabolism ; *Ribosomal Proteins/genetics/metabolism ; Escherichia coli/genetics ; Bacteria/genetics ; Genome, Bacterial ; Phylogeny ; },
abstract = {It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.},
}

*Archaea/genetics/metabolism
*Ribosomal Proteins/genetics/metabolism
Escherichia coli/genetics
Bacteria/genetics
Genome, Bacterial
Phylogeny

@article {pmid38302496,
year = {2024},
author = {Tang, SK and Zhi, XY and Zhang, Y and Makarova, KS and Liu, BB and Zheng, GS and Zhang, ZP and Zheng, HJ and Wolf, YI and Zhao, YR and Jiang, SH and Chen, XM and Li, EY and Zhang, T and Chen, PR and Feng, YZ and Xiang, MX and Lin, ZQ and Shi, JH and Chang, C and Zhang, X and Li, R and Lou, K and Wang, Y and Chang, L and Yin, M and Yang, LL and Gao, HY and Zhang, ZK and Tao, TS and Guan, TW and He, FC and Lu, YH and Cui, HL and Koonin, EV and Zhao, GP and Xu, P},
title = {Addendum: Cellular differentiation into hyphae and spores in halophilic archaea.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {523},
pmid = {38302496},
issn = {2041-1723},
mesh = {*Hyphae ; Spores, Fungal ; *Archaea/genetics ; Phylogeny ; Cell Differentiation ; },
}

*Hyphae
Spores, Fungal
*Archaea/genetics
Phylogeny
Cell Differentiation

@article {pmid38299815,
year = {2024},
author = {Scott, KM and Payne, RR and Gahramanova, A},
title = {Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0155723},
doi = {10.1128/aem.01557-23},
pmid = {38299815},
issn = {1098-5336},
abstract = {Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3[-] supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.},
}

@article {pmid38297167,
year = {2024},
author = {Qin, W and Wei, SP and Zheng, Y and Choi, E and Li, X and Johnston, J and Wan, X and Abrahamson, B and Flinkstrom, Z and Wang, B and Li, H and Hou, L and Tao, Q and Chlouber, WW and Sun, X and Wells, M and Ngo, L and Hunt, KA and Urakawa, H and Tao, X and Wang, D and Yan, X and Wang, D and Pan, C and Weber, PK and Jiang, J and Zhou, J and Zhang, Y and Stahl, DA and Ward, BB and Mayali, X and Martens-Habbena, W and Winkler, MH},
title = {Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38297167},
issn = {2058-5276},
support = {DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; 675459//Simons Foundation/ ; 675459//Simons Foundation/ ; DEB-1664052//National Science Foundation (NSF)/ ; HR0011-17-2-0064//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; HR0011-17-2-0064//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; },
abstract = {Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.},
}

@article {pmid38297006,
year = {2024},
author = {Maza-Márquez, P and Lee, MD and Bebout, BM},
title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2561},
pmid = {38297006},
issn = {2045-2322},
abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.},
}

@article {pmid38292760,
year = {2024},
author = {Candeliere, F and Sola, L and Raimondi, S and Rossi, M and Amaretti, A},
title = {Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis.},
journal = {Synthetic and systems biotechnology},
volume = {9},
number = {1},
pages = {88-98},
doi = {10.1016/j.synbio.2023.12.007},
pmid = {38292760},
issn = {2405-805X},
abstract = {Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.},
}

@article {pmid38280122,
year = {2024},
author = {Rao, A and Driessen, AJM},
title = {Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {1},
pages = {14},
pmid = {38280122},
issn = {1433-4909},
support = {024.003.019//BaSyC - Building a Synthetic Cell/ ; },
mesh = {*Terpenes/metabolism ; *Archaea/genetics/metabolism ; Phospholipids/metabolism ; Oxidoreductases/genetics/chemistry/metabolism ; },
abstract = {The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.},
}

*Terpenes/metabolism
*Archaea/genetics/metabolism
Phospholipids/metabolism
Oxidoreductases/genetics/chemistry/metabolism

@article {pmid38263861,
year = {2024},
author = {Ni, Y and Xu, T and Yan, S and Chen, L and Wang, Y},
title = {Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle-shaped viruses that putatively infect mesophilic ammonia-oxidizing archaea.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13230},
pmid = {38263861},
issn = {1758-2229},
support = {32370151//National Natural Science Foundation of China/ ; 41376135//National Natural Science Foundation of China/ ; },
abstract = {The genome of a putative Nitrosopumilaceae virus with a hypothetical spindle-shaped particle morphology was identified in the Yangshan Harbour metavirome from the East China Sea through protein similarity comparison and structure analysis. This discovery was accompanied by a set of 10 geographically dispersed close relatives found in the environmental virus datasets from typical locations of ammonia-oxidizing archaeon distribution. Its host prediction was supported by iPHoP prediction and protein sequence similarity. The structure of the predicted major capsid protein, together with the overall N-glycosylation site, the transmembrane helices prediction, the hydrophilicity profile, and the docking simulation of the major capsid proteins, indicate that these viruses resemble spindle-shaped viruses. It suggests a similarly assembled structure and, consequently, a possibly spindle-shaped morphology of these newly discovered archaeal viruses.},
}

@article {pmid38261994,
year = {2024},
author = {},
title = {Correction to 'Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome'.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae047},
pmid = {38261994},
issn = {1362-4962},
}

@article {pmid38259951,
year = {2023},
author = {Beeckman, F and Drozdzecki, A and De Knijf, A and Audenaert, D and Beeckman, T and Motte, H},
title = {High-throughput assays to identify archaea-targeting nitrification inhibitors.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1283047},
pmid = {38259951},
issn = {1664-462X},
abstract = {Nitrification is a microbial process that converts ammonia (NH3) to nitrite (NO2 [-]) and then to nitrate (NO3 [-]). The first and rate-limiting step in nitrification is ammonia oxidation, which is conducted by both bacteria and archaea. In agriculture, it is important to control this process as high nitrification rates result in NO3 [-] leaching, reduced nitrogen (N) availability for the plants and environmental problems such as eutrophication and greenhouse gas emissions. Nitrification inhibitors can be used to block nitrification, and as such reduce N pollution and improve fertilizer use efficiency (FUE) in agriculture. Currently applied inhibitors target the bacteria, and do not block nitrification by ammonia-oxidizing archaea (AOA). While it was long believed that nitrification in agroecosystems was primarily driven by bacteria, recent research has unveiled potential significant contributions from ammonia-oxidizing archaea (AOA), especially when bacterial activity is inhibited. Hence, there is also a need for AOA-targeting nitrification inhibitors. However, to date, almost no AOA-targeting inhibitors are described. Furthermore, AOA are difficult to handle, hindering their use to test or identify possible AOA-targeting nitrification inhibitors. To address the need for AOA-targeting nitrification inhibitors, we developed two miniaturized nitrification inhibition assays using an AOA-enriched nitrifying community or the AOA Nitrosospaera viennensis. These assays enable high-throughput testing of candidate AOA inhibitors. We here present detailed guidelines on the protocols and illustrate their use with some examples. We believe that these assays can contribute to the discovery of future AOA-targeting nitrification inhibitors, which could complement the currently applied inhibitors to increase nitrification inhibition efficiency in the field and as such contribute to a more sustainable agriculture.},
}

@article {pmid38246077,
year = {2024},
author = {Tang, M and Chen, Q and Zhong, H and Liu, S and Sun, W},
title = {CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater.},
journal = {Water research},
volume = {251},
number = {},
pages = {121137},
doi = {10.1016/j.watres.2024.121137},
pmid = {38246077},
issn = {1879-2448},
abstract = {The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.},
}

@article {pmid38243071,
year = {2024},
author = {Müller, MC and Lemaire, ON and Kurth, JM and Welte, CU and Wagner, T},
title = {Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {111},
pmid = {38243071},
issn = {2399-3642},
support = {KU 3768/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.},
}

@article {pmid38227606,
year = {2024},
author = {Hackley, RK and Vreugdenhil-Hayslette, A and Darnell, CL and Schmid, AK},
title = {A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.},
journal = {PLoS genetics},
volume = {20},
number = {1},
pages = {e1011115},
doi = {10.1371/journal.pgen.1011115},
pmid = {38227606},
issn = {1553-7404},
abstract = {Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica, TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum, activation of ppsA and repression of pykA, is absent in Har. hispanica. Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica. Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.},
}

@article {pmid38225278,
year = {2024},
author = {Lu, Z and Xia, R and Zhang, S and Pan, J and Liu, Y and Wolf, YI and Koonin, EV and Li, M},
title = {Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {515},
pmid = {38225278},
issn = {2041-1723},
abstract = {The archaeal ancestor of eukaryotes apparently belonged to the phylum Asgardarchaeota, but the ecology and evolution of Asgard archaea are poorly understood. The optimal GDP-binding temperature of a translation elongation factor (EF-1A or EF-Tu) has been previously shown to correlate with the optimal growth temperature of diverse prokaryotes. Here, we reconstruct ancestral EF-1A sequences and experimentally measure the optimal GDP-binding temperature of EF-1A from ancient and extant Asgard archaea, to infer the evolution of optimal growth temperatures in Asgardarchaeota. Our results suggest that the Asgard ancestor of eukaryotes was a moderate thermophile, with an optimal growth temperature around 53 °C. The origin of eukaryotes appears to coincide with a transition from thermophilic to mesophilic lifestyle during the evolution of Asgard archaea.},
}

@article {pmid38203843,
year = {2024},
author = {Cisek, AA and Szymańska, E and Wierzbicka-Rucińska, A and Aleksandrzak-Piekarczyk, T and Cukrowska, B},
title = {Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203843},
issn = {1422-0067},
support = {M34/2019//Children's Memorial Health Institute/ ; 2017/25/N/NZ7/02905//National Science Center/ ; },
mesh = {Humans ; Child ; Archaea/genetics ; *Euryarchaeota ; *Inflammatory Bowel Diseases ; *Colitis, Ulcerative ; *Crohn Disease ; Leukocyte L1 Antigen Complex ; },
abstract = {The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.},
}

Humans
Child
Archaea/genetics
*Euryarchaeota
*Inflammatory Bowel Diseases
*Colitis, Ulcerative
*Crohn Disease
Leukocyte L1 Antigen Complex

@article {pmid38197785,
year = {2024},
author = {Hu, Y and Ma, X and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL},
title = {Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006231},
pmid = {38197785},
issn = {1466-5034},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriaceae/genetics ; *Halobacteriales ; Phosphatidylglycerols ; Soil ; Sulfates ; },
abstract = {Two extremely halophilic archaeal strains, GSLN9[T] and XZYJT29[T], were isolated from the saline soil in different regions of western China. Both strains GSLN9[T] and XZYJT29[T] have two 16S rRNA genes with similarities of 95.1 and 94.8 %, respectively. Strain GSLN9[T] was mostly related to the genus Halomicrococcus based on 16S rRNA (showing 91.0-96.0 % identities) and rpoB' genes (showing 92.0 % identity). Strain XZYJT29[T] showed 92.1-97.6 % (16S rRNA gene) and 91.4-93.1 % (rpoB' gene) sequence similarities to its relatives in the genus Halosimplex, respectively. The polar lipid profile of strain GSLN9[T] included phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate (PGS), sulphated mannosyl glucosyl diether (S-DGD-1) and sulphated galactosyl mannosyl glucosyl diether (S-TGD-1), mostly similar to that of Halomicrococcus hydrotolerans H22[T]. PA, PG, PGP-Me, S-DGD-1 (S-DGD-PA), S2-DGD, S-TGD-1 and an unidentified glycolipid were detected in strain XZYJT29[T]; this polar lipid composition is similar to those of members of the genus Halosimplex. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between these two strains and their relatives of the genera Halomicrococcus and Halosimplex were no more than 82, 27 and 80 %, respectively, much lower than the thresholds for species demarcation. Other phenotypic characterization results indicated that strains GSLN9[T] and XZYJT29[T] can be differentiated from the current species of the genera Halomicrococcus and Halosimplex, respectively. These results revealed that strains GSLN9[T] (=CGMCC 1.15215[T]=JCM 30842[T]) and XZYJT29[T] (=CGMCC 1.15828[T]=JCM 31853[T]) represent novel species of Halomicrococcus and Halosimplex, for which the names Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov. are proposed.},
}

RNA, Ribosomal, 16S/genetics
Phylogeny
Sequence Analysis, DNA
DNA, Bacterial/genetics
Bacterial Typing Techniques
Base Composition
Fatty Acids/chemistry
*Halobacteriaceae/genetics
*Halobacteriales
Phosphatidylglycerols
Soil
Sulfates

@article {pmid38194256,
year = {2024},
author = {Li, XX and Tan, S and Cheng, M and Hu, Y and Ma, X and Hou, J and Cui, HL},
title = {Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov., halophilic archaea isolated from saline soil of an inland solar saltern and offshore sediment.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006220},
pmid = {38194256},
issn = {1466-5034},
mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriaceae/genetics ; *Halobacteriales ; Phosphatidylglycerols ; },
abstract = {Two novel halophilic archaeal strains (XZGYJ-43[T] and ZJ1[T]) were isolated from Mangkang ancient solar saltern (Tibet, PR China) and Zhujiang river inlet (Guangdong, PR China), respectively. The comparison of the 16S rRNA gene sequences revealed that strain XZGYJ-43[T] is related to the current species of the family Halobacteriaceae (89.2-91.7% similarity) and strain ZJ1[T] showed 94.7-98.3% similarity to the current species of the genus Haladaptatus. Phylogenetic analyses based on 16S rRNA genes, rpoB' genes and genomes indicated that strain XZGYJ-43[T] is separate from the related genera, Halocalculus, Salarchaeum and Halarchaeum of the family Halobacteriaceae, and strain ZJ1[T] tightly clusters with the current species of the genus Haladaptatus. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain XZGYJ-43[T] and the current species of the family Halobacteriaceae were 71-75, 20-25 and 59-68 %, and these values between strain ZJ1[T] and the current species of the genus Haladaptatus were 77-81, 27-32 and 76-82 %, respectively, clearly below the thresholds for prokaryotic species demarcation. These two strains could be distinguished from their relatives according to differential phenotypic characteristics. The major polar lipids of strain XZGYJ-43[T] were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), mannosyl glucosyl diether (DGD-1; DGD-PA) and sulphated mannosyl glucosyl diether (S-DGD-1; S-DGD-PA), and those of strain ZJ1[T] were PA, PG, PGP-Me, DGD-PA, S-DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. Based on phenotypic, phylogenetic and genomic data, strain XZGYJ-43[T] (=CGMCC 1.13890[T]=JCM 33735[T]) represents a novel species of a new genus within the family Halobacteriaceae, and strain ZJ1[T] (=CGMCC 1.18785[T]=JCM 34917[T]) represents a novel species of the genus Haladaptatus, for which the names Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov. are proposed, respectively.},
}

Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
DNA, Bacterial/genetics
Bacterial Typing Techniques
Base Composition
Fatty Acids/chemistry
*Halobacteriaceae/genetics
*Halobacteriales
Phosphatidylglycerols

@article {pmid38189270,
year = {2024},
author = {Makarova, KS and Zhang, C and Wolf, YI and Karamycheva, S and Whitaker, RJ and Koonin, EV},
title = {Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0309223},
doi = {10.1128/mbio.03092-23},
pmid = {38189270},
issn = {2150-7511},
abstract = {Only a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells.},
}

@article {pmid38188570,
year = {2023},
author = {Hanišáková, N and Vítězová, M and Vítěz, T and Kushkevych, I and Kotrlová, E and Novák, D and Lochman, J and Zavada, R},
title = {Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1293506},
pmid = {38188570},
issn = {1664-302X},
abstract = {In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.},
}

@article {pmid38185001,
year = {2024},
author = {Mao, Y and Wu, J and Yang, R and Ma, Y and Ye, J and Zhong, J and Deng, N and He, X and Hong, Y},
title = {Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary.},
journal = {Marine environmental research},
volume = {194},
number = {},
pages = {106342},
doi = {10.1016/j.marenvres.2024.106342},
pmid = {38185001},
issn = {1879-0291},
abstract = {The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.},
}

@article {pmid38181064,
year = {2024},
author = {Zhao, H and Wu, H and Guseman, A and Abeykoon, D and Camara, CM and Dalal, Y and Fushman, D and Papoian, GA},
title = {The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.},
journal = {PLoS computational biology},
volume = {20},
number = {1},
pages = {e1011721},
doi = {10.1371/journal.pcbi.1011721},
pmid = {38181064},
issn = {1553-7358},
abstract = {Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.},
}

@article {pmid38179456,
year = {2023},
author = {Medina-Chávez, NO and Torres-Cerda, A and Chacón, JM and Harcombe, WR and De la Torre-Zavala, S and Travisano, M},
title = {Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1276438},
doi = {10.3389/fmicb.2023.1276438},
pmid = {38179456},
issn = {1664-302X},
abstract = {Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.},
}

@article {pmid38172371,
year = {2024},
author = {Guerra, A},
title = {Human associated Archaea: a neglected microbiome worth investigating.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {2},
pages = {60},
pmid = {38172371},
issn = {1573-0972},
mesh = {Child ; Pregnancy ; Humans ; Female ; Animals ; *Archaea ; Infectious Disease Transmission, Vertical ; *Microbiota ; Milk ; Colostrum/microbiology ; },
abstract = {The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.},
}

Child
Pregnancy
Humans
Female
Animals
*Archaea
Infectious Disease Transmission, Vertical
*Microbiota
Milk
Colostrum/microbiology

@article {pmid38138100,
year = {2023},
author = {Hinkle, JE and Mara, P and Beaudoin, DJ and Edgcomb, VP and Teske, AP},
title = {A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
pmid = {38138100},
issn = {2076-2607},
support = {512580/NASA/NASA/United States ; },
abstract = {The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.},
}

@article {pmid38138015,
year = {2023},
author = {Wu, X and Zhang, W and Liu, G and Chen, T and Li, Z},
title = {Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/microorganisms11122871},
pmid = {38138015},
issn = {2076-2607},
abstract = {Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.},
}

@article {pmid38135695,
year = {2023},
author = {Trouche, B and Schauberger, C and Bouderka, F and Auguet, JC and Belser, C and Poulain, J and Thamdrup, B and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L},
title = {Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {133},
pmid = {38135695},
issn = {2730-6151},
abstract = {Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.},
}

@article {pmid38132325,
year = {2023},
author = {Rafiq, M and Hassan, N and Rehman, M and Hayat, M and Nadeem, G and Hassan, F and Iqbal, N and Ali, H and Zada, S and Kang, Y and Sajjad, W and Jamal, M},
title = {Challenges and Approaches of Culturing the Unculturable Archaea.},
journal = {Biology},
volume = {12},
number = {12},
pages = {},
pmid = {38132325},
issn = {2079-7737},
abstract = {Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.},
}