@article {pmid32754597,
year = {2020},
author = {Kulkarni, R and Kale, V},
title = {Physiological Cues Involved in the Regulation of Adhesion Mechanisms in Hematopoietic Stem Cell Fate Decision.},
journal = {Frontiers in cell and developmental biology},
volume = {8},
number = {},
pages = {611},
doi = {10.3389/fcell.2020.00611},
pmid = {32754597},
issn = {2296-634X},
abstract = {Hematopoietic stem cells (HSC) could have several fates in the body; viz. self-renewal, differentiation, migration, quiescence, and apoptosis. These fate decisions play a crucial role in maintaining homeostasis and critically depend on the interaction of the HSCs with their micro-environmental constituents. However, the physiological cues promoting these interactions in vivo have not been identified to a great extent. Intense research using various in vitro and in vivo models is going on in various laboratories to understand the mechanisms involved in these interactions, as understanding of these mechanistic would greatly help in improving clinical transplantations. However, though these elegant studies have identified the molecular interactions involved in the process, harnessing these interactions to the recipients' benefit would ultimately depend on manipulation of environmental cues initiating them in vivo: hence, these need to be identified at the earliest. HSCs reside in the bone marrow, which is a very complex tissue comprising of various types of stromal cells along with their secreted cytokines, extra-cellular matrix (ECM) molecules and extra-cellular vesicles (EVs). These components control the HSC fate decision through direct cell-cell interactions - mediated via various types of adhesion molecules -, cell-ECM interactions - mediated mostly via integrins -, or through soluble mediators like cytokines and EVs. This could be a very dynamic process involving multiple transient interactions acting concurrently or sequentially, and the adhesion molecules involved in various fate determining situations could be different. If the switch mechanisms governing these dynamic states in vivo are identified, they could be harnessed for the development of novel therapeutics. Here, in addition to reviewing the adhesion molecules involved in the regulation of HSCs, we also touch upon recent advances in our understanding of the physiological cues known to initiate specific adhesive interactions of HSCs with the marrow stromal cells or ECM molecules and EVs secreted by them.},
}

@article {pmid32752238,
year = {2020},
author = {Mayfield, AB},
title = {Proteomic Signatures of Corals from Thermodynamic Reefs.},
journal = {Microorganisms},
volume = {8},
number = {8},
pages = {},
doi = {10.3390/microorganisms8081171},
pmid = {32752238},
issn = {2076-2607},
support = {OISE-0852960//National Science Foundation/ ; postdoctoral research fellowship//Khaled bin Sultan Living Oceans Foundation/ ; crowd-sourced funds//Friendly Bear Editorial Service/ ; personal research grant//MacArthur Foundation/ ; },
abstract = {Unlike most parts of the world, coral reefs of Taiwan's deep south have generally been spared from climate change-induced degradation. This has been linked to the oceanographically unique nature of Nanwan Bay, where intense upwelling occurs. Specifically, large-amplitude internal waves cause shifts in temperature of 6-9 °C over the course of several hours, and the resident corals not only thrive under such conditions, but they have also been shown to withstand multi-month laboratory incubations at experimentally elevated temperatures. To gain insight into the sub-cellular basis of acclimation to upwelling, proteins isolated from reef corals (Seriatopora hystrix) featured in laboratory-based reciprocal transplant studies in which corals from upwelling and non-upwelling control reefs (<20 km away) were exposed to stable or variable temperature regimes were analyzed via label-based proteomics (iTRAQ). Corals exposed to their "native" temperature conditions for seven days (1) demonstrated highest growth rates and (2) were most distinct from one another with respect to their protein signatures. The latter observation was driven by the fact that two Symbiodiniaceae lipid trafficking proteins, sec1a and sec34, were marginally up-regulated in corals exposed to their native temperature conditions. Alongside the marked degree of proteomic "site fidelity" documented, this dataset sheds light on the molecular mechanisms underlying acclimatization to thermodynamically extreme conditions in situ.},
}

@article {pmid32751534,
year = {2020},
author = {Moustakas, M and Bayçu, G and Sperdouli, I and Eroğlu, H and Eleftheriou, EP},
title = {Arbuscular Mycorrhizal Symbiosis Enhances Photosynthesis in the Medicinal Herb Salvia fruticosa by Improving Photosystem II Photochemistry.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
doi = {10.3390/plants9080962},
pmid = {32751534},
issn = {2223-7747},
support = {3351//Istanbul Üniversitesi/ ; },
abstract = {We investigated the influence of Salvia fruticosa colonization by the arbuscular mycorrhizal fungi (AMF) Rhizophagus irregularis on photosynthetic function by using chlorophyll fluorescence imaging analysis to evaluate the light energy use in photosystem II (PSII) of inoculated and non-inoculated plants. We observed that inoculated plants used significantly higher absorbed energy in photochemistry (ΦPSII) than non-inoculated and exhibited significant lower excess excitation energy (EXC). However, the increased ΦPSII in inoculated plants did not result in a reduced non-regulated energy loss in PSII (ΦNO), suggesting the same singlet oxygen (1O2) formation between inoculated and non-inoculated plants. The increased ΦPSII in inoculated plants was due to an increased efficiency of open PSII centers to utilize the absorbed light (Fv'/Fm') due to a decreased non-photochemical quenching (NPQ) since there was no difference in the fraction of open reaction centers (qp). The decreased NPQ in inoculated plants resulted in an increased electron-transport rate (ETR) compared to non-inoculated. Yet, inoculated plants exhibited a higher efficiency of the water-splitting complex on the donor side of PSII as revealed by the increased Fv/Fo ratio. A spatial heterogeneity between the leaf tip and the leaf base for the parameters ΦPSII and ΦNPQ was observed in both inoculated and non-inoculated plants, reflecting different developmental zones. Overall, our findings suggest that the increased ETR of inoculated S. fruticosa contributes to increased photosynthetic performance, providing growth advantages to inoculated plants by increasing their aboveground biomass, mainly by increasing leaf biomass.},
}

@article {pmid32384101,
year = {2020},
author = {Hale, RE and Powell, E and Beikmohamadi, L and Alexander, ML},
title = {Effects of arthropod inquilines on growth and reproductive effort among metacommunities of the purple pitcher plant (Sarracenia purpurea var. montana).},
journal = {PloS one},
volume = {15},
number = {5},
pages = {e0232835},
pmid = {32384101},
issn = {1932-6203},
mesh = {Animals ; Arthropods/*physiology ; Biodiversity ; Biota/*physiology ; Chironomidae/growth & development/metabolism ; Copepoda/metabolism ; Culicidae/metabolism ; Flowers/growth & development ; Larva ; Mites/metabolism ; Nitrogen Cycle ; Plant Dispersal ; Plant Leaves/growth & development ; Reproduction ; Sarraceniaceae/*growth & development/metabolism ; Symbiosis/*physiology ; },
abstract = {Many plant species harbor communities of symbionts that release nutrients used by their host plants. However, the importance of these nutrients to plant growth and reproductive effort is not well understood. Here, we evaluate the relationship between the communities that colonize pitcher plant phytotelmata and the pitcher plants' vegetative growth and flower production to better understand the symbiotic role played by phytotelma communities. We focus on the mountain variety purple pitcher plant (Sarracenia purpurea var. montana), which occurs in small and isolated populations in Western North Carolina. We found that greater symbiont community diversity is associated with higher flower production the following season. We then examined geographic variation in communities and found that smaller plant populations supported less diverse symbiont communities. We relate our observations to patterns of community diversity predicted by community ecology theory.},
}

Animals
Arthropods/*physiology
Biodiversity
Biota/*physiology
Chironomidae/growth & development/metabolism
Copepoda/metabolism
Culicidae/metabolism
Flowers/growth & development
Larva
Mites/metabolism
Nitrogen Cycle
Plant Dispersal
Plant Leaves/growth & development
Reproduction
Sarraceniaceae/*growth & development/metabolism
Symbiosis/*physiology

@article {pmid31511342,
year = {2019},
author = {Roder, AC and Wang, Y and Butcher, RA and Stock, SP},
title = {Influence of symbiotic and non-symbiotic bacteria on pheromone production in Steinernema nematodes (Nematoda, Steinernematidae).},
journal = {The Journal of experimental biology},
volume = {222},
number = {Pt 18},
pages = {},
doi = {10.1242/jeb.212068},
pmid = {31511342},
issn = {1477-9145},
mesh = {Animals ; Bacteria ; Bacterial Physiological Phenomena ; Glycolipids/metabolism ; Pheromones/*metabolism ; Rhabditida/*metabolism/*microbiology ; Symbiosis ; *Xenorhabdus ; },
abstract = {In this study, we assessed the effect of symbiotic (cognate and non-cognate) and non-symbiotic bacteria on ascaroside production of first-generation adults in two Steinernema spp.: S. carpocapsae All strain and S. feltiae SN strain. Each nematode species was reared under three bacterial scenarios: (1) cognate symbiotic, (2) non-cognate symbiotic strain and (3) non-cognate symbiotic species. Our results showed S. carpocapsae produced four quantifiable ascaroside molecules: asc-C5, asc-C6, asc-C7 and asc-C11, whereas in S. feltiae only three molecules were detected: asc-C5, asc-C7 and asc-C11. Bacterial conditions did not significantly affect the quantity of the secreted ascarosides in first-generation adults of S. carpocapsae However, in S. feltiae, Xenorhabdus nematophila All strain influenced the production of two ascaroside molecules: asc-C5 and asc-C11.},
}

Animals
Bacteria
Bacterial Physiological Phenomena
Glycolipids/metabolism
Pheromones/*metabolism
Rhabditida/*metabolism/*microbiology
Symbiosis
*Xenorhabdus

@article {pmid32750361,
year = {2020},
author = {Llopis-Belenguer, C and Pavoine, S and Blasco-Costa, I and Antonio Balbuena, J},
title = {Assembly rules of helminth parasite communities in grey mullets: combining components of diversity.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2020.06.006},
pmid = {32750361},
issn = {1879-0135},
abstract = {Organisms aggregate in ecological communities. It has been widely debated whether these associations are explained by deterministic or, in contrast, random processes. The answer may vary, depending on the level of an organisational scale (α, β and γ) and the facet of diversity considered: taxonomic (TD), functional (FD) and phylogenetic (PD). Diversity at the level of a sampling unit (i.e. host individual) is the α diversity; β diversity represents the extent of dissimilarity in diversity among sampling units (within a level of an organisational scale, β1; between levels of an organisational scale, β2); and the total diversity of a system is γ diversity. Thus, the combination of facets and levels of a scale may be useful to disentangle the mechanisms driving the composition of a parasite community. Using helminth parasite TD, FD, and a proxy for PD (PPD) of three species of grey mullets (Teleostei: Mugilidae) from the Mediterranean Sea, we show that random and deterministic processes of different nature explain the assemblage of parasite communities. The parasite community at a host individual (α) was invariably a random subset of the total diversity in the community for the three facets of diversity. At the β1 level, TD was lower than expected by chance, whereas FD and PPD were random. At the β2 level, diversity patterns suggested environmental filtering of the parasite assemblage: species, trait, and phylogenetic compositions of parasite communities seemed to depend primarily on the species of host, but also on the locality and season. Our study shows that parasite communities are not totally understood if any of the components (i.e. facets and levels) of diversity is neglected.},
}

@article {pmid32750052,
year = {2020},
author = {Lao, A and Cabezas, H and Orosz, Á and Friedler, F and Tan, R},
title = {Socio-ecological network structures from process graphs.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0232384},
doi = {10.1371/journal.pone.0232384},
pmid = {32750052},
issn = {1932-6203},
abstract = {We propose a process graph (P-graph) approach to develop ecosystem networks from knowledge of the properties of the component species. Originally developed as a process engineering tool for designing industrial plants, the P-graph framework has key advantages over conventional ecological network analysis techniques based on input-output models. A P-graph is a bipartite graph consisting of two types of nodes, which we propose to represent components of an ecosystem. Compartments within ecosystems (e.g., organism species) are represented by one class of nodes, while the roles or functions that they play relative to other compartments are represented by a second class of nodes. This bipartite graph representation enables a powerful, unambiguous representation of relationships among ecosystem compartments, which can come in tangible (e.g., mass flow in predation) or intangible form (e.g., symbiosis). For example, within a P-graph, the distinct roles of bees as pollinators for some plants and as prey for some animals can be explicitly represented, which would not otherwise be possible using conventional ecological network analysis. After a discussion of the mapping of ecosystems into P-graph, we also discuss how this framework can be used to guide understanding of complex networks that exist in nature. Two component algorithms of P-graph, namely maximal structure generation (MSG) and solution structure generation (SSG), are shown to be particularly useful for ecological network analysis. These algorithms enable candidate ecosystem networks to be deduced based on current scientific knowledge on the individual ecosystem components. This method can be used to determine the (a) effects of loss of specific ecosystem compartments due to extinction, (b) potential efficacy of ecosystem reconstruction efforts, and (c) maximum sustainable exploitation of human ecosystem services by humans. We illustrate the use of P-graph for the analysis of ecosystem compartment loss using a small-scale stylized case study, and further propose a new criticality index that can be easily derived from SSG results.},
}

@article {pmid32749730,
year = {2020},
author = {Kale, V},
title = {Transforming growth factor beta boosts the functionality of human bone marrow-derived mesenchymal stromal cells.},
journal = {Cell biology international},
volume = {},
number = {},
pages = {},
doi = {10.1002/cbin.11437},
pmid = {32749730},
issn = {1095-8355},
abstract = {Transforming Growth Factor beta1 (TGFβ1) is a negative regulator of hematopoiesis, and yet, it is frequently found at the active sites of hematopoiesis. Here we show, for the first time, that bone marrow-derived mononuclear cells (MNCs) secrete TGFβ1in response to erythropoietin (EPO). We further show that human bone marrow-derived MSCs (BMSCs) briefly exposed to the conditioned medium of EPO-primed MNCs, or purified TGFβ1; gain significantly increased hematopoiesis-supportive ability. Mechanistically, we show that this phenomenon involves TGFβ1-mediated activation of nitric oxide (NO) signalling pathway in the BMSCs. The data suggest that EPO-MNC-TGFβ1 could be one of the regulatory axes operative in the bone marrow microenvironment involved in maintaining the functionality of the resident BMSCs. This article is protected by copyright. All rights reserved.},
}

@article {pmid32746782,
year = {2020},
author = {Pecoraro, L and Wang, X and Venturella, G and Gao, W and Wen, T and Gafforov, Y and Gupta, VK},
title = {Molecular evidence supports simultaneous association of the achlorophyllous orchid Chamaegastrodia inverta with ectomycorrhizal Ceratobasidiaceae and Russulaceae.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {236},
doi = {10.1186/s12866-020-01906-4},
pmid = {32746782},
issn = {1471-2180},
abstract = {BACKGROUND: Achlorophyllous orchids are mycoheterotrophic plants, which lack photosynthetic ability and associate with fungi to acquire carbon from different environmental sources. In tropical latitudes, achlorophyllous forest orchids show a preference to establish mycorrhizal relationships with saprotrophic fungi. However, a few of them have been recently found to associate with ectomycorrhizal fungi and there is still much to be learned about the identity of fungi associated with tropical orchids. The present study focused on mycorrhizal diversity in the achlorophyllous orchid C. inverta, an endangered species, which is endemic to southern China. The aim of this work was to identify the main mycorrhizal partners of C. inverta in different plant life stages, by means of morphological and molecular methods.

RESULTS: Microscopy showed that the roots of analysed C. inverta samples were extensively colonized by fungal hyphae forming pelotons in root cortical cells. Fungal ITS regions were amplified by polymerase chain reaction, from DNA extracted from fungal mycelia isolated from orchid root samples, as well as from total root DNA. Molecular sequencing and phylogenetic analyses showed that the investigated orchid primarily associated with ectomycorrhizal fungi belonging to a narrow clade within the family Ceratobasidiaceae, which was previously detected in a few fully mycoheterotrophic orchids and was also found to show ectomycorrhizal capability on trees and shrubs. Russulaceae fungal symbionts, showing high similarity with members of the ectomycorrhizal genus Russula, were also identified from the roots of C. inverta, at young seedling stage. Ascomycetous fungi including Chaetomium, Diaporthe, Leptodontidium, and Phomopsis genera, and zygomycetes in the genus Mortierella were obtained from orchid root isolated strains with unclear functional role.

CONCLUSIONS: This study represents the first assessment of root fungal diversity in the rare, cryptic and narrowly distributed Chinese orchid C. inverta. Our results provide new insights on the spectrum of orchid-fungus symbiosis suggesting an unprecedented mixed association between the studied achlorophyllous forest orchid and ectomycorrhizal fungi belonging to Ceratobasidiaceae and Russulaceae. Ceratobasidioid fungi as dominant associates in the roots of C. inverta represent a new record of the rare association between the identified fungal group and fully mycoheterotrophic orchids in nature.},
}

@article {pmid31471302,
year = {2019},
author = {Rothman, JA and Leger, L and Kirkwood, JS and McFrederick, QS},
title = {Cadmium and Selenate Exposure Affects the Honey Bee Microbiome and Metabolome, and Bee-Associated Bacteria Show Potential for Bioaccumulation.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {21},
pages = {},
pmid = {31471302},
issn = {1098-5336},
mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Bees/drug effects/*microbiology ; Bioaccumulation/*physiology ; Biodiversity ; Cadmium/*metabolism/toxicity ; Drug Resistance, Bacterial/drug effects ; Gastrointestinal Microbiome/drug effects/genetics/*physiology ; Lactobacillus/genetics/metabolism ; Metabolome ; Plants ; Pollination ; RNA, Ribosomal, 16S/metabolism ; Selenic Acid/*metabolism/toxicity ; Symbiosis ; },
abstract = {Honey bees are important insect pollinators used heavily in agriculture and can be found in diverse environments. Bees may encounter toxicants such as cadmium and selenate by foraging on plants growing in contaminated areas, which can result in negative health effects. Honey bees are known to have a simple and consistent microbiome that conveys many benefits to the host, and toxicant exposure may impact this symbiotic microbial community. We used 16S rRNA gene sequencing to assay the effects that sublethal cadmium and selenate treatments had over 7 days and found that both treatments significantly but subtly altered the composition of the bee microbiome. Next, we exposed bees to cadmium and selenate and then used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to show that chemical exposure changed the bees' metabolite profiles and that compounds which may be involved in detoxification, proteolysis, and lipolysis were more abundant in treatments. Finally, we exposed several strains of bee-associated bacteria in liquid culture and found that each strain removed cadmium from its medium but that only Lactobacillus Firm-5 microbes assimilated selenate, indicating the possibility that these microbes may reduce the metal and metalloid burden on their host. Overall, our report shows that metal and metalloid exposure can affect the honey bee microbiome and metabolome and that strains of bee-associated bacteria can bioaccumulate these toxicants.IMPORTANCE Bees are important insect pollinators that may encounter environmental pollution when foraging upon plants grown in contaminated areas. Despite the pervasiveness of pollution, little is known about the effects of these toxicants on honey bee metabolism and their symbiotic microbiomes. Here, we investigated the impact of selenate and cadmium exposure on the gut microbiome and metabolome of honey bees. We found that exposure to these chemicals subtly altered the overall composition of the bees' microbiome and metabolome and that exposure to toxicants may negatively impact both host and microbe. As the microbiome of animals can reduce mortality upon metal or metalloid challenge, we grew bee-associated bacteria in media spiked with selenate or cadmium. We show that some bacteria can remove these toxicants from their media in vitro and suggest that bacteria may reduce metal burden in their hosts.},
}

Animals
Bacteria/classification/genetics/isolation & purification/*metabolism
Bees/drug effects/*microbiology
Bioaccumulation/*physiology
Biodiversity
Cadmium/*metabolism/toxicity
Drug Resistance, Bacterial/drug effects
Gastrointestinal Microbiome/drug effects/genetics/*physiology
Lactobacillus/genetics/metabolism
Metabolome
Plants
Pollination
RNA, Ribosomal, 16S/metabolism
Selenic Acid/*metabolism/toxicity
Symbiosis

@article {pmid32741527,
year = {2020},
author = {Vavougios, GD and Zarogiannis, SG and Krogfelt, KA and Stamoulis, G and Gourgoulianis, KI},
title = {Epigenetic regulation of apoptosis via the PARK7 interactome in peripheral blood mononuclear cells donated by tuberculosis patients vs. healthy controls and the response to treatment: A systems biology approach.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {123},
number = {},
pages = {101938},
doi = {10.1016/j.tube.2020.101938},
pmid = {32741527},
issn = {1873-281X},
abstract = {AIMS: The aims of our study were to determine for the first time differentially expressed genes (DEGs) and enriched molecular pathways involving the PARK7 interactome in PBMCs donated from tuberculosis patients.

METHODS: Data on a previously reconstructed PARK7 interactome (Vavougios et al., 2017) from datasets GDS4966 (Case-Control) and GDS4781 (Treatment Series) were retrieved from the Gene Expression Omnibus (GEO) repository. Gene Enrichment analysis was performed via the STRING algorithm and the GeneTrail2 software.

RESULTS: 17 and 22 PARK7 interactores were determined as DEGs in the active TB vs HD and Treatment Series subset analyses, correspondingly, associated with significantly enriched pathways (FDR <0.05) involving p53 and PTEN mediated, stress responsive apoptosis regulation pathways. The treatment subset was characterized by the emergence of an additional layer of transcriptional regulation mediated by polycomb proteins among others, as well as TLR-mediated and cytokine survival signaling. Finally, the enrichment of a Parkinson's disease signature including PARK7 interactors was determined by its differential regulation both in the exploratory analyses (FDR = 0.024), as well as the confirmatory analyses (FDR = 1.81e-243).

CONCLUSIONS: Our in silico analysis revealed for the first time the role of PARK7's interactome in regulating the epigenetics of the PBMC lifecycle and Mtb symbiosis.},
}

@article {pmid32371877,
year = {2020},
author = {Schroeder, JW and Dobson, A and Mangan, SA and Petticord, DF and Herre, EA},
title = {Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2204},
doi = {10.1038/s41467-020-16047-5},
pmid = {32371877},
issn = {2041-1723},
mesh = {Algorithms ; *Ecosystem ; Feedback, Physiological/physiology ; Host Microbial Interactions ; Models, Theoretical ; Mycorrhizae/classification/*physiology ; Plants/classification/*metabolism/microbiology ; Soil/*chemistry ; *Soil Microbiology ; Species Specificity ; Symbiosis/*physiology ; },
abstract = {Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.},
}

Algorithms
*Ecosystem
Feedback, Physiological/physiology
Host Microbial Interactions
Models, Theoretical
Mycorrhizae/classification/*physiology
Plants/classification/*metabolism/microbiology
Soil/*chemistry
*Soil Microbiology
Species Specificity
Symbiosis/*physiology

@article {pmid32366903,
year = {2020},
author = {Herren, JK and Mbaisi, L and Mararo, E and Makhulu, EE and Mobegi, VA and Butungi, H and Mancini, MV and Oundo, JW and Teal, ET and Pinaud, S and Lawniczak, MKN and Jabara, J and Nattoh, G and Sinkins, SP},
title = {A microsporidian impairs Plasmodium falciparum transmission in Anopheles arabiensis mosquitoes.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2187},
pmid = {32366903},
issn = {2041-1723},
support = {107372/WT_/Wellcome Trust/United Kingdom ; 200274/WT_/Wellcome Trust/United Kingdom ; 202888/WT_/Wellcome Trust/United Kingdom ; BB/R005338/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Anopheles/microbiology/*parasitology ; Host-Pathogen Interactions ; Humans ; Kenya ; Malaria, Falciparum/*parasitology/prevention & control/transmission ; Microsporidia/physiology ; Mosquito Control/methods ; Mosquito Vectors/microbiology/*parasitology ; Plasmodium falciparum/*physiology ; Sporozoites/physiology ; Symbiosis ; },
abstract = {A possible malaria control approach involves the dissemination in mosquitoes of inherited symbiotic microbes to block Plasmodium transmission. However, in the Anopheles gambiae complex, the primary African vectors of malaria, there are limited reports of inherited symbionts that impair transmission. We show that a vertically transmitted microsporidian symbiont (Microsporidia MB) in the An. gambiae complex can impair Plasmodium transmission. Microsporidia MB is present at moderate prevalence in geographically dispersed populations of An. arabiensis in Kenya, localized to the mosquito midgut and ovaries, and is not associated with significant reductions in adult host fecundity or survival. Field-collected Microsporidia MB infected An. arabiensis tested negative for P. falciparum gametocytes and, on experimental infection with P. falciparum, sporozoites aren't detected in Microsporidia MB infected mosquitoes. As a microbe that impairs Plasmodium transmission that is non-virulent and vertically transmitted, Microsporidia MB could be investigated as a strategy to limit malaria transmission.},
}

Animals
Anopheles/microbiology/*parasitology
Host-Pathogen Interactions
Humans
Kenya
Malaria, Falciparum/*parasitology/prevention & control/transmission
Microsporidia/physiology
Mosquito Control/methods
Mosquito Vectors/microbiology/*parasitology
Plasmodium falciparum/*physiology
Sporozoites/physiology
Symbiosis

@article {pmid31522940,
year = {2019},
author = {Yoshida, S and Kim, S and Wafula, EK and Tanskanen, J and Kim, YM and Honaas, L and Yang, Z and Spallek, T and Conn, CE and Ichihashi, Y and Cheong, K and Cui, S and Der, JP and Gundlach, H and Jiao, Y and Hori, C and Ishida, JK and Kasahara, H and Kiba, T and Kim, MS and Koo, N and Laohavisit, A and Lee, YH and Lumba, S and McCourt, P and Mortimer, JC and Mutuku, JM and Nomura, T and Sasaki-Sekimoto, Y and Seto, Y and Wang, Y and Wakatake, T and Sakakibara, H and Demura, T and Yamaguchi, S and Yoneyama, K and Manabe, RI and Nelson, DC and Schulman, AH and Timko, MP and dePamphilis, CW and Choi, D and Shirasu, K},
title = {Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism.},
journal = {Current biology : CB},
volume = {29},
number = {18},
pages = {3041-3052.e4},
doi = {10.1016/j.cub.2019.07.086},
pmid = {31522940},
issn = {1879-0445},
mesh = {Animals ; Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Germination ; Host-Parasite Interactions/*genetics ; Orobanchaceae/genetics ; Parasites/genetics/metabolism ; Plant Roots ; Seeds ; Striga/*genetics ; Symbiosis ; },
abstract = {Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.},
}

Animals
Biological Evolution
Evolution, Molecular
Gene Transfer, Horizontal/genetics
Germination
Host-Parasite Interactions/*genetics
Orobanchaceae/genetics
Parasites/genetics/metabolism
Plant Roots
Seeds
Striga/*genetics
Symbiosis

@article {pmid31175851,
year = {2019},
author = {Wang, Y},
title = {Pollination-mutualisms in a two-patch system with dispersal.},
journal = {Journal of theoretical biology},
volume = {476},
number = {},
pages = {51-61},
doi = {10.1016/j.jtbi.2019.06.004},
pmid = {31175851},
issn = {1095-8541},
mesh = {Animals ; *Ecosystem ; *Models, Biological ; Plants/*metabolism ; Pollination/*physiology ; Symbiosis/*physiology ; },
abstract = {In this paper, we consider a two-patch pollination-mutualism model with dispersal, which is derived from resource-service exchange between the plant and pollinator. The pollinator is assumed to persist in one patch in the presence of pollination-mutualisms, while it can (or cannot) survive alone in the other. Rigorous study on the model exhibits that solutions of the equations are nonnegative and bounded, and there exist stable positive equilibria under conditions. Theoretical analysis on the equilibria demonstrates that if the pollinator can survive alone in the other patch, a small dispersal can make the pollinator approach higher total population abundance than if non-dispersing. If the pollinator cannot survive alone in the other patch, a small or large dispersal can make the pollinator approach higher size than if non-dispersing, which is not intuitive. A novel prediction of this work is that the pollinator with dispersal can reach high population abundance even though the mutualistic plant approaches a low density, while constructing a high-quality patch for pollinator can lead to extra individuals for both plant and pollinator via dispersal. Numerical simulations confirm and extend our results.},
}

Animals
*Ecosystem
*Models, Biological
Plants/*metabolism
Pollination/*physiology
Symbiosis/*physiology

@article {pmid32734058,
year = {2018},
author = {Chellapandi, P and Bharathi, M and Sangavai, C and Prathiviraj, R},
title = {Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review.},
journal = {Veterinary and animal science},
volume = {6},
number = {},
pages = {86-94},
pmid = {32734058},
issn = {2451-943X},
abstract = {Methanobacterium formicicum (Methanobacteriaceae family) is an endosymbiotic methanogenic Archaean found in the digestive tracts of ruminants and elsewhere. It has been significantly implicated in global CH4 emission during enteric fermentation processes. In this review, we discuss current genomic and metabolic aspects of this microorganism for the purpose of the discovery of novel veterinary therapeutics. This microorganism encompasses a typical H2 scavenging system, which facilitates a metabolic symbiosis across the H2 producing cellulolytic bacteria and fumarate reducing bacteria. To date, five genome-scale metabolic models (iAF692, iMG746, iMB745, iVS941 and iMM518) have been developed. These metabolic reconstructions revealed the cellular and metabolic behaviors of methanogenic archaea. The characteristics of its symbiotic behavior and metabolic crosstalk with competitive rumen anaerobes support understanding of the physiological function and metabolic fate of shared metabolites in the rumen ecosystem. Thus, systems biological characterization of this microorganism may provide a new insight to realize its metabolic significance for the development of a healthy microbiota in ruminants. An in-depth knowledge of this microorganism may allow us to ensure a long term sustainability of ruminant-based agriculture.},
}

@article {pmid32733401,
year = {2020},
author = {Pasqualetti, C and Szokoli, F and Rindi, L and Petroni, G and Schrallhammer, M},
title = {The Obligate Symbiont "Candidatus Megaira polyxenophila" Has Variable Effects on the Growth of Different Host Species.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1425},
doi = {10.3389/fmicb.2020.01425},
pmid = {32733401},
issn = {1664-302X},
abstract = {"Candidatus Megaira polyxenophila" is a recently described member of Rickettsiaceae which comprises exclusively obligate intracellular bacteria. Interestingly, these bacteria can be found in a huge diversity of eukaryotic hosts (protist, green algae, metazoa) living in marine, brackish or freshwater habitats. Screening of amplicon datasets revealed a high frequency of these bacteria especially in freshwater environments, most likely associated to eukaryotic hosts. The relationship of "Ca. Megaira polyxenophila" with their hosts and their impact on host fitness have not been studied so far. Even less is known regarding the responses of these intracellular bacteria to potential stressors. In this study, we used two phylogenetically close species of the freshwater ciliate Paramecium, Paramecium primaurelia and Paramecium pentaurelia (Ciliophora, Oligohymenophorea) naturally infected by "Ca. Megaira polyxenophila". In order to analyze the effect of the symbiont on the fitness of these two species, we compared the growth performance of both infected and aposymbiotic paramecia at different salinity levels in the range of freshwater and oligohaline brackish water i.e., at 0, 2, and 4.5 ppt. For the elimination of "Ca. Megaira polyxenophila" we established an antibiotic treatment to obtain symbiont-free lines and confirmed its success by fluorescence in situ hybridization (FISH). The population and infection dynamics during the growth experiment were observed by cell density counts and FISH. Paramecia fitness was compared applying generalized additive mixed models. Surprisingly, both infected Paramecium species showed higher densities under all salinity concentrations. The tested salinity concentrations did not significantly affect the growth of any of the two species directly, but we observed the loss of the endosymbiont after prolonged exposure to higher salinity levels. This experimental data might explain the higher frequency of "Ca. M. polyxenophila" in freshwater habitats as observed from amplicon data.},
}

@article {pmid32733173,
year = {2019},
author = {Moran, NA and Ochman, H and Hammer, TJ},
title = {Evolutionary and ecological consequences of gut microbial communities.},
journal = {Annual review of ecology, evolution, and systematics},
volume = {50},
number = {1},
pages = {451-475},
doi = {10.1146/annurev-ecolsys-110617-062453},
pmid = {32733173},
issn = {1543-592X},
abstract = {Animals are distinguished by having guts: organs that must extract nutrients from food while barring invasion by pathogens. Most guts are colonized by non-pathogenic microorganisms, but the functions of these microbes, or even the reasons why they occur in the gut, vary widely among animals. Sometimes these microorganisms have co-diversified with hosts; sometimes they live mostly elsewhere in the environment. Either way, gut microorganisms often benefit hosts. Benefits may reflect evolutionary "addiction" whereby hosts incorporate gut microorganisms into normal developmental processes. But benefits often include novel ecological capabilities; for example, many metazoan clades exist by virtue of gut communities enabling new dietary niches. Animals vary immensely in their dependence on gut microorganisms, from lacking them entirely, to using them as food, to obligate dependence for development, nutrition, or protection. Many consequences of gut microorganisms for hosts can be ascribed to microbial community processes and the host's ability to shape these processes.},
}

@article {pmid32732998,
year = {2020},
author = {Wong, JEMM and Gysel, K and Birkefeldt, TG and Vinther, M and Muszyński, A and Azadi, P and Laursen, NS and Sullivan, JT and Ronson, CW and Stougaard, J and Andersen, KR},
title = {Structural signatures in EPR3 define a unique class of plant carbohydrate receptors.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3797},
doi = {10.1038/s41467-020-17568-9},
pmid = {32732998},
issn = {2041-1723},
support = {DNRF79//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; OPP11772165//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; DE-SC0015662//DOE | SC | Basic Energy Sciences (BES)/ ; },
abstract = {Receptor-mediated perception of surface-exposed carbohydrates like lipo- and exo-polysaccharides (EPS) is important for non-self recognition and responses to microbial associated molecular patterns in mammals and plants. In legumes, EPS are monitored and can either block or promote symbiosis with rhizobia depending on their molecular composition. To establish a deeper understanding of receptors involved in EPS recognition, we determined the structure of the Lotus japonicus (Lotus) exopolysaccharide receptor 3 (EPR3) ectodomain. EPR3 forms a compact structure built of three putative carbohydrate-binding modules (M1, M2 and LysM3). M1 and M2 have unique βαββ and βαβ folds that have not previously been observed in carbohydrate binding proteins, while LysM3 has a canonical βααβ fold. We demonstrate that this configuration is a structural signature for a ubiquitous class of receptors in the plant kingdom. We show that EPR3 is promiscuous, suggesting that plants can monitor complex microbial communities though this class of receptors.},
}

@article {pmid32730346,
year = {2020},
author = {Sun, B and Ma, M and Li, Y and Zheng, L},
title = {Analysis on the stability and evolutionary trend of the symbiosis system in the supply chain of fresh agricultural products.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0236334},
doi = {10.1371/journal.pone.0236334},
pmid = {32730346},
issn = {1932-6203},
abstract = {In order to increase the stability of fresh agricultural product supply chain, farmers and enterprises need to evolve into a symbiotic system of supply chain. At the present stage, symbiotic relations and evolutionary trends in a symbiotic system for fresh agricultural product supply chains lack quantitative methods for determining symbiotic criteria. In the sense of quantification -oriented criteria, symbiotic systems for fresh agricultural product supply chains are defined, and an improved stationary state analysis method is proposed. Three key steps in this method are quantifying a symbiotic energy model with an evaluation model of ecological carrying capacity, setting up a system evolution model based on the logistic growth function, and verifying the symbiotic system's singularity and phase transition boundary by Lyapunov indirect method. MATLAB numerical simulation shows that types of singularity and the phase transition boundary of symbiotic system are divided effectively. And in both conditions, infinite exponential growth and convergence to steady state, the mutualism mode is the optimal choice for the symbiotic system we defined, symbiotic relations between farmers and cooperative companies are stable and long-term at this time. Those conclusions provide a reference approach to enhance the overall prospective benefits to the fresh agricultural products supply chain.},
}

@article {pmid32730262,
year = {2020},
author = {Nguyen, PL and van Baalen, M},
title = {On the difficult evolutionary transition from the free-living lifestyle to obligate symbiosis.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0235811},
doi = {10.1371/journal.pone.0235811},
pmid = {32730262},
issn = {1932-6203},
abstract = {Obligate symbiosis evolved from free-living individuals most likely via the intermediate stage of facultative symbiosis. However, why should facultative symbionts, who can live independently but also benefit from their partners if these are available, give up this best of both worlds? Using the adaptive dynamics approach, we analyse a simple model, focusing on one partner of the symbiosis, to gain more insight into the selective forces that make individuals forgo the ability to reproduce in the free-living state. Our results suggest that, similar to the parasitism-mutualism continuum, the free-living way of life and obligate symbiosis are two extremes of a continuum of the ability to reproduce independently of a partner. More importantly, facultative symbiosis should be the rule as for many parameter combinations completely giving up independent reproduction or adopting a pure free-living strategy is not so easy. We also show that if host encounter comes at a cost, individuals that put more effort into increasing the chances to meet with their partners are more likely to give up the ability to reproduce independently. Finally, our model does not specify the ecological interactions between hosts and symbionts but we discuss briefly how the ecological nature of an interaction can influence the transition from facultative to obligate symbiosis.},
}

@article {pmid32728495,
year = {2020},
author = {Roodi, D and Millner, JP and McGill, C and Johnson, RD and Jauregui, R and Card, SD},
title = {Methylobacterium, a major component of the culturable bacterial endophyte community of wild Brassica seed.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9514},
doi = {10.7717/peerj.9514},
pmid = {32728495},
issn = {2167-8359},
abstract = {Background: Plants are commonly colonized by a wide diversity of microbial species and the relationships created can range from mutualistic through to parasitic. Microorganisms that typically form symptomless associations with internal plant tissues are termed endophytes. Endophytes associate with most plant species found in natural and managed ecosystems. They are extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Plant domestication has reduced endophyte diversity and therefore the wild relatives of many crop species remain untapped reservoirs of beneficial microbes. Brassica species display immense diversity and consequently provide the greatest assortment of products used by humans from a single plant genus important for agriculture, horticulture, bioremediation, medicine, soil conditioners, composting crops, and in the production of edible and industrial oils. Many endophytes are horizontally transmitted, but some can colonize the plant's reproductive tissues, and this gives these symbionts an efficient mechanism of propagation via plant seed (termed vertical transmission).

Methods: This study surveyed 83 wild and landrace Brassica accessions composed of 14 different species with a worldwide distribution for seed-originating bacterial endophytes. Seed was stringently disinfected, sown within sterile tissue culture pots within a sterile environment and incubated. After approximately 1-month, direct isolation techniques were used to recover bacterial endophytes from roots and shoots of symptomless plants. Bacteria were identified based on the PCR amplification of partial 16S rDNA gene sequences and annotated using the BLASTn program against the NCBI rRNA database. A diversity index was used as a quantitative measure to reflect how many different bacterial species there were in the seed-originating microbial community of the Brassica accessions sampled.

Results: Bacterial endophytes were recovered from the majority of the Brassica accessions screened. 16S rDNA gene sequencing identified 19 different bacterial species belonging to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria with the most frequently isolated species being Methylobacterium fujisawaense, Stenotrophomonas rhizophila and Pseudomonas lactis. Methylobacterium was the dominant genus composing 56% of the culturable isolated bacterial community and was common in 77% of accessions possessing culturable bacterial endophytes. Two selected isolates of Methylobacterium significantly promoted plant growth when inoculated into a cultivar of oilseed rape and inhibited the growth of the pathogen Leptosphaeria maculans in dual culture. This is the first report that investigates the seed-originating endophytic microorganisms of wild Brassica species and highlights the Brassica microbiome as a resource for plant growth promoting bacteria and biological control agents.},
}

@article {pmid32203477,
year = {2020},
author = {Ives, AR and Barton, BT and Penczykowski, RM and Harmon, JP and Kim, KL and Oliver, K and Radeloff, VC},
title = {Self-perpetuating ecological-evolutionary dynamics in an agricultural host-parasite system.},
journal = {Nature ecology & evolution},
volume = {4},
number = {5},
pages = {702-711},
doi = {10.1038/s41559-020-1155-0},
pmid = {32203477},
issn = {2397-334X},
mesh = {Animals ; *Aphids ; *Parasites ; Symbiosis ; },
abstract = {Ecological and evolutionary processes may become intertwined when they operate on similar time scales. Here we show ecological-evolutionary dynamics between parasitoids and aphids containing heritable symbionts that confer resistance against parasitism. In a large-scale field experiment, we manipulated the aphid's host plant to create ecological conditions that either favoured or disfavoured the parasitoid. The result was rapid evolutionary divergence of aphid resistance between treatment populations. Consistent with ecological-evolutionary dynamics, the resistant aphid populations then had reduced parasitism and increased population growth rates. We fit a model to quantify costs (reduced intrinsic rates of increase) and benefits of resistance. We also performed genetic assays on 5 years of field samples that showed persistent but highly variable frequencies of aphid clones containing protective symbionts; these patterns were consistent with simulations from the model. Our results show (1) rapid evolution that is intertwined with ecological dynamics and (2) variation in selection that prevents traits from becoming fixed, which together generate self-perpetuating ecological-evolutionary dynamics.},
}

Animals
*Aphids
*Parasites
Symbiosis

@article {pmid31540983,
year = {2019},
author = {Tian, PP and Chang, CY and Miao, NH and Li, MY and Liu, XD},
title = {Infections with Arsenophonus Facultative Endosymbionts Alter Performance of Aphids (Aphis gossypii) on an Amino-Acid-Deficient Diet.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {23},
pages = {},
pmid = {31540983},
issn = {1098-5336},
mesh = {Amino Acids/deficiency ; Animals ; Aphids/growth & development/*microbiology ; Cucumis sativus ; *Food Chain ; Gammaproteobacteria/*physiology ; Gossypium ; Nymph/growth & development/microbiology ; *Symbiosis ; },
abstract = {Genetic polymorphism and endosymbiont infection are ubiquitous in aphid populations. It has been known that the obligate symbiont Buchnera provides aphids with essential amino acids which cannot be ingested from plant sap. Buchnera often coexists with facultative endosymbionts in aphids. However, it is unclear whether the facultative endosymbionts affect the aphid's amino acid requirements from diet. In this study, we found that the facultative endosymbiont status in populations of the cotton-melon aphid Aphis gossypii was associated with aphid genotype or host plant. The infection frequency of Arsenophonus in aphids living on cotton was significantly higher than that in aphids on cucumber, and cucumber leaves contained higher titers of free amino acids than cotton leaves, especially amino acids Leu, Arg, Ile, Val, and Phe. The net reproductive rates of five aphid genotypes infected with Arsenophonus were not different on the complete-amino-acid diet, but the values were significantly different among seven Arsenophonus-free aphid genotypes. Moreover, the net reproductive rates of aphids on the amino-acid-deficient diet were significantly affected by Arsenophonus infection and aphid genotype. Arsenophonus infection decreased aphid performance on the Phe-free diet but improved performance on the Leu-free diet and did not affect the performance on the Ile-free or Val-free diet. Arsenophonus infections altered aphid requirements for amino acids that were significantly different in cotton and cucumber leaves, suggesting this endosymbiont would modulate the host specialization of this aphid.IMPORTANCE The facultative endosymbiont Arsenophonus plays an important role in regulating reproduction through son killing, enemy resistance, and the dietary breadth of its insect hosts. In this study, we found Arsenophonus could alter aphid performance on the amino-acid-deficient diets. Arsenophonus infection increased aphid requirements for the amino acid Phe, but decreased requirements for the Leu. Cotton and cucumber leaves contained drastically different titers of free amino acids Phe and Leu, and aphids living on these two plants were infected with different incidences of Arsenophonus We hypothesize that host specialization or the host plant range of aphids may be mediated by Arsenophonus.},
}

Amino Acids/deficiency
Animals
Aphids/growth & development/*microbiology
Cucumis sativus
*Food Chain
Gammaproteobacteria/*physiology
Gossypium
Nymph/growth & development/microbiology
*Symbiosis

@article {pmid32723830,
year = {2020},
author = {Maire, J and Parisot, N and Galvao Ferrarini, M and Vallier, A and Gillet, B and Hughes, S and Balmand, S and Vincent-Monégat, C and Zaidman-Rémy, A and Heddi, A},
title = {Spatial and morphological reorganization of endosymbiosis during metamorphosis accommodates adult metabolic requirements in a weevil.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.2007151117},
pmid = {32723830},
issn = {1091-6490},
abstract = {Bacterial intracellular symbiosis (endosymbiosis) is widespread in nature and impacts many biological processes. In holometabolous symbiotic insects, metamorphosis entails a complete and abrupt internal reorganization that creates a constraint for endosymbiont transmission from larvae to adults. To assess how endosymbiosis copes-and potentially evolves-throughout this major host-tissue reorganization, we used the association between the cereal weevil Sitophilus oryzae and the bacterium Sodalis pierantonius as a model system. S. pierantonius are contained inside specialized host cells, the bacteriocytes, that group into an organ, the bacteriome. Cereal weevils require metabolic inputs from their endosymbiont, particularly during adult cuticle synthesis, when endosymbiont load increases dramatically. By combining dual RNA-sequencing analyses and cell imaging, we show that the larval bacteriome dissociates at the onset of metamorphosis and releases bacteriocytes that undergo endosymbiosis-dependent transcriptomic changes affecting cell motility, cell adhesion, and cytoskeleton organization. Remarkably, bacteriocytes turn into spindle cells and migrate along the midgut epithelium, thereby conveying endosymbionts to midgut sites where future mesenteric caeca will develop. Concomitantly, endosymbiont genes encoding a type III secretion system and a flagellum apparatus are transiently up-regulated while endosymbionts infect putative stem cells and enter their nuclei. Infected cells then turn into new differentiated bacteriocytes and form multiple new bacteriomes in adults. These findings show that endosymbiosis reorganization in a holometabolous insect relies on a synchronized host-symbiont molecular and cellular "choreography" and illustrates an adaptive feature that promotes bacteriome multiplication to match increased metabolic requirements in emerging adults.},
}

@article {pmid32723477,
year = {2020},
author = {Fang, H and Labandeira, CC and Ma, Y and Zheng, B and Ren, D and Wei, X and Liu, J and Wang, Y},
title = {Lichen mimesis in mid-Mesozoic lacewings.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
doi = {10.7554/eLife.59007},
pmid = {32723477},
issn = {2050-084X},
support = {31970383//National Natural Science Foundation of China/ ; 31730087,41688103//National Natural Science Foundation of China/ ; 31770022//National Natural Science Foundation of China/ ; 5192002//Natural Science Foundation of Beijing Municipality/ ; 19530050144//Capacity Building for Sci-Tech Innovation - Fundamental Scientific Research Funds/ ; IRT-17R75//Program for Changjiang Scholars and Innovative Research Team in University/ ; IDHT20180518//Support Project of High Level Teachers in Beijing Municipal Universities/ ; 028175534000,028185511700//Graduate Student Program for International Exchange and Joint Supervision at Capital Normal University/ ; },
abstract = {Animals mimicking other organisms or using camouflage to deceive predators are vital survival strategies. Modern and fossil insects can simulate diverse objects. Lichens are an ancient symbiosis between a fungus and an alga or a cyanobacterium that sometimes have a plant-like appearance and occasionally are mimicked by modern animals. Nevertheless, lichen models are almost absent in fossil record of mimicry. Here, we provide the earliest fossil evidence of a mimetic relationship between the moth lacewing mimic Lichenipolystoechotes gen. nov. and its co-occurring fossil lichen model Daohugouthallus ciliiferus. We corroborate the lichen affinity of D. ciliiferus and document this mimetic relationship by providing structural similarities and detailed measurements of the mimic's wing and correspondingly the model's thallus. Our discovery of lichen mimesis predates modern lichen-insect associations by 165 million years, indicating that during the mid-Mesozoic, the lichen-insect mimesis system was well established and provided lacewings with highly honed survival strategies.},
}

@article {pmid32722489,
year = {2020},
author = {Herrera, H and Sanhueza, T and Martiarena, R and Valadares, R and Fuentes, A and Arriagada, C},
title = {Mycorrhizal Fungi Isolated from Native Terrestrial Orchids from Region of La Araucanía, Southern Chile.},
journal = {Microorganisms},
volume = {8},
number = {8},
pages = {},
doi = {10.3390/microorganisms8081120},
pmid = {32722489},
issn = {2076-2607},
support = {3200134//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1170931//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
abstract = {Mycorrhizal interactions of orchids are influenced by several environmental conditions. Hence, knowledge of mycorrhizal fungi associated with orchids inhabiting different ecosystems is essential to designing recovery strategies for threatened species. This study analyzes the mycorrhizal associations of terrestrial orchids colonizing grassland and understory in native ecosystems of the region of La Araucanía in southern Chile. Mycorrhizal fungi were isolated from peloton-containing roots and identified based on the sequence of the ITS region. Their capacities for seed germination were also investigated. We detected Tulasnella spp. and Ceratobasidium spp. in the pelotons of the analyzed orchids. Additionally, we showed that some Ceratobasidium isolates effectively induce seed germination to differing degrees, unlike Tulasnella spp., which, in most cases, fail to achieve protocorm growth. This process may underline a critical step in the life cycle of Tulasnella-associated orchids, whereas the Ceratobasidium-associated orchids were less specific for fungi and were effectively germinated with mycorrhizal fungi isolated from adult roots.},
}

@article {pmid32721312,
year = {2020},
author = {Genc, O and Kurt, A and Yazan, DM and Erdis, E},
title = {Circular eco-industrial park design inspired by nature: An integrated non-linear optimization, location, and food web analysis.},
journal = {Journal of environmental management},
volume = {270},
number = {},
pages = {110866},
doi = {10.1016/j.jenvman.2020.110866},
pmid = {32721312},
issn = {1095-8630},
abstract = {Industrial symbiosis (IS) is one of the alternative ways of using natural resources in industrial processes. Eco-industrial parks (EIPs), as commonly known areas of IS practices, increase resource efficacy and reduce environmental effects by implementing waste/by product exchanges among tenant plants. Although there is an increasing but limited number of EIPs around the world, their circularity is not ensured due to high dynamic market and business conditions. This paper aims at offering an innovative design approach for EIPs taking into account the potential waste exchanges between the plants potentially to be co-located within EIPs with the goal of eliminating adverse impacts of market and business dynamicity. To this end, first an analysis of an existing IS database is conducted and the sectors potentially to be co-located are identified. Second, inspired by natural eco-systems, the food web (FW) metrics are defined to measure the potential EIPs' circularity. Third, a non-linear optimization method, namely branch and bound algorithm, is adopted to decide which plants should be included in the EIP designs to maximize the cyclicity of the networks. Lastly, a location analysis is conducted in order to co-locate the plants and to minimize the operational costs of implementing and running the EIPs. The use of this integrated approach is illustrated in a scenario analysis for four theoretical EIPs, two taking the construction industry as an anchor industry and two considering the random inclusion of various industries that can exchange wastes with the constructions industry. These EIPs' FW metric values are compared with the biological FW averages of natural ecosystems. The results support the method's ability to design sustainable and circular EIPs and point out practical implications for practitioners and policy-makers. The study is a seminal one integrating three methodologies for the first time to design IS networks in the form of EIPs.},
}

@article {pmid31640545,
year = {2019},
author = {Akami, M and Ren, XM and Qi, X and Mansour, A and Gao, B and Cao, S and Niu, CY},
title = {Symbiotic bacteria motivate the foraging decision and promote fecundity and survival of Bactrocera dorsalis (Diptera: Tephritidae).},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {229},
pmid = {31640545},
issn = {1471-2180},
mesh = {Animals ; Appetitive Behavior ; Bacteria/genetics/*growth & development ; Female ; Fertility ; Genetic Fitness ; Longevity ; Male ; Symbiosis ; Tephritidae/genetics/*microbiology/*physiology ; },
abstract = {BACKGROUND: The gut bacteria of tephritid fruit flies play prominent roles in nutrition, reproduction, maintenance and ecological adaptations of the host. Here, we adopted an approach based on direct observation of symbiotic or axenic flies feeding on dishes seeded with drops of full diet (containing all amino acids) or full diet supplemented with bacteria at similar concentrations to explore the effects of intestinal bacteria on foraging decision and fitness of Bactrocera dorsalis.

RESULTS: The results show that intestinal probiotics elicit beneficial foraging decision and enhance the female reproduction fitness and survival of B. dorsalis (symbiotic and axenic), yet preferences for probiotic diets were significantly higher in axenic flies to which they responded faster compared to full diet. Moreover, females fed diet supplemented with Pantoea dispersa and Enterobacter cloacae laid more eggs but had shorter lifespan while female fed Enterococcus faecalis and Klebsiella oxytoca enriched diets lived longer but had lower fecundity compared to the positive control. Conversely, flies fed sugar diet (negative control) were not able to produce eggs, but lived longer than those from the positive control.

CONCLUSIONS: These results suggest that intestinal bacteria can drive the foraging decision in a way which promotes the reproduction and survival of B. dorsalis. Our data highlight the potentials of gut bacterial isolates to control the foraging behavior of the fly and empower the sterile insect technique (SIT) program through the mass rearing.},
}

Animals
Appetitive Behavior
Bacteria/genetics/*growth & development
Female
Fertility
Genetic Fitness
Longevity
Male
Symbiosis
Tephritidae/genetics/*microbiology/*physiology

@article {pmid31621176,
year = {2020},
author = {Venice, F and Ghignone, S and Salvioli di Fossalunga, A and Amselem, J and Novero, M and Xianan, X and Sędzielewska Toro, K and Morin, E and Lipzen, A and Grigoriev, IV and Henrissat, B and Martin, FM and Bonfante, P},
title = {At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions.},
journal = {Environmental microbiology},
volume = {22},
number = {1},
pages = {122-141},
doi = {10.1111/1462-2920.14827},
pmid = {31621176},
issn = {1462-2920},
mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Base Sequence ; Gene Transfer, Horizontal ; Genome, Fungal/genetics ; Glomeromycota/genetics/*physiology ; Microbiota/genetics ; Mycorrhizae/*physiology ; Plant Roots/*microbiology ; Plants/*microbiology ; Symbiosis/*physiology ; },
abstract = {As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.},
}

Bacteria/classification/genetics
*Bacterial Physiological Phenomena
Base Sequence
Gene Transfer, Horizontal
Genome, Fungal/genetics
Glomeromycota/genetics/*physiology
Microbiota/genetics
Mycorrhizae/*physiology
Plant Roots/*microbiology
Plants/*microbiology
Symbiosis/*physiology

@article {pmid32317381,
year = {2020},
author = {Mendoza-Suárez, MA and Geddes, BA and Sánchez-Cañizares, C and Ramírez-González, RH and Kirchhelle, C and Jorrin, B and Poole, PS},
title = {Optimizing Rhizobium-legume symbioses by simultaneous measurement of rhizobial competitiveness and N2 fixation in nodules.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {18},
pages = {9822-9831},
pmid = {32317381},
issn = {1091-6490},
support = {BB/L011484/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N003608/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N013387/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Fabaceae/*genetics/metabolism/microbiology ; Green Fluorescent Proteins/genetics ; High-Throughput Nucleotide Sequencing ; Nitrogen/metabolism ; Nitrogen Fixation/*genetics ; Peas/genetics/metabolism ; Plasmids/genetics ; Rhizobium leguminosarum/*genetics/metabolism ; Root Nodules, Plant/genetics/metabolism ; Soil Microbiology ; Symbiosis/*genetics ; Synthetic Biology ; },
abstract = {Legumes tend to be nodulated by competitive rhizobia that do not maximize nitrogen (N2) fixation, resulting in suboptimal yields. Rhizobial nodulation competitiveness and effectiveness at N2 fixation are independent traits, making their measurement extremely time-consuming with low experimental throughput. To transform the experimental assessment of rhizobial competitiveness and effectiveness, we have used synthetic biology to develop reporter plasmids that allow simultaneous high-throughput measurement of N2 fixation in individual nodules using green fluorescent protein (GFP) and barcode strain identification (Plasmid ID) through next generation sequencing (NGS). In a proof-of-concept experiment using this technology in an agricultural soil, we simultaneously monitored 84 different Rhizobium leguminosarum strains, identifying a supercompetitive and highly effective rhizobial symbiont for peas. We also observed a remarkable frequency of nodule coinfection by rhizobia, with mixed occupancy identified in ∼20% of nodules, containing up to six different strains. Critically, this process can be adapted to multiple Rhizobium-legume symbioses, soil types, and environmental conditions to permit easy identification of optimal rhizobial inoculants for field testing to maximize agricultural yield.},
}

Fabaceae/*genetics/metabolism/microbiology
Green Fluorescent Proteins/genetics
High-Throughput Nucleotide Sequencing
Nitrogen/metabolism
Nitrogen Fixation/*genetics
Peas/genetics/metabolism
Plasmids/genetics
Rhizobium leguminosarum/*genetics/metabolism
Root Nodules, Plant/genetics/metabolism
Soil Microbiology
Symbiosis/*genetics
Synthetic Biology

@article {pmid32714300,
year = {2020},
author = {Wang, X and Sun, S and Yang, X and Cheng, J and Wei, H and Li, Z and Michaud, JP and Liu, X},
title = {Variability of Gut Microbiota Across the Life Cycle of Grapholita molesta (Lepidoptera: Tortricidae).},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1366},
doi = {10.3389/fmicb.2020.01366},
pmid = {32714300},
issn = {1664-302X},
abstract = {Grapholita molesta, the oriental fruit moth, is a serious global pest of many Rosaceae fruit trees. Gut microorganisms play important roles in host nutrition, digestion, detoxification, and resistance to pathogens. However, there are few studies on the microbiota of G. molesta, particularly during metamorphosis. Here, the diversity of gut microbiota across the holometabolous life cycle of G. molesta was investigated comprehensively by Illumina high-throughput sequencing technology. The results showed that the microbiota associated with eggs had a high number of operational taxonomic units (OTUs). OTU and species richness in early-instar larvae (first and second instars) were significantly higher than those in late-instar larvae (third to fifth instars). Species richness increased again in male pupae and adults, apparently during the process of metamorphosis, compared to late-instar larvae. Proteobacteria and Firmicutes were the dominant phyla in the gut and underwent notable changes during metamorphosis. At the genus level, gut microbial community shifts from Gluconobacter and Pantoea in early-instar larvae to Enterococcus and Enterobacter in late-instar larvae and to Serratia in pupae were apparent, in concert with host developmental changes. Principal coordinate analysis (PCoA) and linear discriminant analysis effect size (LEfSe) analyses confirmed the differences in the structure of gut microbiota across different developmental stages. In addition, sex-dependent bacterial community differences were observed. Microbial interaction network analysis showed different correlations among intestinal microbes at each developmental stage of G. molesta, which may result from the different abundance and diversity of gut microbiota at different life stages. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated that most functional prediction categories of gut microbiota were related to membrane transport, carbohydrate and amino acid metabolism, and DNA replication and repair. Bacteria isolated by conventional culture-dependent methods belonged to Proteobacteria, Firmicutes, and Actinobacteria, which was consistent with high-throughput sequencing results. In conclusion, exploration of gut bacterial community composition in the gut of G. molesta should shed light into deeper understanding about the intricate associations between microbiota and host and might provide clues to the development of novel pest management strategies against fruit borers.},
}

@article {pmid32713966,
year = {2020},
author = {Rubia, MI and Ramachandran, VK and Arrese-Igor, C and Larrainzar, E and Poole, PS},
title = {A novel biosensor to monitor proline in pea root exudates and nodules under osmotic stress and recovery.},
journal = {Plant and soil},
volume = {452},
number = {1},
pages = {413-422},
doi = {10.1007/s11104-020-04577-2},
pmid = {32713966},
issn = {0032-079X},
abstract = {Background and aims: Plant and bacteria are able to synthesise proline, which acts as a compound to counteract the negative effects of osmotic stresses. Most methodologies rely on the extraction of compounds using destructive methods. This work describes a new proline biosensor that allows the monitoring of proline levels in a non-invasive manner in root exudates and nodules of legume plants.

Methods: The proline biosensor was constructed by cloning the promoter region of pRL120553, a gene with high levels of induction in the presence of proline, in front of the lux cassette in Rhizobium leguminosarum bv. viciae.

Results: Free-living assays show that the proline biosensor is sensitive and specific for proline. Proline was detected in both root exudates and nodules of pea plants. The luminescence detected in bacteroids did not show variations during osmotic stress treatments, but significantly increased during recovery.

Conclusions: This biosensor is a useful tool for the in vivo monitoring of proline levels in root exudates and bacteroids of symbiotic root nodules, and it contributes to our understanding of the metabolic exchange occurring in nodules under abiotic stress conditions.},
}

@article {pmid32710518,
year = {2020},
author = {Allgeier, JE and Andskog, MA and Hensel, E and Appaldo, R and Layman, C and Kemp, DW},
title = {Rewiring coral: Anthropogenic nutrients shift diverse coral-symbiont nutrient and carbon interactions toward symbiotic algal dominance.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.15230},
pmid = {32710518},
issn = {1365-2486},
support = {OCE #0746164//National Science Foundation/ ; OCE #2023507//National Science Foundation/ ; OCE #1948622//National Science Foundation/ ; //University of Alabama at Birmingham/ ; },
abstract = {Improving coral reef conservation requires heightened understanding of the mechanisms by which coral cope with changing environmental conditions to maintain optimal health. We used a long-term (10 month) in situ experiment with two phylogenetically diverse scleractinians (Acropora palmata and Porites porites) to test how coral-symbiotic algal interactions changed under real-world conditions that were a priori expected to be beneficial (fish-mediated nutrients) and to be harmful, but non-lethal, for coral (fish + anthropogenic nutrients). Analyzing nine response variables of nutrient stoichiometry and stable isotopes per coral fragment, we found that nutrients from fish positively affected coral growth, and moderate doses of anthropogenic nutrients had no additional effects. While growing, coral maintained homeostasis in their nutrient pools, showing tolerance to the different nutrient regimes. Nonetheless, structural equation models revealed more nuanced relationships, showing that anthropogenic nutrients reduced the diversity of coral-symbiotic algal interactions and caused nutrient and carbon flow to be dominated by the symbiont. Our findings show that nutrient and carbon pathways are fundamentally "rewired" under anthropogenic nutrient regimes in ways that could increase corals' susceptibility to further stressors. We hypothesize that our experiment captured coral in a previously unrecognized transition state between mutualism and antagonism. These findings highlight a notable parallel between how anthropogenic nutrients promote symbiont dominance with the holobiont, and how they promote macroalgal dominance at the coral reef scale. Our findings suggest more realistic experimental conditions, including studies across gradients of anthropogenic nutrient enrichment as well as the incorporation of varied nutrient and energy pathways, may facilitate conservation efforts to mitigate coral loss.},
}

@article {pmid32709946,
year = {2020},
author = {Barcoto, MO and Carlos-Shanley, C and Fan, H and Ferro, M and Nagamoto, NS and Bacci, M and Currie, CR and Rodrigues, A},
title = {Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12384},
doi = {10.1038/s41598-020-68448-7},
pmid = {32709946},
issn = {2045-2322},
support = {2015/16415-0//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo/ ; 2016/02767-5//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo/ ; 2017/04824-9//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo/ ; 2012/25299-6//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo/ ; 05269/2018-6//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#x00ED;fico e Tecnol&#x00F3;gico (National Council for Scientific and Technological Development)/ ; },
abstract = {Some lineages of ants, termites, and beetles independently evolved a symbiotic association with lignocellulolytic fungi cultivated for food, in a lifestyle known as fungiculture. Fungus-growing insects' symbiosis also hosts a bacterial community thought to integrate their physiology. Similarities in taxonomic composition support the microbiota of fungus-growing insects as convergent, despite differences in fungus-rearing by these insects. Here, by comparing fungus-growing insects to several hosts ranging diverse dietary patterns, we investigate whether the microbiota taxonomic and functional profiles are characteristic of the fungiculture environment. Compared to other hosts, the microbiota associated with fungus-growing insects presents a distinctive taxonomic profile, dominated by Gammaproteobacteria at class level and by Pseudomonas at genera level. Even with a functional profile presenting similarities with the gut microbiota of herbivorous and omnivorous hosts, some differentially abundant features codified by the microbiota of fungus-growing insects suggest these communities occupying microhabitats that are characteristic of fungiculture. These features include metabolic pathways involved in lignocellulose breakdown, detoxification of plant secondary metabolites, metabolism of simple sugars, fungal cell wall deconstruction, biofilm formation, antimicrobials biosynthesis, and metabolism of diverse nutrients. Our results suggest that the microbiota could be functionally adapted to the fungiculture environment, codifying metabolic pathways potentially relevant to the fungus-growing insects' ecosystems functioning.},
}

@article {pmid32709725,
year = {2020},
author = {Del Cerro, P and Ayala-García, P and Buzón, P and Castells-Graells, R and López-Baena, FJ and Ollero, FJ and Pérez-Montaño, F},
title = {OnfD, an AraC-type transcriptional regulator of Rhizobium tropici CIAT 899 involved in Nod factor synthesis and symbiosis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01297-20},
pmid = {32709725},
issn = {1098-5336},
abstract = {Rhizobium tropici CIAT 899 is a broad host-range rhizobial strain that establishes symbiotic interactions with legumes and tolerates different environmental stresses such as heat, acidity or salinity. This rhizobial strain produces a wide variety of symbiotically active nodulation factors (NF) induced by the presence of plant-released flavonoids, but also under osmotic stress conditions, through the LysR-type transcriptional regulators NodD1 (flavonoids) and NodD2 (osmotic stress). However, the activation of NodD2 under high osmotic conditions remains elusive. In this paper, we have studied the role of a new AraC-type regulator (named as OnfD) in the symbiotic interaction of R. tropici CIAT 899 with Phaseolus vulgaris and Lotus plants. We determined that OnfD is required under salt stress conditions for the transcriptional activation of the nodulation genes and therefore the synthesis and export of NF, which are required for a successful symbiosis with P. vulgaris Moreover, using bacterial two-hybrid analysis, we demonstrated that the OnfD and NodD2 proteins form homodimers and OnfD/NodD2 form heterodimers, which could be involved in the production of NF in the presence of osmotic stress conditions since both regulators are required for NF synthesis in the presence of salt. A structural model of OnfD is presented and discussed.ImportanceThe synthesis and export of rhizobial NF are mediated by a conserved group of LysR-type regulators, the NodD proteins. In this manuscript, we have demonstrated that a non-LysR-type regulator, an AraC-type protein, is required for the transcriptional activation of symbiotic genes and for the synthesis of symbiotically active NF under salt stress conditions.},
}

@article {pmid32708808,
year = {2020},
author = {Lindsey, ARI},
title = {Sensing, Signaling, and Secretion: A Review and Analysis of Systems for Regulating Host Interaction in Wolbachia.},
journal = {Genes},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/genes11070813},
pmid = {32708808},
issn = {2073-4425},
support = {R01AI144430//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {Wolbachia (Anaplasmataceae) is an endosymbiont of arthropods and nematodes that resides within host cells and is well known for manipulating host biology to facilitate transmission via the female germline. The effects Wolbachia has on host physiology, combined with reproductive manipulations, make this bacterium a promising candidate for use in biological- and vector-control. While it is becoming increasingly clear that Wolbachia's effects on host biology are numerous and vary according to the host and the environment, we know very little about the molecular mechanisms behind Wolbachia's interactions with its host. Here, I analyze 29 Wolbachia genomes for the presence of systems that are likely central to the ability of Wolbachia to respond to and interface with its host, including proteins for sensing, signaling, gene regulation, and secretion. Second, I review conditions under which Wolbachia alters gene expression in response to changes in its environment and discuss other instances where we might hypothesize Wolbachia to regulate gene expression. Findings will direct mechanistic investigations into gene regulation and host-interaction that will deepen our understanding of intracellular infections and enhance applied management efforts that leverage Wolbachia.},
}

@article {pmid32708770,
year = {2020},
author = {Song, F and Bai, F and Wang, J and Wu, L and Jiang, Y and Pan, Z},
title = {Influence of Citrus Scion/Rootstock Genotypes on Arbuscular Mycorrhizal Community Composition under Controlled Environment Condition.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {7},
pages = {},
doi = {10.3390/plants9070901},
pmid = {32708770},
issn = {2223-7747},
support = {2019YFD1001400//National Key R&D Program of China/ ; 2016-620-000-001-030//Hubei Provincial Agriculture Research System, Hubei Provincial Characteristic Fruit Innovation, and Hubei Agricultural Science and Technology Innovation Fund/ ; },
abstract = {Citrus is vegetatively propagated by grafting for commercial production, and most rootstock cultivars of citrus have scarce root hairs, thus heavily relying on mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community composition, and its differences under different citrus scion/rootstock genotypes, were largely unknown. In this study, we investigated the citrus root-associated AMF diversity and richness, and assessed the influence of citrus scion/rootstock genotypes on the AMF community composition in a controlled condition, in order to exclude interferences from environmental factors and agricultural practices. As a result, a total of 613,408 Glomeromycota tags were detected in the citrus roots, and 46 AMF species were annotated against the MAARJAM database. Of these, 39 species belonged to Glomus, indicating a dominant role of the Glomus AMF in the symbiosis with citrus. PCoA analysis indicated that the AMF community's composition was significantly impacted by both citrus scion and rootstock genotypes, but total samples were clustered according to rootstock genotype rather than scion genotype. In addition, AMF α diversity was significantly affected merely by rootstock genotype. Thus, rootstock genotype might exert a greater impact on the AMF community than scion genotype. Taken together, this study provides a comprehensive insight into the AMF community in juvenile citrus plants, and reveals the important effects of citrus genotype on AMF community composition.},
}

@article {pmid32708248,
year = {2020},
author = {Tran, T and Grandvalet, C and Verdier, F and Martin, A and Alexandre, H and Tourdot-Maréchal, R},
title = {Microbial Dynamics between Yeasts and Acetic Acid Bacteria in Kombucha: Impacts on the Chemical Composition of the Beverage.},
journal = {Foods (Basel, Switzerland)},
volume = {9},
number = {7},
pages = {},
doi = {10.3390/foods9070963},
pmid = {32708248},
issn = {2304-8158},
abstract = {Kombucha is a traditional low-alcoholic beverage made from sugared tea and transformed by a complex microbial consortium including yeasts and acetic acid bacteria (AAB). To study the microbial interactions and their impact on the chemical composition of the beverage, an experimental design with nine couples associating one yeast strain and one AAB strain isolated from original black tea kombucha was set up. Three yeast strains belonging to the genera Brettanomyces, Hanseniaspora, and Saccharomyces and three strains of Acetobacter and Komagataeibacter species were chosen. Monocultures in sugared tea were analyzed to determine their individual microbial behaviors. Then, cultivation of the original kombucha consortium and cocultures in sugared tea were compared to determine the interactive microbial effects during successive phases in open and closed incubation conditions. The results highlight the main impact of yeast metabolism on the product's chemical composition and the secondary impact of bacterial species on the composition in organic acids. The uncovered microbial interactions can be explained by different strategies for the utilization of sucrose. Yeasts and AAB unable to perform efficient sucrose hydrolysis rely on yeasts with high invertase activity to access released monosaccharides. Moreover, the presence of AAB rerouted the metabolism of Saccharomycescerevisiae towards higher invertase and fermentative activities.},
}

@article {pmid32704792,
year = {2019},
author = {Pyles, MB and Fowler, AL and Bill, VT and Harlow, BE and Crum, AD and Hayes, SH and Flythe, MD and Lawrence, LM},
title = {Effect of maternal diet on select fecal bacteria of foals.},
journal = {Translational animal science},
volume = {3},
number = {1},
pages = {204-211},
pmid = {32704792},
issn = {2573-2102},
abstract = {Adult horses depend on the microbial community in the hindgut to digest fiber and produce short-chain fatty acids that are use for energy. Colonization of the foal gastrointestinal tract is essential to develop this symbiosis. However, factors affecting colonization are not well understood. The objectives of this study were to evaluate the age-related changes and effects of maternal diet on select fecal bacterial groups in foals from 1 to 28 d of age. Thoroughbred foals (n = 18) were from dams fed forage and one of two concentrates: an oat-based (OB) or corn and wheat middlings-based (CWB) pelleted concentrate. The mares had access to assigned concentrates, along with a mixed hay and cool-season grass pasture, 28 d before and 28 d after parturition. Fecal samples were collected from foals at 1 d (14 to 36 h), 4, 14, and 28 d after birth. Fecal samples were serially diluted with phosphate-buffered saline before inoculation of enriched, selective media to enumerate Lactobacillus spp., amylolytic bacteria, and cellulolytic bacteria. Enumeration data were log-transformed then analyzed with mixed model analysis of variance with repeated measures (SAS 9.3) to test the main effects of maternal diet (OB or CWB), time of sample, and interaction between maternal diet and time. Cellulolytic bacteria first appeared in foal feces between 4 and 14 d of age and increased with age (P < 0.05). Amylolytic bacteria and lactobacilli were abundant at 1 d and then increased with age (P < 0.05). There was an interaction between maternal diet and time for Lactobacillus spp. with OB foals having more lactobacilli than CWB foals at 1 and 4 d (P < 0.05); however, there were no differences observed at 14 d (P > 0.05). Maternal diet did not influence amylolytic or cellulolytic bacteria (P > 0.05). These results indicate that colonization of the hindgut is a sequential process beginning early in the foal's life and that maternal diet may influence some bacteria in the gastrointestinal tract of foals.},
}

@article {pmid32706881,
year = {2020},
author = {Sogawa, A and Takahashi, I and Kyo, M and Imaizumi-Anraku, H and Tajima, S and Nomura, M},
title = {Requirements of Qa-SNARE LjSYP132s for nodulation and seed development in Lotus japonicus.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaa099},
pmid = {32706881},
issn = {1471-9053},
abstract = {SNARE (soluble N-ethyl maleimide sensitive factor attachment protein receptor) mediates membrane fusion of vesicle transport in eukaryotic cells. LjSYP132s is a member of Qa-SNAREs in Lotus japonicus, and two isoforms, LjSYP132a and LjSYP132b, are generated by alternative splicing. Immunoblot analysis showed LjSYP132s antibody was expressed strongly in infected root nodules and seeds by post-transcriptional modification. In LjSYP132a or LjSYP132b silencing roots (RNAi-LjSYP132a, RNAi-LjSYP132b), infection thread (IT) was not elongated, suggesting that both LjSYP132a and LjSYP132b have a role in IT progression. The results were consistent with the data of qRT-PCR that both genes expressed at the early stage of infection. However, during the nodulation only LjSYP132a was induced. LjSYP132s protein was observed in the M. loti-inoculated roots of mutants, nfr1, castor, and pollux, suggesting that LjSYP132s can be induced without Nod factor signaling. Accumulation of LjSYP132s in the PBM suggests the function of not only IT formation but also nutrient transport. In contrast, qRT-PCR showed that LjSYP132b was expressed in the seeds. A stable transgenic plant of LjSYP132b, R132b, was produced by RNAi silencing. In the R132b plants, small pods with a few seeds and abnormal tip growth of the pollen tubes were observed, suggesting LjSYP132b has a role in pollen tube growth as well as nutrient transport in the plasma membrane of seeds.},
}

@article {pmid32704060,
year = {2020},
author = {Lin, C and Wang, Y and Liu, M and Li, Q and Xiao, W and Song, X},
title = {Effects of nitrogen deposition and phosphorus addition on arbuscular mycorrhizal fungi of Chinese fir (Cunninghamia lanceolata).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12260},
doi = {10.1038/s41598-020-69213-6},
pmid = {32704060},
issn = {2045-2322},
support = {2016YFD0600201//National Key Research and Development Program of China/ ; 2016YFD0600201//National Key Research and Development Program of China/ ; 2016YFD0600201//National Key Research and Development Program of China/ ; 2016YFD0600201//National Key Research and Development Program of China/ ; 2016YFD0600201//National Key Research and Development Program of China/ ; 2016YFD0600201//National Key Research and Development Program of China/ ; 2016SY06//Province-Academy Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; 2016SY06//Province-Academy Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; 2016SY06//Province-Academy Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; 2016SY06//Province-Academy Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; 2016SY06//Province-Academy Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; 2016SY06//Province-Academy Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; },
abstract = {Nitrogen (N) deposition is a key factor that affects terrestrial biogeochemical cycles with a growing trend, especially in the southeast region of China, where shortage of available phosphorus (P) is particularly acute and P has become a major factor limiting plant growth and productivity. Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with plants, and play an important role in enhancing plant stress resistance. However, the response of AMF to the combined effects of N deposition and P additions is poorly understood. Thus, in this study, a field experiment was conducted in 10-year Chinese fir forests to estimate the effects of simulated nitrogen (N) deposition (low-N, 30 kg ha-1 year-1 and high-N, 60 kg ha-1 year-1) and phosphorus (P) addition treatments (low-P, 20 mg kg-1 and high-P, 40 mg kg-1) on AMF since April 2017, which was reflected in AMF root colonization rates and spore density of rhizosphere soil. Our results showed that N deposition significantly decreased AMF root colonization rates and spore density. In N-free plots, P addition significantly decreased AMF root colonization rates, but did not significantly alter spore density. In low-N plots, colonization rates significantly decreased under low P addition, but significantly increased under high P addition, and spore density exhibited a significant decline under high P additions. In high-N plots, colonization rates and spore density significantly increased under P additions. Interactive effects of simulated N deposition and P addition on both colonization rates and spore density were significant. Moderate N deposition or P addition can weaken the symbiotic relationship between plants and AMF, significantly reducing AMF colonization rates and inhibiting spore production. However, a moderate addition of P greatly enhances spore yield. In the case of interactive effects, the AMF colonization rates and spore density are affected by the relative content of N and P in the soil.},
}

@article {pmid32294136,
year = {2020},
author = {Raza, MF and Wang, Y and Cai, Z and Bai, S and Yao, Z and Awan, UA and Zhang, Z and Zheng, W and Zhang, H},
title = {Gut microbiota promotes host resistance to low-temperature stress by stimulating its arginine and proline metabolism pathway in adult Bactrocera dorsalis.},
journal = {PLoS pathogens},
volume = {16},
number = {4},
pages = {e1008441},
pmid = {32294136},
issn = {1553-7374},
mesh = {Animals ; Arginine/*metabolism ; Cold Temperature ; *Gastrointestinal Microbiome ; Klebsiella/genetics/growth & development/isolation & purification/physiology ; Male ; Proline/*metabolism ; Stress, Physiological ; Symbiosis ; Tephritidae/*microbiology/physiology ; },
abstract = {Gut symbiotic bacteria have a substantial impact on host physiology and ecology. However, the contribution of gut microbes to host fitness during long-term low-temperature stress is still unclear. This study examined the role of gut microbiota in host low-temperature stress resistance at molecular and biochemical levels in the oriental fruit fly Bactrocera dorsalis. The results showed that after the gut bacteria of flies were removed via antibiotic treatment, the median survival time was significantly decreased to approximately 68% of that in conventional flies following exposure to a temperature stress of 10°C. Furthermore, we found that Klebsiella michiganensis BD177 is a key symbiotic bacterium, whose recolonization in antibiotic treated (ABX) flies significantly extended the median survival time to 160% of that in the ABX control, and restored their lifespan to the level of conventional flies. Notably, the relative levels of proline and arginine metabolites were significantly downregulated by 34- and 10-fold, respectively, in ABX flies compared with those in the hemolymph of conventional flies after exposure to a temperature stress of 10°C whereas recolonization of ABX flies by K. michiganensis BD177 significantly upregulated the levels of proline and arginine by 13- and 10- fold, respectively, compared with those found in the hemolymph of ABX flies. qPCR analysis also confirmed that K. michiganensis-recolonized flies significantly stimulated the expression of transcripts from the arginine and proline metabolism pathway compared with the ABX controls, and RNAi mediated silencing of two key genes Pro-C and ASS significantly reduced the survival time of conventional flies, postexposure low-temperature stress. We show that microinjection of L-arginine and L-proline into ABX flies significantly increased their survival time following exposure to temperature stress of 10°C. Transmission electron microscopy (TEM) analysis further revealed that low-temperature stress caused severe destruction in cristae structures and thus resulted in abnormal circular shapes of mitochondria in ABX flies gut, while the recolonization of live K. michiganensis helped the ABX flies to maintain mitochondrial functionality to a normal status, which is important for the arginine and proline induction. Our results suggest that gut microbiota plays a vital role in promoting the host resistance to low-temperature stress in B. dorsalis by stimulating its arginine and proline metabolism pathway.},
}

Animals
Arginine/*metabolism
Cold Temperature
*Gastrointestinal Microbiome
Klebsiella/genetics/growth & development/isolation & purification/physiology
Male
Proline/*metabolism
Stress, Physiological
Symbiosis
Tephritidae/*microbiology/physiology

@article {pmid32282850,
year = {2020},
author = {Lewis, MD and Paun, A and Romano, A and Langston, H and Langner, CA and Moore, IN and Bock, KW and Francisco, AF and Brenchley, JM and Sacks, DL},
title = {Fatal progression of experimental visceral leishmaniasis is associated with intestinal parasitism and secondary infection by commensal bacteria, and is delayed by antibiotic prophylaxis.},
journal = {PLoS pathogens},
volume = {16},
number = {4},
pages = {e1008456},
pmid = {32282850},
issn = {1553-7374},
mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Antibiotic Prophylaxis ; Bacteria/classification/genetics/isolation & purification ; Bacterial Infections/*prevention & control ; Bacterial Physiological Phenomena ; Coinfection/microbiology/*prevention & control ; Cricetinae ; Disease Progression ; Female ; Gastrointestinal Microbiome ; Humans ; Intestinal Diseases, Parasitic/*parasitology ; Leishmania donovani/physiology ; Leishmaniasis, Visceral/complications/*parasitology ; Male ; Mesocricetus ; Mice ; Mice, Inbred C57BL ; Symbiosis ; },
abstract = {Leishmania donovani causes visceral leishmaniasis (VL), which is typically fatal without treatment. There is substantial variation between individuals in rates of disease progression, response to treatment and incidence of post-treatment sequelae, specifically post-kala-azar dermal leishmaniasis (PKDL). Nevertheless, the majority of infected people are asymptomatic carriers. Hamsters and mice are commonly used as models of fatal and non-fatal VL, respectively. Host and parasite genetics are likely to be important factors, but in general the reasons for heterogeneous disease presentation in humans and animal models are poorly understood. Host microbiota has become established as a factor in cutaneous forms of leishmaniasis but this has not been studied in VL. We induced intestinal dysbiosis in mice and hamsters by long-term treatment with broad-spectrum antibiotics in their drinking water. There were no significant differences in disease presentation in dysbiotic mice. In contrast, dysbiotic hamsters infected with L. donovani had delayed onset and progression of weight loss. Half of control hamsters had a rapid progression phenotype compared with none of the ABX-treated animals and the nine-month survival rate was significantly improved compared to untreated controls (40% vs. 10%). Antibiotic-treated hamsters also had significantly less severe hepatosplenomegaly, which was accompanied by a distinct cytokine gene expression profile. The protective effect was not explained by differences in parasite loads or haematological profiles. We further found evidence that the gut-liver axis is a key aspect of fatal VL progression in hamsters, including intestinal parasitism, bacterial translocation to the liver, malakoplakia and iron sequestration, none of which occurred in non-progressing murine VL. Diverse bacterial genera were cultured from VL affected livers, of which Rodentibacter was specifically absent from ABX-treated hamsters, indicating this pathobiont may play a role in promoting disease progression. The results provide experimental support for antibiotic prophylaxis against secondary bacterial infections as an adjunct therapy in human VL patients.},
}

Animals
Anti-Bacterial Agents/*administration & dosage
Antibiotic Prophylaxis
Bacteria/classification/genetics/isolation & purification
Bacterial Infections/*prevention & control
Bacterial Physiological Phenomena
Coinfection/microbiology/*prevention & control
Cricetinae
Disease Progression
Female
Gastrointestinal Microbiome
Humans
Intestinal Diseases, Parasitic/*parasitology
Leishmania donovani/physiology
Leishmaniasis, Visceral/complications/*parasitology
Male
Mesocricetus
Mice
Mice, Inbred C57BL
Symbiosis

@article {pmid32157312,
year = {2020},
author = {Dellagi, A and Quillere, I and Hirel, B},
title = {Beneficial soil-borne bacteria and fungi: a promising way to improve plant nitrogen acquisition.},
journal = {Journal of experimental botany},
volume = {71},
number = {15},
pages = {4469-4479},
doi = {10.1093/jxb/eraa112},
pmid = {32157312},
issn = {1460-2431},
abstract = {Nitrogen (N) is an essential element for plant productivity, thus, it is abundantly applied to the soil in the form of organic or chemical fertilizers that have negative impacts on the environment. Exploiting the potential of beneficial microbes and identifying crop genotypes that can capitalize on symbiotic associations may be possible ways to significantly reduce the use of N fertilizers. The best-known example of symbiotic association that can reduce the use of N fertilizers is the N2-fixing rhizobial bacteria and legumes. Bacterial taxa other than rhizobial species can develop associative symbiotic interactions with plants and also fix N. These include bacteria of the genera Azospirillum, Azotobacter, and Bacillus, some of which are commercialized as bio-inoculants. Arbuscular mycorrhizal fungi are other microorganisms that can develop symbiotic associations with most terrestrial plants, favoring access to nutrients in a larger soil volume through their extraradical mycelium. Using combinations of different beneficial microbial species is a promising strategy to boost plant N acquisition and foster a synergistic beneficial effect between symbiotic microorganisms. Complex biological mechanisms including molecular, metabolic, and physiological processes dictate the establishment and efficiency of such multipartite symbiotic associations. In this review, we present an overview of the current knowledge and future prospects regarding plant N nutrition improvement through the use of beneficial bacteria and fungi associated with plants, individually or in combination.},
}

@article {pmid31131325,
year = {2019},
author = {Hong, SW and O, E and Lee, JY and Lee, M and Han, D and Ko, HJ and Sprent, J and Surh, CD and Kim, KS},
title = {Food antigens drive spontaneous IgE elevation in the absence of commensal microbiota.},
journal = {Science advances},
volume = {5},
number = {5},
pages = {eaaw1507},
pmid = {31131325},
issn = {2375-2548},
mesh = {Allergens/immunology ; Animals ; Antigens/*immunology ; Bone Marrow Cells/metabolism ; CD4-Positive T-Lymphocytes/cytology ; CD40 Antigens/metabolism ; CD40 Ligand/metabolism ; Food Hypersensitivity/*immunology ; Gastrointestinal Microbiome/*immunology ; Germ-Free Life ; Immune System ; Immunoglobulin E/blood/*immunology ; Lymph Nodes/pathology ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Symbiosis ; },
abstract = {Immunoglobulin E (IgE), a key mediator in allergic diseases, is spontaneously elevated in mice with disrupted commensal microbiota such as germ-free (GF) and antibiotics-treated mice. However, the underlying mechanisms for aberrant IgE elevation are still unclear. Here, we demonstrate that food antigens drive spontaneous IgE elevation in GF and antibiotics-treated mice by generating T helper 2 (TH2)-skewed T follicular helper (TFH) cells in gut-associated lymphoid tissues (GALTs). In these mice, depriving contact with food antigens results in defective IgE elevation as well as impaired generation of TFH cells and IgE-producing cells in GALT. Food antigen-driven TFH cells in GF mice are mostly generated in early life, especially during the weaning period. We also reveal that food antigen-driven TFH cells in GF mice are actively depleted by colonization with commensal microbiota. Thus, our findings provide a possible explanation for why the perturbation of commensal microbiota in early life increases the occurrence of allergic diseases.},
}

Allergens/immunology
Animals
Antigens/*immunology
Bone Marrow Cells/metabolism
CD4-Positive T-Lymphocytes/cytology
CD40 Antigens/metabolism
CD40 Ligand/metabolism
Food Hypersensitivity/*immunology
Gastrointestinal Microbiome/*immunology
Germ-Free Life
Immune System
Immunoglobulin E/blood/*immunology
Lymph Nodes/pathology
Lymphocyte Activation
Mice
Mice, Inbred C57BL
Symbiosis

@article {pmid32702541,
year = {2020},
author = {Li, H and Zhong, Y and Huang, H and Tan, Z and Sun, Y and Liu, H},
title = {Simultaneous nitrogen and phosphorus removal by interactions between phosphate accumulating organisms (PAOs) and denitrifying phosphate accumulating organisms (DPAOs) in a sequencing batch reactor.},
journal = {The Science of the total environment},
volume = {744},
number = {},
pages = {140852},
doi = {10.1016/j.scitotenv.2020.140852},
pmid = {32702541},
issn = {1879-1026},
abstract = {The identification of phosphate-accumulating organisms (PAOs), denitrifying phosphate-accumulating organisms (DPAOs) and their relationship is a key pathway for optimizing nitrate and phosphate removal efficiency in activated sludge. In this study, the acclimatization of microorganisms in sequencing batch reactor were performed with anaerobic/aerobic (A/O) and anaerobic/anoxic (A/A) cycles, the biomass changes of PAOs and DPAOs and the correlations were then discussed. The results indicated that after acclimatization, the nutrient removal efficiencies reached to 85.34% (COD), 93.64% (PO43--P) and 92.34% (NO3--N), respectively, with NO3--N:PO43-P of 1.5:1. The successful enrichment of PAOs and DPAOs (reached 97.9%) was verified by the change of relative metabolic activities, which was further proved by the change of bacterial diversity. The number of Candidatus Accumulibacter, Zoogloea, and Dechloromonas all increased at A/O and A/A stages while the number of Acinetobacter only increased at A/O stage. So Accumulibacter sp. was DPAO while Acinetobacter sp. was only PAO in this process, and genera Accumulibacter, Dechloromonas and Zoogloea greatly coordinated in denitrification and accumulating phosphorous though RDA and chord plot. This was worthy of attention and development to explore enhanced biological phosphorus removal (EBPR) in practical wastewater treatment via improving identification of bacterial species and symbiosis of bacteria community.},
}

@article {pmid32701945,
year = {2020},
author = {Koester, LR and Poole, DH and Serão, NVL and Schmitz-Esser, S},
title = {Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0229192},
doi = {10.1371/journal.pone.0229192},
pmid = {32701945},
issn = {1932-6203},
abstract = {Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungus Epichloë coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. The objective of this study was to identify bacterial and fungal communities associated with fescue toxicosis tolerance. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance groups according to their growth performance (weight gain). 20 HT and 20 LT cattle balanced by farm were selected for amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (q<0.05) different bacterial and fungal microbiota between HT and LT cattle, and indicates that fungal phylotypes may be important for an animal's response to fescue toxicosis: We found that fungal phylotypes affiliating to the Neocallimastigaceae, which are known to be important fiber-degrading fungi, were consistently more abundant in the HT cattle. Whereas fungal phylotypes related to the genus Thelebolus were more abundant in the LT cattle. This study also found more pronounced shifts in the microbiota in animals receiving higher amounts of the toxin. We identified fungal phylotypes which were consistently more abundant either in HT or LT cattle and may thus be associated with the respective animal's response to fescue toxicosis. Our results thus suggest that some fungal phylotypes might be involved in mitigating fescue toxicosis.},
}

@article {pmid32695865,
year = {2020},
author = {Gogoleva, NE and Kataev, VY and Balkin, AS and Plotnikov, AO and Shagimardanova, EI and Subbot, AM and Cherkasov, SV and Gogolev, YV},
title = {Dataset for transcriptome analysis of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S response to starvation.},
journal = {Data in brief},
volume = {31},
number = {},
pages = {106008},
pmid = {32695865},
issn = {2352-3409},
abstract = {Salmonella enterica is an ubiquitous pathogen throughout the world causing gastroenteritis in humans and animals. Survival of pathogenic bacteria in the external environment may be associated with the ability to overcome the stress caused by starvation. The bacterial response to starvation is well understood in laboratory cultures with a sufficiently high cell density. However, bacterial populations often have a small size when facing this challenge in natural biotopes. The aim of this work was to find out if there are differences in the transcriptomes of S. enterica depending on the factor of cell density during starvation. Here we present transcriptome data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S grown in carbon rich or carbon deficient medium with high or low cell density. These data will help identify genes involved in adaptation of low-density bacterial populations to starvation conditions.},
}

@article {pmid32695802,
year = {2020},
author = {Thakur, S and Storewala, P and Basak, U and Jalan, N and Pethe, P},
title = {Clocking the circadian genes in human embryonic stem cells.},
journal = {Stem cell investigation},
volume = {7},
number = {},
pages = {9},
pmid = {32695802},
issn = {2306-9759},
abstract = {Multicellular organisms respond to changing environment which is primarily driven by light from the sun. Essential cyclical processes such as digestion, sleep, migration and breeding are controlled by set of genes know as circadian genes. The core circadian genes comprise of CLOCK, BMAL-1, PERIOD and CYRPTOCHROME that are expressed cyclically and they regulate expression of several genes downstream. The expression of circadian genes has been well studied in multicellular animals; however, it has been shown that stem cells also possess active circadian cycle genes. The circadian cycle genes have been studied in mouse embryonic stem cells and in adult human stem cells. However, there are only few reports of circadian cycle genes in human pluripotent stem cells. We used human embryonic stem cells to investigate the expression of CLOCK, BMAL-1, PERIOD and CYRPTOCHORME genes by RT-PCR at 6, 18 and 22 hours in undifferentiated and differentiated cells. We differentiated human embryonic stem cells spontaneously by adding 10% fetal bovine serum (FBS), and the cells primarily differentiated into ectoderm and mesoderm. We report that CLOCK and BMAL-1 are differentially expressed while PERIOD and CRYPTOCHROME show cyclicity in differentiated and undifferentiated cells. Our results show circadian genes are active in human embryonic stem cells and this needs to be further investigated as human pluripotent stem cells have potential to be used for cell therapy, where they need to synchronize with the body's circadian cycle.},
}

@article {pmid32689478,
year = {2002},
author = {Leggat, W and Marendy, EM and Baillie, B and Whitney, SM and Ludwig, M and Badger, MR and Yellowlees, D},
title = {Dinoflagellate symbioses: strategies and adaptations for the acquisition and fixation of inorganic carbon.},
journal = {Functional plant biology : FPB},
volume = {29},
number = {3},
pages = {309-322},
doi = {10.1071/PP01202},
pmid = {32689478},
issn = {1445-4416},
abstract = {Dinoflagellates exist in symbiosis with a number of marine invertebrates including giant clams, which are the largest of these symbiotic organisms. The dinoflagellates (Symbiodinium sp.) live intercellularly within tubules in the mantle of the host clam. The transport of inorganic carbon (Ci) from seawater to Symbiodinium (=zooxanthellae) is an essential function of hosts that derive the majority of their respiratory energy from the photosynthate exported by the zooxanthellae. Immunolocalisation studies show that the host has adapted its physiology to acquire, rather than remove CO2, from the haemolymph and clam tissues. Two carbonic anhydrase (CA) isoforms (32 and 70 kDa) play an essential part in this process. These have been localised to the mantle and gill tissues where they catalyse the interconversion of HCO3- to CO2, which then diffuses into the host tissues. The zooxanthellae exhibit a number of strategies to maximise Ci acquisition and utilisation. This is necessary as they express a form II Rubisco that has poor discrimination between CO2 and O2. Evidence is presented for a carbon concentrating mechanism (CCM) to overcome this disadvantage. The CCM incorporates the presence of a light-activated CA activity, a capacity to take up both HCO3-and CO2, an ability to accumulate an elevated concentration of Ci within the algal cell, and localisation of Rubisco to the pyrenoid. These algae also express both external and intracellular CAs, with the intracellular isoforms being localised to the thylakoid lumen and pyrenoid. These results have been incorporated into a model that explains the transport of Ci from seawater through the clam to the zooxanthellae.},
}

@article {pmid32689285,
year = {2006},
author = {Murray, J and Geil, R and Wagg, C and Karas, B and Szczyglowski, K and Peterson, RL},
title = {Genetic supressors of Lotus japonicus har1-1 hypernodulation show altered interactions with Glomus intraradices.},
journal = {Functional plant biology : FPB},
volume = {33},
number = {8},
pages = {749-755},
doi = {10.1071/FP06083},
pmid = {32689285},
issn = {1445-4416},
abstract = {Mutant lines of Lotus japonicus (Regel) Larsen that show defects in nodulation as well as in mycorrhiza formation are valuable resources for studying the events required for the establishment of functional symbioses. In this study, 11 mutant lines derived from a screen for genetic suppressors of har1-1 hypernodulation were assessed quantitatively for their ability to form arbuscular mycorrhizal (AM) symbiosis. The presence of extraradical mycelia, appressoria, intraradical hyphae, arbuscules and vesicles were scored. Roots of the har1-1 parental line were heavily colonised by six weeks after inoculation with the AM fungus Glomus intraradices showing the typical Arum-type colonisation pattern. Five mutants lacked internal root colonisation with blocks either at the surface of epidermal cells or at the outer tangential wall of cortical cells. These AM- lines showed some differences in relation to the amount of extraradical hyphae, the number of appressoria, and the degree of abnormal appressorium morphology. Four mutants had internal root colonisation but at a lower level than the parental line. Two mutants showed no difference from the parental line. Results of this study provide additional genetic resources for studying the mechanism of root colonisation by AM fungi.},
}

@article {pmid32689284,
year = {2006},
author = {Hohnjec, N and Henckel, K and Bekel, T and Gouzy, J and Dondrup, M and Goesmann, A and Küster, H},
title = {Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula.},
journal = {Functional plant biology : FPB},
volume = {33},
number = {8},
pages = {737-748},
doi = {10.1071/FP06079},
pmid = {32689284},
issn = {1445-4416},
abstract = {The arbuscular mycorrhizal (AM) association between terrestrial plants and soil fungi of the phylum Glomeromycota is the most widespread beneficial plant-microbe interaction on earth. In the course of the symbiosis, fungal hyphae colonise plant roots and supply limiting nutrients, in particular phosphorus, in exchange for carbon compounds. Owing to the obligate biotrophy of mycorrhizal fungi and the lack of genetic systems to study them, targeted molecular studies on AM symbioses proved to be difficult. With the emergence of plant genomics and the selection of suitable models, an application of untargeted expression profiling experiments became possible. In the model legume Medicago truncatula, high-throughput expressed sequence tag (EST)-sequencing in conjunction with in silico and experimental transcriptome profiling provided transcriptional snapshots that together defined the global genetic program activated during AM. Owing to an asynchronous development of the symbiosis, several hundred genes found to be activated during the symbiosis cannot be easily correlated with symbiotic structures, but the expression of selected genes has been extended to the cellular level to correlate gene expression with specific stages of AM development. These approaches identified marker genes for the AM symbiosis and provided the first insights into the molecular basis of gene expression regulation during AM.},
}

@article {pmid32689281,
year = {2006},
author = {Kinkema, M and Scott, PT and Gresshoff, PM},
title = {Legume nodulation: successful symbiosis through short- and long-distance signalling.},
journal = {Functional plant biology : FPB},
volume = {33},
number = {8},
pages = {707-721},
doi = {10.1071/FP06056},
pmid = {32689281},
issn = {1445-4416},
abstract = {Nodulation in legumes provides a major conduit of available nitrogen into the biosphere. The development of nitrogen-fixing nodules results from a symbiotic interaction between soil bacteria, commonly called rhizobia, and legume plants. Molecular genetic analysis in both model and agriculturally important legume species has resulted in the identification of a variety of genes that are essential for the establishment, maintenance and regulation of this symbiosis. Autoregulation of nodulation (AON) is a major internal process by which nodule numbers are controlled through prior nodulation events. Characterisation of AON-deficient mutants has revealed a novel systemic signal transduction pathway controlled by a receptor-like kinase. This review reports our present level of understanding on the short- and long-distance signalling networks controlling early nodulation events and AON.},
}

@article {pmid32689208,
year = {2006},
author = {Diouf, D and Duponnois, R and Tidiane Ba, A and Neyra, M and Lesueur, D},
title = {Symbiosis of Acacia auriculiformis and Acacia mangium with mycorrhizal fungi and Bradyrhizobium spp. improves salt tolerance in greenhouse conditions.},
journal = {Functional plant biology : FPB},
volume = {32},
number = {12},
pages = {1143-1152},
doi = {10.1071/FP04069},
pmid = {32689208},
issn = {1445-4416},
abstract = {The aim of our work was to assess the growth and mineral nutrition of salt stressed Acacia auriculiformis A. Cunn. ex Benth. and Acacia mangium Willd. seedlings inoculated with a combination of selected microsymbionts (bradyrhizobia and mycorrhizal fungi). Plants were grown in greenhouse conditions in non-sterile soil, irrigated with a saline nutrient solution (0, 50 and 100 mm NaCl). The inoculation combinations consisted of the Bradyrhizobium strain Aust 13c for A. mangium and Aust 11c for A. auriculiformis, an arbuscular mycorrhizal fungus (Glomus intraradices, DAOM 181602) and an ectomycorrhizal fungus (Pisolithus albus, strain COI 007). The inoculation treatments were designed to identify the symbionts that might improve the salt tolerance of both Acacia species. The main effect of salinity was reduced tree growth in both acacias. However, it appeared that, compared with controls, both rhizobial and mycorrhizal inoculation improved the growth of the salt-stressed plants, while inoculation with the ectomycorrhizal fungus strain appeared to have a small effect on their growth and mineral nutrition levels. Endomycorrhizal inoculation combined with rhizobial inoculation usually gave good results. Analysis of foliar proline accumulation confirmed that dual inoculation gave the trees better tolerance to salt stress and suggested that the use of this dual inoculum might be beneficial for inoculation of both Acacia species in soils with moderate salt constraints.},
}

@article {pmid32688821,
year = {2008},
author = {Mathesius, U},
title = {Auxin: at the root of nodule development?.},
journal = {Functional plant biology : FPB},
volume = {35},
number = {8},
pages = {651-668},
doi = {10.1071/FP08177},
pmid = {32688821},
issn = {1445-4416},
abstract = {Root nodules are formed as a result of an orchestrated exchange of chemical signals between symbiotic nitrogen fixing bacteria and certain plants. In plants that form nodules in symbiosis with actinorhizal bacteria, nodules are derived from lateral roots. In most legumes, nodules are formed de novo from pericycle and cortical cells that are re-stimulated for division and differentiation by rhizobia. The ability of plants to nodulate has only evolved recently and it has, therefore, been suggested that nodule development is likely to have co-opted existing mechanisms for development and differentiation from lateral root formation. Auxin is an important regulator of cell division and differentiation, and changes in auxin accumulation and transport are essential for lateral root development. There is growing evidence that rhizobia alter the root auxin balance as a prerequisite for nodule formation, and that nodule numbers are regulated by shoot-to-root auxin transport. Whereas auxin requirements appear to be similar for lateral root and nodule primordium activation and organ differentiation, the major difference between the two developmental programs lies in the specification of founder cells. It is suggested that differing ratios of auxin and cytokinin are likely to specify the precursors of the different root organs.},
}

@article {pmid32688631,
year = {2009},
author = {McCully, ME and Canny, MJ and Huang, CX},
title = {Invited Review: Cryo-scanning electron microscopy (CSEM) in the advancement of functional plant biology. Morphological and anatomical applications.},
journal = {Functional plant biology : FPB},
volume = {36},
number = {2},
pages = {97-124},
doi = {10.1071/FP08304},
pmid = {32688631},
issn = {1445-4416},
abstract = {Cryo-scanning electron microscopy (CSEM) is reviewed by exploring how the images obtained have changed paradigms of plant functions and interactions with their environment. Its power to arrest and stabilise plant parts in milliseconds, and to preserve them at full hydration for examination at micrometre resolution has changed many views of plant function. For example, it provides the only feasible way of accurately measuring stomatal aperture during active transpiration, and volume and shape changes in guard cells, or examining the contents of laticifers. It has revealed that many xylem conduits contain gas, not liquid, during the day, and that they can be refilled with sap and resume water transport. It has elucidated the management of ice to prevent cell damage in frost tolerant plants and has revealed for the first time inherent biological and physical features of root/soil interactions in the field. CSEM is increasingly used to reveal complementary structural information in studies of metabolism, fungal infection and symbiosis, molecular and genetic analysis.},
}

@article {pmid31726316,
year = {2019},
author = {Fiers, WD and Gao, IH and Iliev, ID},
title = {Gut mycobiota under scrutiny: fungal symbionts or environmental transients?.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {79-86},
pmid = {31726316},
issn = {1879-0364},
support = {F32 DK120228/DK/NIDDK NIH HHS/United States ; R01 DK113136/DK/NIDDK NIH HHS/United States ; R21 AI146957/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Fungi/genetics/*physiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; Mice ; *Mycobiome ; Symbiosis/*genetics/immunology ; },
abstract = {The human gastrointestinal tract is home to a thriving community of microbes including the fungal 'mycobiota'. Although sequencing methodology has enumerated diverse fungal genera within this niche, discerning persistent symbiotic residents from contaminants and purely environmental transients remains a challenge. Recent advances in culturomics and sequencing employing metagenomics, metatranscriptomics and longitudinal studies have begun to reveal a human symbiont 'core mycobiome' that may contribute to human health and disease. Trans-kingdom interactions between the bacterial microbiota and evolution within the niche have defined C. albicans as a true symbiont, setting a bar for defining other fungi. Additionally, elegant investigations of mammalian antifungal immunity have examined mononuclear phagocytes, neutrophils, antigen-specific recognition by T cells and other mechanisms important for local and systemic effects on the host, providing further evidence supporting gut persistence. In this review we discuss current research aimed at investigating the symbiotic mycobiota and propose four criteria aiding in the differentiation of fungal symbionts from environmental transients.},
}

Animals
Fungi/genetics/*physiology
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Metagenomics
Mice
*Mycobiome
Symbiosis/*genetics/immunology

@article {pmid31707219,
year = {2019},
author = {Stubbendieck, RM and Li, H and Currie, CR},
title = {Convergent evolution of signal-structure interfaces for maintaining symbioses.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {71-78},
pmid = {31707219},
issn = {1879-0364},
support = {T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; Ants/microbiology ; Decapodiformes/microbiology ; *Evolution, Molecular ; Fabaceae/microbiology ; *Host Microbial Interactions ; Humans ; *Microbiota ; *Symbiosis ; },
abstract = {Symbiotic microbes are essential to the ecological success and evolutionary diversification of multicellular organisms. The establishment and stability of bipartite symbioses are shaped by mechanisms ensuring partner fidelity between host and symbiont. In this minireview, we demonstrate how the interface of chemical signals and host structures influences fidelity between legume root nodules and rhizobia, Hawaiian bobtail squid light organs and Allivibrio fischeri, and fungus-growing ant crypts and Pseudonocardia. Subsequently, we illustrate the morphological diversity and widespread phylogenetic distribution of specialized structures used by hosts to house microbial symbionts, indicating the importance of signal-structure interfaces across the history of multicellular life. These observations, and the insights garnered from well-studied bipartite associations, demonstrate the need to concentrate on the signal-structure interface in complex and multipartite systems, including the human microbiome.},
}

Animals
Ants/microbiology
Decapodiformes/microbiology
*Evolution, Molecular
Fabaceae/microbiology
*Host Microbial Interactions
Humans
*Microbiota
*Symbiosis

@article {pmid31666377,
year = {2020},
author = {Munson-McGee, JH and Rooney, C and Young, MJ},
title = {An Uncultivated Virus Infecting a Nanoarchaeal Parasite in the Hot Springs of Yellowstone National Park.},
journal = {Journal of virology},
volume = {94},
number = {3},
pages = {},
pmid = {31666377},
issn = {1098-5514},
mesh = {Archaeal Viruses/classification/genetics/*isolation & purification/*physiology ; Base Sequence ; DNA Viruses/genetics ; Genome, Viral ; Host Specificity ; Hot Springs/*virology ; Metagenome ; Metagenomics ; Nanoarchaeota/genetics/*virology ; Parks, Recreational ; Symbiosis ; United States ; },
abstract = {The Nanoarchaeota are small cells with reduced genomes that are found attached to and dependent on a second archaeal cell for their growth and replication. Initially found in marine hydrothermal environments and subsequently in terrestrial geothermal hot springs, the Nanoarchaeota species that have been described are obligate ectobionts, each with a different host species. However, no viruses had been described that infect the Nanoarchaeota. Here, we identify a virus infecting Nanoarchaeota by the use of a combination of viral metagenomic and bioinformatic approaches. This virus, tentatively named Nanoarchaeota Virus 1 (NAV1), consists of a 35.6-kb circular DNA genome coding for 52 proteins. We further demonstrate that this virus is broadly distributed among Yellowstone National Park hot springs. NAV1 is one of the first examples of a virus infecting a single-celled organism that is itself an ectobiont of another single-celled organism.IMPORTANCE Here, we present evidence of the first virus found to infect Nanoarchaeota, a symbiotic archaean found in acidic hot springs of Yellowstone National Park, USA. Using culture-independent techniques, we provide the genome sequence and identify the archaeal host species of a novel virus, NAV1. NAV1 is the first example of a virus infecting an archaeal species that is itself an obligate symbiont and dependent on a second host organism for growth and cellular replication. On the basis of annotation of the NAV1 genome, we propose that this virus is the founding member of a new viral family, further demonstrating the remarkable genetic diversity of archaeal viruses.},
}

Archaeal Viruses/classification/genetics/*isolation & purification/*physiology
Base Sequence
DNA Viruses/genetics
Genome, Viral
Host Specificity
Hot Springs/*virology
Metagenome
Metagenomics
Nanoarchaeota/genetics/*virology
Parks, Recreational
Symbiosis
United States

@article {pmid31629912,
year = {2019},
author = {Kokkoris, V and Pogiatzis, A and Hart, MM},
title = {Contrasting common measures of arbuscular mycorrhizal fungal root colonization.},
journal = {Journal of microbiological methods},
volume = {167},
number = {},
pages = {105727},
doi = {10.1016/j.mimet.2019.105727},
pmid = {31629912},
issn = {1872-8359},
mesh = {Flax/microbiology ; Image Processing, Computer-Assisted/*methods ; Microscopy/*methods ; Mycorrhizae/*physiology ; Photography/methods ; Plant Roots/*microbiology ; Symbiosis ; },
abstract = {Estimating the abundance of arbuscular mycorrhizal fungi relies entirely on indirect methods, meaning all measures are associated with some variability. The most common methods use microscopic estimates of the relative proportion of root length colonized by fungal structures. These methods typically examine root subsamples. While such methods are inexpensive and relatively simple, significant variation within single root system means there is opportunity for sampling bias. We evaluated the two most common methods of percent root length colonization for AM fungi both as a subsample and for the entire root system of flax plants. We compared these measures to a novel technique that returns projected fungal surface area (fungal coverage), by using microphotography and imaging analysis. Both microscopic methods overestimated the colonization intensity compared to image analysis. Among the microscopic methods, the method which incorporated colonization intensity (Trouvelot) was significantly more similar to imaging method results, than the method that is based on the presence/absence of the fungus (McGonigle).},
}

Flax/microbiology
Image Processing, Computer-Assisted/*methods
Microscopy/*methods
Mycorrhizae/*physiology
Photography/methods
Plant Roots/*microbiology
Symbiosis

@article {pmid31585390,
year = {2019},
author = {Kuthyar, S and Manus, MB and Amato, KR},
title = {Leveraging non-human primates for exploring the social transmission of microbes.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {8-14},
doi = {10.1016/j.mib.2019.09.001},
pmid = {31585390},
issn = {1879-0364},
mesh = {Animals ; *Behavior, Animal ; Environment ; *Host Microbial Interactions ; Humans ; *Microbiota ; Movement ; Primates/*microbiology ; *Social Behavior ; Symbiosis ; },
abstract = {Host social interactions can provide multiple complex pathways for microbial transmission. Here, we suggest non-human primates as models to study the social transmission of commensal or mutualistic microbes due to their high sociality, wide range of group compositions and dominance structures, and diverse group interactions. Microbial sharing from social interactions can positively impact host health by promoting microbial diversity and influencing immunity. Microbes may also drive their own transmission by shaping host behavior, which could lead to fitness benefits for both microbes and hosts. Variation in patterns of social interactions at both the individual and group scale make non-human primates an ideal system to explore the relationship between social behavior, microbial sharing, and their impact on host health and evolution.},
}

Animals
*Behavior, Animal
Environment
*Host Microbial Interactions
Humans
*Microbiota
Movement
Primates/*microbiology
*Social Behavior
Symbiosis

@article {pmid31474424,
year = {2019},
author = {Derrien, M and Alvarez, AS and de Vos, WM},
title = {The Gut Microbiota in the First Decade of Life.},
journal = {Trends in microbiology},
volume = {27},
number = {12},
pages = {997-1010},
doi = {10.1016/j.tim.2019.08.001},
pmid = {31474424},
issn = {1878-4380},
mesh = {Child ; Child, Preschool ; *Diet ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Appreciation of the importance of the gut microbiome is growing, and it is becoming increasingly relevant to identify preventive or therapeutic solutions targeting it. The composition and function of the gut microbiota are relatively well described for infants (less than 3 years) and adults, but have been largely overlooked in pre-school (3-6 years) and primary school-age (6-12 years) children, as well as teenagers (12-18 years). Early reports suggested that the infant microbiota would attain an adult-like structure at the age of 3 years, but recent studies have suggested that microbiota development may take longer. This development time is of key importance because there is evidence to suggest that deviations in this development may have consequences in later life. In this review, we provide an overview of current knowledge concerning the gut microbiota, its evolution, variation, and response to dietary challenges during the first decade of life with a focus on healthy pre-school and primary school-age children (up to 12 years) from various populations around the globe. This knowledge should facilitate the identification of diet-based approaches targeting individuals of this age group, to promote the development of a healthy microbiota in later life.},
}

Child
Child, Preschool
*Diet
*Gastrointestinal Microbiome
Humans
RNA, Ribosomal, 16S/genetics
Symbiosis

@article {pmid31451346,
year = {2019},
author = {Voulgari-Kokota, A and McFrederick, QS and Steffan-Dewenter, I and Keller, A},
title = {Drivers, Diversity, and Functions of the Solitary-Bee Microbiota.},
journal = {Trends in microbiology},
volume = {27},
number = {12},
pages = {1034-1044},
doi = {10.1016/j.tim.2019.07.011},
pmid = {31451346},
issn = {1878-4380},
mesh = {Animals ; Bees/*microbiology/*physiology ; *Biodiversity ; Environment ; Female ; Male ; *Microbiota ; *Social Behavior ; Social Isolation ; Symbiosis ; },
abstract = {Accumulating reports of global bee declines have drawn much attention to the bee microbiota and its importance. Most research has focused on social bees, while solitary species have received scant attention despite their enormous biodiversity, ecological importance, and agroeconomic value. We review insights from several recent studies on diversity, function, and drivers of the solitary-bee microbiota, and compare these factors with those relevant to the social-bee microbiota. Despite basic similarities, the social-bee model, with host-specific core microbiota and social transmission, is not representative of the vast majority of bee species. The solitary-bee microbiota exhibits greater variability and biodiversity, with a strong impact of environmental acquisition routes. Our synthesis identifies outstanding questions that will build understanding of these interactions, responses to environmental threats, and consequences for health.},
}

Animals
Bees/*microbiology/*physiology
*Biodiversity
Environment
Female
Male
*Microbiota
*Social Behavior
Social Isolation
Symbiosis

@article {pmid31422731,
year = {2019},
author = {Wari, D and Alamgir, KM and Mujiono, K and Hojo, Y and Tani, A and Shinya, T and Nakatani, H and Galis, I},
title = {Brown planthopper honeydew-associated symbiotic microbes elicit momilactones in rice.},
journal = {Plant signaling & behavior},
volume = {14},
number = {11},
pages = {1655335},
pmid = {31422731},
issn = {1559-2324},
mesh = {Animals ; Cucumis melo/*microbiology/*parasitology ; Diterpenes/*metabolism ; Hemiptera/*physiology ; Lactones/*metabolism ; Oryza/*microbiology/*parasitology ; Plant Leaves/metabolism ; *Symbiosis ; },
abstract = {Plants use many natural products to counter pests and diseases in nature. In rice, direct defense mechanisms include broad range of secondary metabolites, such as phenolamides (PA), diterpene phytoalexins, and flavonoid sakuranetin. Recently, accumulation of PAs in rice was shown to be under control of microbial symbionts in honeydew (HD), digestive waste from the rice brown planthopper (Nilaparvata lugens; BPH), but whether HD microbiota can also promote diterpene phytoalexins, momilactone A (MoA) and MoB, has not been reported. Here, we demonstrate that crude HD, but not a filtered one, induces MoA and MoB in rice, suggesting the involvement of BPH-HD endosymbionts. Consequently, microbial strains previously isolated from HD could promote MoA and MoB levels in wounded rice leaves, suggesting that rice indeed responds to BPH by cumulative chemical defense that involves both PA and diterpene phytoalexin pathways.},
}

Animals
Cucumis melo/*microbiology/*parasitology
Diterpenes/*metabolism
Hemiptera/*physiology
Lactones/*metabolism
Oryza/*microbiology/*parasitology
Plant Leaves/metabolism
*Symbiosis

@article {pmid31299010,
year = {2019},
author = {Lee, HY and Lee, SH and Lee, JH and Lee, WJ and Min, KJ},
title = {The role of commensal microbes in the lifespan of Drosophila melanogaster.},
journal = {Aging},
volume = {11},
number = {13},
pages = {4611-4640},
pmid = {31299010},
issn = {1945-4589},
mesh = {Age Factors ; Animals ; Bacterial Load ; Drosophila melanogaster/*microbiology/physiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; Host Microbial Interactions ; *Longevity ; Symbiosis ; },
abstract = {Commensal microbes have mutualistic relationships with their host and mainly live in the host intestine. There are many studies on the relationships between commensal microbes and host physiology. However, there are inconsistent results on the effects of commensal microbes on host lifespan. To clarify this controversy, we generated axenic flies by using two controlled methods - bleaching and antibiotic treatment - and investigated the relationship between the commensal microbes and host lifespan in Drosophila melanogaster. The removal of microbes by using bleaching and antibiotic treatments without detrimental effects increased fly lifespan. Furthermore, a strain of flies colonized with a high load of microbiota showed a greater effect on lifespan extension when the microbes were eliminated, suggesting that commensal bacteria abundance may be a critical determinant of host lifespan. Consistent with those observations, microbial flora of aged fly gut significantly decreased axenic fly lifespan via an increase in bacterial load rather than through a change of bacterial composition. Our elaborately controlled experiments showed that the elimination of commensal microbes without detrimental side effects increased fly lifespan, and that bacterial load was a significant determinant of lifespan. Furthermore, our results indicate the presence of a deterministic connection between commensal microbes and host lifespan.},
}

Age Factors
Animals
Bacterial Load
Drosophila melanogaster/*microbiology/physiology
*Gastrointestinal Microbiome
Germ-Free Life
Host Microbial Interactions
*Longevity
Symbiosis

@article {pmid32691527,
year = {2020},
author = {Parmentier, T and De Laender, F and Bonte, D},
title = {The topology and drivers of ant-symbiont networks across Europe.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.12634},
pmid = {32691527},
issn = {1469-185X},
support = {BOF17/PDO/084//Bijzonder Onderzoeksfonds/ ; 1203020N//Fonds Wetenschappelijk Onderzoek/ ; W0.003.16N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Intimate associations between different species drive community composition across ecosystems. Understanding the ecological and evolutionary drivers of these symbiotic associations is challenging because their structure eventually determines stability and resilience of the entire species network. Here, we compiled a detailed database on naturally occurring ant-symbiont networks in Europe to identify factors that affect symbiont network topology. These networks host an unrivalled diversity of macrosymbiotic associations, spanning the entire mutualism-antagonism continuum, including: (i) myrmecophiles - commensalistic and parasitic arthropods; (ii) trophobionts - mutualistic aphids, scale insects, planthoppers and caterpillars; (iii) social parasites - parasitic ant species; (iv) parasitic helminths; and (v) parasitic fungi. We dissected network topology to investigate what determines host specificity, symbiont species richness, and the capacity of different symbiont types to switch hosts. We found 722 macrosymbionts (multicellular symbionts) associated with European ants. Symbiont type explained host specificity and the average relatedness of the host species. Social parasites were associated with few hosts that were phylogenetically highly related, whereas the other symbiont types interacted with a larger number of hosts across a wider taxonomic distribution. The hosts of trophobionts were the least phylogenetically related across all symbiont types. Colony size, host range and habitat type predicted total symbiont richness: ant hosts with larger colony size, a larger distribution range or with a wider habitat range contained more symbiont species. However, we found that different sets of host factors affected diversity in the different types of symbionts. Ecological factors, such as colony size, host range and niche width predominantly determined myrmecophile species richness, whereas host phylogeny was the most important predictor of mutualistic trophobiont, social parasite and parasitic helminth species richness. Lastly, we found that hosts with a common biogeographic history support a more similar community of symbionts. Phylogenetically related hosts also shared more trophobionts, social parasites and helminths, but not myrmecophiles. Taken together, these results suggest that ecological and evolutionary processes structure host specificity and symbiont richness in large-scale ant-symbiont networks, but these drivers may shift in importance depending on the type of symbiosis. Our findings highlight the potential of well-characterized bipartite networks composed of different types of symbioses to identify candidate processes driving community composition.},
}

@article {pmid32690192,
year = {2020},
author = {Zhang, J and Peng, S and Shang, Y and Brunel, B and Li, S and Zhao, Y and Liu, Y and Chen, W and Wang, E and Singh, RP and James, EK},
title = {Genomic diversity of chickpea-nodulating rhizobia in Ningxia (north central China) and gene flow within symbiotic Mesorhizobium muleiense populations.},
journal = {Systematic and applied microbiology},
volume = {43},
number = {4},
pages = {126089},
doi = {10.1016/j.syapm.2020.126089},
pmid = {32690192},
issn = {1618-0984},
abstract = {Diversity and taxonomic affiliation of chickpea rhizobia were investigated from Ningxia in north central China and their genomic relationships were compared with those from northwestern adjacent regions (Gansu and Xinjiang). Rhizobia were isolated from root-nodules after trapping by chickpea grown in soils from a single site of Ningxia and typed by IGS PCR-RFLP. Representative strains were phylogenetically analyzed on the basis of the 16S rRNA, housekeeping (atpD, recA and glnII) and symbiosis (nodC and nifH) genes. Genetic differentiation and gene flow were estimated among the chickpea microsymbionts from Ningxia, Gansu and Xinjiang. Fifty chickpea rhizobial isolates were obtained and identified as Mesorhizobium muleiense. Their symbiosis genes nodC and nifH were highly similar (98.4 to 100%) to those of other chickpea microsymbionts, except for one representative strain (NG24) that showed low nifH similarities with all the defined Mesorhizobium species. The rhizobial population from Ningxia was genetically similar to that from Gansu, but different from that in Xinjiang as shown by high chromosomal gene flow/low differentiation with the Gansu population but the reverse with the Xinjiang population. This reveals a biogeographic pattern with two main populations in M. muleiense, the Xinjiang population being chromosomally differentiated from Ningxia-Gansu one. M. muleiense was found as the sole main chickpea-nodulating rhizobial symbiont of Ningxia and it was also found in Gansu sharing alkaline-saline soils with Ningxia. Introduction of chickpea in recently cultivated areas in China seems to select from alkaline-saline soils of M. muleiense that acquired symbiotic genes from symbiovar ciceri.},
}

@article {pmid32453775,
year = {2020},
author = {O'Connor, RM and Nepveux V, FJ and Abenoja, J and Bowden, G and Reis, P and Beaushaw, J and Bone Relat, RM and Driskell, I and Gimenez, F and Riggs, MW and Schaefer, DA and Schmidt, EW and Lin, Z and Distel, DL and Clardy, J and Ramadhar, TR and Allred, DR and Fritz, HM and Rathod, P and Chery, L and White, J},
title = {A symbiotic bacterium of shipworms produces a compound with broad spectrum anti-apicomplexan activity.},
journal = {PLoS pathogens},
volume = {16},
number = {5},
pages = {e1008600},
pmid = {32453775},
issn = {1553-7374},
support = {R21 AT009174/AT/NCCIH NIH HHS/United States ; U19 TW008163/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; *Antiprotozoal Agents/metabolism/pharmacology ; Apicomplexa/*growth & development ; Bivalvia/*microbiology ; Gammaproteobacteria/*metabolism ; Mice ; Protozoan Infections/drug therapy ; *Symbiosis ; },
abstract = {Apicomplexan parasites cause severe disease in both humans and their domesticated animals. Since these parasites readily develop drug resistance, development of new, effective drugs to treat infection caused by these parasites is an ongoing challenge for the medical and veterinary communities. We hypothesized that invertebrate-bacterial symbioses might be a rich source of anti-apicomplexan compounds because invertebrates are susceptible to infections with gregarines, parasites that are ancestral to all apicomplexans. We chose to explore the therapeutic potential of shipworm symbiotic bacteria as they are bona fide symbionts, are easily grown in axenic culture and have genomes rich in secondary metabolite loci [1,2]. Two strains of the shipworm symbiotic bacterium, Teredinibacter turnerae, were screened for activity against Toxoplasma gondii and one strain, T7901, exhibited activity against intracellular stages of the parasite. Bioassay-guided fractionation identified tartrolon E (trtE) as the source of the activity. TrtE has an EC50 of 3 nM against T. gondii, acts directly on the parasite itself and kills the parasites after two hours of treatment. TrtE exhibits nanomolar to picomolar level activity against Cryptosporidium, Plasmodium, Babesia, Theileria, and Sarcocystis; parasites representing all branches of the apicomplexan phylogenetic tree. The compound also proved effective against Cryptosporidium parvum infection in neonatal mice, indicating that trtE may be a potential lead compound for preclinical development. Identification of a promising new compound after such limited screening strongly encourages further mining of invertebrate symbionts for new anti-parasitic therapeutics.},
}

Animals
*Antiprotozoal Agents/metabolism/pharmacology
Apicomplexa/*growth & development
Bivalvia/*microbiology
Gammaproteobacteria/*metabolism
Mice
Protozoan Infections/drug therapy
*Symbiosis

@article {pmid31752998,
year = {2019},
author = {Sweet, M and Burian, A and Fifer, J and Bulling, M and Elliott, D and Raymundo, L},
title = {Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {139},
pmid = {31752998},
issn = {2049-2618},
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria/*pathogenicity ; *Coral Reefs ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Micronesia ; Symbiosis/*physiology ; },
abstract = {BACKGROUND: Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome.

RESULTS: Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named 'grey-patch disease', is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals' microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of 'infection clusters' in the microbiomes of apparently healthy corals.

CONCLUSIONS: Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase β-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the 'healthy' coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals' defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.},
}

Animals
*Anthozoa/microbiology/physiology
Bacteria/*pathogenicity
*Coral Reefs
Microbial Interactions/*physiology
Microbiota/*physiology
Micronesia
Symbiosis/*physiology

@article {pmid31300838,
year = {2020},
author = {White, JA and Styer, A and Rosenwald, LC and Curry, MM and Welch, KD and Athey, KJ and Chapman, EG},
title = {Endosymbiotic Bacteria Are Prevalent and Diverse in Agricultural Spiders.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {472-481},
pmid = {31300838},
issn = {1432-184X},
support = {0224651//U.S. Department of Agriculture/ ; 148-502-16-377//Kentucky Science and Engineering Foundation/ ; 148-502-10-261//Kentucky Science and Engineering Foundation/ ; },
mesh = {Animals ; Bacteria/classification/*isolation & purification ; Bacterial Physiological Phenomena ; Bacteriological Techniques/*methods ; Entomology/*methods ; Food Deprivation ; High-Throughput Nucleotide Sequencing ; Kentucky ; *Microbiota/genetics ; Polymerase Chain Reaction ; Spiders/*microbiology ; Symbiosis/*physiology ; },
abstract = {Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Additional strains included Rickettsiella, Spiroplasma, Rhabdochlamydia, and a novel Rickettsiales, all of which could range from pathogenic to mutualistic in their effects upon their hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.},
}

Animals
Bacteria/classification/*isolation & purification
Bacterial Physiological Phenomena
Bacteriological Techniques/*methods
Entomology/*methods
Food Deprivation
High-Throughput Nucleotide Sequencing
Kentucky
*Microbiota/genetics
Polymerase Chain Reaction
Spiders/*microbiology
Symbiosis/*physiology

@article {pmid32687170,
year = {2020},
author = {Yang, LL and Jiang, Z and Li, Y and Wang, ET and Zhi, XY},
title = {Plasmids related to the symbiotic nitrogen fixation are not only cooperated functionally, but also may have evolved over a time span in family Rhizobiaceae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaa152},
pmid = {32687170},
issn = {1759-6653},
abstract = {Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analysed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host's physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.},
}

@article {pmid32686981,
year = {2020},
author = {Safronova, V and Guro, P and Sazanova, A and Kuznetsova, I and Belimov, A and Yakubov, V and Chirak, E and Afonin, A and Gogolev, Y and Andronov, E and Tikhonovich, I},
title = {Rhizobial microsymbionts of the narrowly endemic Oxytropis species growing in Kamchatka are characterized by significant genetic diversity and possess a set of genes that are associated with T3SS and T6SS secretion systems and can affect the development of symbiosis.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-05-20-0114-R},
pmid = {32686981},
issn = {0894-0282},
abstract = {A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica and O. pumilio originated from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S rRNA gene sequence showed a significant diversity of isolates belonging to families Rhizobiaceae (genus Rhizobium), Phyllobacteriaceae (genera Mesorhizobium, Phyllobacterium) and Bradyrhizobiaceae (genera Bosea, Tardiphaga). Plant nodulation assay showed that only strains belonging to the genus Mesorhizobium could form nitrogen-fixing nodules on Oxytropis plants. The strains M. loti 582 and M. huakuii 583, in addition to symbiotic clusters, possessed genes of the T3SS and T6SS secretion systems, which can influence the host specificity of strains. These strains formed nodules of two types (elongated and rounded) on O. kamtschatica roots. We suggest this phenomenon may result from Nod-factor dependent and independent nodulation strategies. The obtained strains are of interest for further study of the T3SS and T6SS gene function and their role in the development of rhizobium-legume symbiosis. The prospects of using rhizobia having both gene systems related to symbiotic and non-symbiotic nodulation strategies to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing nodulation efficiency are discussed.},
}

@article {pmid32686279,
year = {2020},
author = {Kashkouli, M and Castelli, M and Floriano, AM and Bandi, C and Epis, S and Fathipour, Y and Mehrabadi, M and Sassera, D},
title = {Characterization of a novel Pantoea symbiont allows inference of a pattern of convergent genome reduction in bacteria associated with Pentatomidae.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15169},
pmid = {32686279},
issn = {1462-2920},
abstract = {Phytophagous stink bugs typically harbor nutritional symbiotic bacteria in their midgut, to integrate their unbalanced diet. In the Pentatomidae, most symbionts are affiliated to the genus Pantoea, and are polyphyletic. This suggests a scenario of an ancestral establishment of symbiosis, followed by multiple symbiont replacement events by akin environmental bacteria in different host lineages. In this study, a novel Pantoea species ("Candidatus Pantoea persica") was characterized from the gut of pentatomid Acrosternum arabicum, and shown to be highly abundant in a specific portion of the gut and necessary for the host development. The genome of the symbiont (2.9 Mb), while presenting putative host-supportive metabolic pathways, including those for amino acids and vitamin synthesis, showed high level of pseudogenization, indicating ongoing genome reduction. Comparative analyses with other free-living and symbiotic Pantoea highlighted a convergent pattern of genome reduction in symbionts of pentatomids, putatively following the typical phases modelized in obligate nutritional symbionts of insects. Additionally, this system has distinctive traits, as hosts are closely related, and symbionts originated multiple independent times from closely related free-living bacteria, displaying convergent and independent conspicuous genome reduction. Due to such peculiarities, this may become an ideal model to study genome evolutionary processes in insect symbionts. This article is protected by copyright. All rights reserved.},
}

@article {pmid32686173,
year = {2020},
author = {Appert, O and Garcia, AR and Frei, R and Roduit, C and Constancias, F and Neuzil-Bunesova, V and Ferstl, R and Zhang, J and Akdis, C and Lauener, R and Lacroix, C and Schwab, C},
title = {Initial butyrate producers during infant gut microbiota development are endospore formers.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15167},
pmid = {32686173},
issn = {1462-2920},
abstract = {The acquisition of the infant gut microbiota is key to establishing a host-microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation-derived short chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate-forming bacterial population is taxonomically and functionally diverse and includes endospore formers with high transmission potential. Succession, and contribution of butyrate-producing taxa have been little investigated. We determined abundance of major butyrate-forming groups and fermentation metabolites in feces, isolated, cultivated and characterized the heat-resistant cell population, which included endospores, and compared butyrate formation efficiency of representative taxa in batch cultures. Our study showed that pioneer butyrate formers were members of the Clostridium sensu stricto. We observed an increase in abundance of Faecalibacterium prausnitzii, butyrate-producing Lachnospiraceae and fecal butyrate levels with age that is likely explained by higher butyrate production capacity of contributing taxa compared to Clostridium sensu stricto. Our data suggest that a successional arrangement of butyrate-forming populations and an overall increase in abundance of butyrate forming populations occur during the first year of life, which is associated with an increase of intestinal butyrate formation capacity. This article is protected by copyright. All rights reserved.},
}

@article {pmid32015496,
year = {2020},
author = {Geier, B and Sogin, EM and Michellod, D and Janda, M and Kompauer, M and Spengler, B and Dubilier, N and Liebeke, M},
title = {Spatial metabolomics of in situ host-microbe interactions at the micrometre scale.},
journal = {Nature microbiology},
volume = {5},
number = {3},
pages = {498-510},
doi = {10.1038/s41564-019-0664-6},
pmid = {32015496},
issn = {2058-5276},
mesh = {Animals ; Bacteria/genetics/metabolism ; Bivalvia/*microbiology ; Host Microbial Interactions/*physiology ; In Situ Hybridization, Fluorescence ; Metabolome ; Metabolomics/*methods ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Symbiosis ; Tandem Mass Spectrometry ; },
abstract = {Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defence molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry to image host-microbe symbioses and their metabolic interactions. The metaFISH pipeline aligns and integrates metabolite and fluorescent images at the micrometre scale to provide a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts and variation in metabolic phenotypes within a single symbiont 16S rRNA phylotype, and enabled the discovery of specialized metabolites from the host-microbe interface. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ and is a powerful tool for microbiologists across fields.},
}

Animals
Bacteria/genetics/metabolism
Bivalvia/*microbiology
Host Microbial Interactions/*physiology
In Situ Hybridization, Fluorescence
Metabolome
Metabolomics/*methods
Microbiota/genetics/*physiology
RNA, Ribosomal, 16S/genetics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Symbiosis
Tandem Mass Spectrometry

@article {pmid32681431,
year = {2020},
author = {Chibeba, AM and Kyei-Boahen, S and de Fátima Guimarães, M and Nogueira, MA and Hungria, M},
title = {Towards sustainable yield improvement: field inoculation of soybean with Bradyrhizobium and co-inoculation with Azospirillum in Mozambique.},
journal = {Archives of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00203-020-01976-y},
pmid = {32681431},
issn = {1432-072X},
support = {N2Africa Project//Bill and Melinda Gates Foundation/ ; },
abstract = {The effects of sole inoculation of soybean (Glycine max L. Merrill) with Bradyrhizobium and co-inoculation with Bradyrhizobium and Azospirillum on nodulation, plant growth and yields were investigated in the 2013/2014 and 2014/2015 cropping seasons under field conditions in Mozambique. The treatments included (1) Control (non-inoculated control, with symbiosis depending on indigenous rhizobia), (2) Urea (non-inoculated, receiving 200 kg ha-1 of N), (3) Sole inoculation with B. diazoefficiens strain USDA 110, and (4) Co-inoculation with B. diazoefficiens strain USDA 110 and A. brasilense strains Ab-V5 and Ab-V6, evaluated in a randomized complete block design with five replications. Nodule number and dry weight, shoot dry weight, biological and grain yields, grain dry weight, and harvest index were evaluated. In general, both sole inoculation and co-inoculation enhanced nodulation in relation to control. Sole inoculation increased grain yield by 22% (356 kg ha-1), the same enhancement magnitude attained under mineral N treatment, suggesting that Bradyrhizobium inoculation provides ecological and economic sustainability to the soybean crop in Mozambique or other countries with similar agro-climatic conditions. Co-inoculation did not increase grain yields in relation to neither the control nor sole inoculation, indicating that further research with adapted and high yielding soybean varieties along with effective rhizobial strains is required in Mozambique to attune the beneficial Azospirillum-plant cultivar-rhizobia interactions that have been reported in other countries for several legumes, including soybean.},
}

@article {pmid32679802,
year = {2020},
author = {Kami, D and Gojo, S},
title = {From Cell Entry to Engraftment of Exogenous Mitochondria.},
journal = {International journal of molecular sciences},
volume = {21},
number = {14},
pages = {},
doi = {10.3390/ijms21144995},
pmid = {32679802},
issn = {1422-0067},
abstract = {Mitochondrial transfer has been recognized to play a role in a variety of processes, ranging from fertilization to cancer and neurodegenerative diseases as well as mammalian horizontal gene transfer. It is achieved through either exogeneous or intercellular mitochondrial transfer. From the viewpoint of evolution, exogeneous mitochondrial transfer is quite akin to the initial process of symbiosis between α-protobacterium and archaea, although the progeny have developed more sophisticated machinery to engulf environmental materials, including nutrients, bacteria, and viruses. A molecular-based knowledge of endocytosis, including macropinocytosis and endosomal escape involving bacteria and viruses, could provide mechanistic insights into exogeneous mitochondrial transfer. We focus on exogeneous mitochondrial transfer in this review to facilitate the clinical development of the use of isolated mitochondria to treat various pathological conditions. Several kinds of novel procedures to enhance exogeneous mitochondrial transfer have been developed and are summarized in this review.},
}

@article {pmid32678761,
year = {2020},
author = {Lu, RR and Hu, ZH and Zhang, QL and Li, YQ and Lin, M and Wang, XL and Wu, XN and Yang, JT and Zhang, LQ and Jing, YX and Peng, CL},
title = {The effect of Funneliformis mosseae on the plant growth, Cd translocation and accumulation in the new Cd-hyperaccumulator Sphagneticola calendulacea.},
journal = {Ecotoxicology and environmental safety},
volume = {203},
number = {},
pages = {110988},
doi = {10.1016/j.ecoenv.2020.110988},
pmid = {32678761},
issn = {1090-2414},
abstract = {The screening and identification of hyperaccumulators is the key to the phytoremediation of soils contaminated by heavy metal (HM). Arbuscular mycorrhizal fungus (AMF) can improve plant growth and tolerance to HM; therefore, AMF-assisted phytoextraction has been regarded as a potential technique for the remediation of HM-polluted soils. A greenhouse pot experiment was conducted to determine whether Sphagneticola calendulacea is a Cd-hyperaccumulator and to investigate the effect of the AMF-Funneliformis mosseae (FM) on plant growth and on the accumulation, subcellular distribution and chemical form of Cd in S. calendulacea grown in soils supplemented with different Cd levels. At 25, 50 and 100 mg Cd kg-1 level, S. calendulacea showed high Cd tolerance, the translocation factor and the bioconcentration factor exceeded 1, and accumulation of more than 100 mg Cd kg-1 was observed in the aboveground parts of the plant, meeting the requirements for a Cd-hyperaccumulator. Moreover, FM colonization significantly increased both biomasses and Cd concentration in S. calendulacea. After FM inoculation, the Cd concentrations and proportions increased in the cell walls, but exhibited no significant change in the organelles of the shoots. Meanwhile, FM symbiosis contributed to the conversion of Cd from highly toxic chemical forms (extracted by 80% ethanol and deionized water) to less toxic chemical forms (extracted by 1 M NaCl, 2% acetic acid, 0.6 M HCl) of Cd in the shoots. Overall, S. calendulacea is a typical Cd-hyperaccumulator, and FM symbiosis relieved the phytotoxicity of Cd and promoted plant growth and Cd accumulation, and thus greatly increasing the efficiency of phytoextraction for Cd-polluted soil. Our study provides a theoretical basis and application guidance for the remediation of Cd-contaminated soil by the symbiont of S. calendulacea with FM.},
}

@article {pmid32676756,
year = {2020},
author = {Aridhi, F and Sghaier, H and Gaitanaros, A and Khadri, A and Aschi-Smiti, S and Brouquisse, R},
title = {Nitric oxide production is involved in maintaining energy state in Alfalfa (Medicago sativa L.) nodulated roots under both salinity and flooding.},
journal = {Planta},
volume = {252},
number = {2},
pages = {22},
doi = {10.1007/s00425-020-03422-1},
pmid = {32676756},
issn = {1432-2048},
support = {Grant N° 17G0904//PHC Utique/ ; Grant N° 17G0904//PHC Utique/ ; },
abstract = {MAIN CONCLUSION: In Medicago sativa nodulated roots, NR-dependent NO production is involved in maintaining energy state, presumably through phytoglobin NO respiration, under both salinity and hypoxia stress. The response to low and average salinity stress and to a 5 day-long flooding period was analyzed in M. sativa nodulated roots. The two treatments result in a decrease in the biological nitrogen fixation capacity and the energy state (evaluated by the ATP/ADP ratio), and conversely in an increase nitric oxide (NO) production. Under salinity and hypoxia treatments, the use of either sodium tungstate, an inhibitor of nitrate reductase (NR), or carboxy-PTIO, a NO scavenger, results in a decrease in NO production and ATP/ADP ratio, meaning that NR-dependent NO production participates to the maintenance of the nodulated roots energy state.},
}

@article {pmid32676060,
year = {2020},
author = {Gupta, A and Nair, S},
title = {Dynamics of Insect-Microbiome Interaction Influence Host and Microbial Symbiont.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1357},
doi = {10.3389/fmicb.2020.01357},
pmid = {32676060},
issn = {1664-302X},
abstract = {Insects share an intimate relationship with their gut microflora and this symbiotic association has developed into an essential evolutionary outcome intended for their survival through extreme environmental conditions. While it has been clearly established that insects, with very few exceptions, associate with several microbes during their life cycle, information regarding several aspects of these associations is yet to be fully unraveled. Acquisition of bacteria by insects marks the onset of microbial symbiosis, which is followed by the adaptation of these bacterial species to the gut environment for prolonged sustenance and successful transmission across generations. Although several insect-microbiome associations have been reported and each with their distinctive features, diversifications and specializations, it is still unclear as to what led to these diversifications. Recent studies have indicated the involvement of various evolutionary processes operating within an insect body that govern the transition of a free-living microbe to an obligate or facultative symbiont and eventually leading to the establishment and diversification of these symbiotic relationships. Data from various studies, summarized in this review, indicate that the symbiotic partners, i.e., the bacteria and the insect undergo several genetic, biochemical and physiological changes that have profound influence on their life cycle and biology. An interesting outcome of the insect-microbe interaction is the compliance of the microbial partner to its eventual genome reduction. Endosymbionts possess a smaller genome as compared to their free-living forms, and thus raising the question what is leading to reductive evolution in the microbial partner. This review attempts to highlight the fate of microbes within an insect body and its implications for both the bacteria and its insect host. While discussion on each specific association would be too voluminous and outside the scope of this review, we present an overview of some recent studies that contribute to a better understanding of the evolutionary trajectory and dynamics of the insect-microbe association and speculate that, in the future, a better understanding of the nature of this interaction could pave the path to a sustainable and environmentally safe way for controlling economically important pests of crop plants.},
}

@article {pmid32675449,
year = {2020},
author = {Ansari, H and Yeravdekar, R},
title = {Respectful maternity care during childbirth in India: A systematic review and meta-analysis.},
journal = {Journal of postgraduate medicine},
volume = {66},
number = {3},
pages = {133-140},
doi = {10.4103/jpgm.JPGM_648_19},
pmid = {32675449},
issn = {0972-2823},
abstract = {Background: Respectful maternity care is a rightful expectation of women. However, disrespectful maternity care is prevalent in various settings. Therefore, a systematic review and meta-analysis were conducted to identify various forms of ill-treatment, determinants, and pooled prevalence of disrespectful maternity care in India.

Methods: A systematic review was performed in various databases. After quality assessment, seven studies were included. Pooled prevalence was estimated using the inverse variance method and the random-effects model using Review Manager Software.

Results: Individual study prevalence ranged from 20.9% to 100%. The overall pooled prevalence of disrespectful maternity care was 71.31% (95% CI 39.84-102.78). Pooled prevalence in community-based studies was 77.32% (95% CI 56.71-97.93), which was higher as compared to studies conducted in health facilities, this being 65.38% (95% CI 15.76-115.01). The highest reported form of ill-treatment was non-consent (49.84%), verbal abuse (25.75%) followed by threats (23.25%), physical abuse (16.96%), and discrimination (14.79%). Besides, other factors identified included lack of dignity, delivery by unqualified personnel, lack of privacy, demand for informal payments, and lack of basic infrastructure, hygiene, and sanitation. The determinants identified for disrespect and abuse were sociocultural factors including age, socioeconomic status, caste, parity, women autonomy, empowerment, comorbidities, and environmental factors including infrastructural issues, overcrowding, ill-equipped health facilities, supply constraints, and healthcare access.

Conclusion: The high prevalence of disrespectful maternity care indicates an urgent need to improve maternity care in India by making it more respectful, dignified, and women-centered. Interventions, policies, and programs should be implemented that will protect the fundamental rights of women.},
}

@article {pmid32674446,
year = {2020},
author = {Solis-Miranda, J and Fonseca-García, C and Nava, N and Pacheco, R and Quinto, C},
title = {Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis.},
journal = {Genes},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/genes11070793},
pmid = {32674446},
issn = {2073-4425},
support = {DGAPA grant (IN201118)//Universidad Nacional Autónoma de México/ ; Fronteras de la ciencia (FC) grant: FC-2016/1503//Consejo Nacional de Ciencia y Tecnología in Mexico (CONACyT)/ ; fellowships 463767, 823333 and 268158//Consejo Nacional de Ciencia y Tecnología in Mexico (CONACyT)/ ; },
abstract = {The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume-rhizobia symbiosis.},
}

@article {pmid32674305,
year = {2020},
author = {Chialva, M and Lanfranco, L and Guazzotti, G and Santoro, V and Novero, M and Bonfante, P},
title = {Gigaspora margarita and Its Endobacterium Modulate Symbiotic Marker Genes in Tomato Roots under Combined Water and Nutrient Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {7},
pages = {},
doi = {10.3390/plants9070886},
pmid = {32674305},
issn = {2223-7747},
support = {727929//European Commission/ ; },
abstract = {As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF) may be effective in enhancing plant resilience to drought, one of the major limiting factors threatening crop productivity. AMF host their own microbiota and previous data demonstrated that endobacteria thriving in Gigaspora margarita modulate fungal antioxidant responses. Here, we used the G. margarita-Candidatus Glomeribacter gigasporarum system to test whether the tripartite interaction between tomato, G. margarita and its endobacteria may improve plant resilience to combined water/nutrient stress. Tomato plants were inoculated with spores containing endobacteria (B+) or not (B-), and exposed to combined water/nutrient stress. Plants traits, AM colonization and expression of AM marker genes were measured. Results showed that mycorrhizal frequency was low and no growth effect was observed. Under control conditions, B+ inoculated plants were more responsive to the symbiosis, as they showed an up-regulation of three AM marker genes involved in phosphate and lipids metabolism compared with B- inoculated or not-inoculated plants. When combined stress was imposed, the difference between fungal strains was still evident for one marker gene. These results indicate that the fungal endobacteria finely modulate plant metabolism, even in the absence of growth response.},
}

@article {pmid32674026,
year = {2020},
author = {Fokin, SI},
title = {Prof. H.-D. Görtz and his contribution to our knowledge of protozoan symbiosis.},
journal = {European journal of protistology},
volume = {75},
number = {},
pages = {125725},
doi = {10.1016/j.ejop.2020.125725},
pmid = {32674026},
issn = {1618-0429},
abstract = {Since the beginning of the 1980s, the Paramecium-Holospora system has become an important model and a subject of international scientific cooperation in symbiosis studies, established by Prof. H.-D. Görtz. In the article, a brief sketch of the scientist's life, his areas of interest, expertise and his contribution to our knowledge of protozoan symbiosis are discussed.},
}

@article {pmid32672816,
year = {2020},
author = {Hou, Q and Kolodkin-Gal, I},
title = {Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaa142},
pmid = {32672816},
issn = {1574-6941},
abstract = {A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.},
}

@article {pmid32672376,
year = {2020},
author = {Soldá, A and Rodríguez-García, AM},
title = {The EYCN and the Power of Networking.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1002/chem.202003020},
pmid = {32672376},
issn = {1521-3765},
abstract = {Networking is a symbiosis-it is about establishing, building and cultivating relationships that you will maintain over a long time and which may lead to mutually beneficial exchanges in your future. Your professional contacts might also become your close friends, since you frequently share the same experiences or merely have similar scientific and general interests or nerdy humour. Chemical societies are a fantastic way to expand your network and engaging or following the activities of the European Young Chemists Network (EYCN) might be the perfect starting point for you.},
}

@article {pmid32669419,
year = {2020},
author = {Rutten, L and Miyata, K and Roswanjaya, YP and Huisman, R and Bu, F and Hartog, M and Linders, S and Velzen, RV and Zeijl, AV and Bisseling, T and Kohlen, W and Geurts, R},
title = {Duplication of symbiotic Lysine Motif-receptors predates the evolution of nitrogen-fixing nodule symbiosis.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1104/pp.19.01420},
pmid = {32669419},
issn = {1532-2548},
abstract = {Rhizobium nitrogen-fixing nodule symbiosis occurs in two taxonomic lineages: legumes (Fabaceae) and Parasponia (Cannabaceae). Both symbioses are initiated upon the perception of rhizobium-secreted lipo-chitooligosaccharides (LCOs), called Nod factors. Studies in the model legumes Lotus japonicus (lotus) and Medicago truncatula (medicago) showed that rhizobium LCOs are perceived by a heteromeric receptor complex of distinct Lysine Motif (LysM)-type transmembrane receptors named NOD FACTOR RECEPTOR1 (LjNFR1)-LjNFR5 (lotus) and LYSM DOMAIN CONTAINING RECEPTOR KINASE3 (MtLYK3)-NOD FACTOR PERCEPTION (MtNFP) (medicago). Recent phylogenomic comparative analyses indicated that the nodulation trait of legumes, Parasponia, as well as of so-called actinorhizal plants that establish a symbiosis with diazotrophic Frankia bacteria, share an evolutionary origin about 110 million years ago. However, the evolutionary trajectory of LysM-type LCO receptors remains elusive. By conducting phylogenetic analysis, trans-complementation studies, and CRISPR-Cas9 mutagenesis in Parasponia andersonii (parasponia), we obtained insight to the origin of LCO receptors essential for nodulation. We identified four LysM-type receptors controlling nodulation in parasponia: PanLYK1, PanLYK3, PanNFP1 and PanNFP2. These genes evolved upon ancient duplication events predating and coinciding with the origin of nodulation. Phylogenetic and functional analysis associated the occurrence of a functional NFP2-orthologous receptor to LCO-driven nodulation. Legumes and Parasponia use orthologous LysM-type receptors to perceive rhizobium LCOs, suggesting a shared evolutionary origin of LCO-driven nodulation. Furthermore, we found that both PanLYK1 and PanLYK3 are essential for intracellular arbuscule formation of mutualistic endomycorrhizal fungi. PanLYK3 also acts as a chitin oligomer receptor essential for innate immune signalling, demonstrating functional analogy to CHITIN ELECITOR RECEPTOR KINASE (CERK)-type receptors.},
}

@article {pmid32669390,
year = {2020},
author = {Mauvais-Jarvis, F},
title = {Aging, Male Sex, Obesity, and Metabolic Inflammation Create the Perfect Storm for COVID-19.},
journal = {Diabetes},
volume = {},
number = {},
pages = {},
doi = {10.2337/dbi19-0023},
pmid = {32669390},
issn = {1939-327X},
abstract = {Coronavirus disease 2019 (COVID-19) is a novel threat that seems to result from the collusion between a new pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and an existing pandemic of metabolic disease driven by obesity. This Perspective explores the evolving epidemiological, clinical, biological, and molecular evidence to propose an unfolding paradigm in which old age, chronic metabolic disease (such as obesity, type 2 diabetes, and metabolic syndrome), and male biological sex produce a deadly symbiosis of dysregulated immunometabolism and chronic systemic inflammation that intensifies virally induced hyperinflammation associated with SARS-CoV-2 infection. It is intended to inspire new research directions and stimulate funding in this field.},
}

@article {pmid32669363,
year = {2020},
author = {Bell, A and Severi, E and Lee, MO and Monaco, S and Latousakis, D and Angulo, J and Thomas, GH and Naismith, J and Juge, N},
title = {Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA120.014454},
pmid = {32669363},
issn = {1083-351X},
abstract = {The human gut symbiont Ruminococcus gnavus scavenges host-derived N-acetylneuraminic acid (Neu5Ac) from mucins, by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into R. gnavus ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D nuclear magnetic resonance (NMR), we elucidated the multistep enzymatic mechanism of the oxidoreductase (RgNanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-DANA intermediate and NAD+ regeneration. The crystal structure of RgNanOx in complex with the NAD+ cofactor showed a protein dimer with a Rossman fold. Guided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of RgNanOx homologues across Gram negative and Gram positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionisation spray mass spectrometry (ESI-MS) that the Escherichia coli homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that E. coli could catabolise 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry (DSF) analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using E. coli mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in E. coli was dependent on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in E. coli.},
}

@article {pmid32646993,
year = {2020},
author = {Harrison, O},
title = {Poised for tissue repair.},
journal = {Science (New York, N.Y.)},
volume = {369},
number = {6500},
pages = {152-153},
doi = {10.1126/science.abc5618},
pmid = {32646993},
issn = {1095-9203},
mesh = {CD8-Positive T-Lymphocytes/immunology ; Humans ; Immune System ; Microbiota/*immunology ; Skin/*immunology/*microbiology ; Staphylococcus epidermidis/*immunology ; Symbiosis ; Wound Healing/*immunology ; },
}

CD8-Positive T-Lymphocytes/immunology
Humans
Immune System
Microbiota/*immunology
Skin/*immunology/*microbiology
Staphylococcus epidermidis/*immunology
Symbiosis
Wound Healing/*immunology

@article {pmid32324730,
year = {2020},
author = {Song, C and Saavedra, S},
title = {Telling ecological networks apart by their structure: An environment-dependent approach.},
journal = {PLoS computational biology},
volume = {16},
number = {4},
pages = {e1007787},
pmid = {32324730},
issn = {1553-7358},
mesh = {*Biota ; Computational Biology/*methods ; *Environment ; *Models, Biological ; Symbiosis/physiology ; Temperature ; },
abstract = {The network architecture of an ecological community describes the structure of species interactions established in a given place and time. It has been suggested that this architecture presents unique features for each type of ecological interaction: e.g., nested and modular architectures would correspond to mutualistic and antagonistic interactions, respectively. Recently, Michalska-Smith and Allesina (2019) proposed a computational challenge to test whether it is indeed possible to differentiate ecological interactions based on network architecture. Contrary to the expectation, they found that this differentiation is practically impossible, moving the question to why it is not possible to differentiate ecological interactions based on their network architecture alone. Here, we show that this differentiation becomes possible by adding the local environmental information where the networks were sampled. We show that this can be explained by the fact that environmental conditions are a confounder of ecological interactions and network architecture. That is, the lack of association between network architecture and type of ecological interactions changes by conditioning on the local environmental conditions. Additionally, we find that environmental conditions are linked to the stability of ecological networks, but the direction of this effect depends on the type of interaction network. This suggests that the association between ecological interactions and network architectures exists, but cannot be fully understood without attention to the environmental conditions acting upon them.},
}

*Biota
Computational Biology/*methods
*Environment
*Models, Biological
Symbiosis/physiology
Temperature

@article {pmid32287291,
year = {2020},
author = {Li, Z and Wu, N and Meng, S and Wu, F and Liu, T},
title = {Arbuscular mycorrhizal fungi (AMF) enhance the tolerance of Euonymus maackii Rupr. at a moderate level of salinity.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231497},
pmid = {32287291},
issn = {1932-6203},
mesh = {Antioxidants ; Ecosystem ; Euonymus/growth & development/*metabolism ; Mycorrhizae/growth & development/*metabolism ; Photosynthesis ; Plant Development ; Plant Leaves/growth & development ; Plant Roots/growth & development ; Plant Shoots/growth & development ; Plants ; Salinity ; Salt Stress/*physiology ; Salt Tolerance/physiology ; Seedlings ; Symbiosis ; },
abstract = {Salt stress is one of the major environmental constraints for plant growth. Although the ways in which mycorrhizal plants deal with salt stress have been well documented, it still is blank for Euonymus maackii, an important local ecological restoration tree, to arbuscular mycorrhizal fungi (AMF) inoculation and salt stress. In this study, we tested the effect of different salt levels (0, 50, 100,150 and 200 mM) and AMF inoculation on E. maackii growth rate, photosynthesis, antioxidant enzymes, nutrient absorption and salt ion distribution. The results indicated negative effect of salt on height, photosynthesis capacity, nutrition accumulation, while salt stimulated the antioxidant defense system and salt ions accumulation. The toxic symptom by excessive accumulation of salt ions worsen with salt level increased gradually (except for the 50 mM NaCl treatment). AMF inoculation alleviated the toxic symptom under moderate salt levels (100 and 150 mM) by increasing photosynthesis capacity, accelerating nutrient absorption and activating antioxidant enzyme activities under salt stress. Meanwhile, effect of AMF was not detected on seedlings under slight (0 and 50 mM) and high (200 mM) NaCl concentration. Our study indicated AMF had positive impact on E. maackii subjected to salt, which suggested potential application of AMF- E. maackii on restoration of salt ecosystems.},
}

Antioxidants
Ecosystem
Euonymus/growth & development/*metabolism
Mycorrhizae/growth & development/*metabolism
Photosynthesis
Plant Development
Plant Leaves/growth & development
Plant Roots/growth & development
Plant Shoots/growth & development
Plants
Salinity
Salt Stress/*physiology
Salt Tolerance/physiology
Seedlings
Symbiosis

@article {pmid32198474,
year = {2020},
author = {Lu, S and Guan, X and Liu, C},
title = {Electricity-powered artificial root nodule.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1505},
pmid = {32198474},
issn = {2041-1723},
support = {S10 OD025017/OD/NIH HHS/United States ; },
mesh = {Ammonia ; Biomass ; *Electricity ; Electrochemistry/*methods ; Fertilizers ; Models, Theoretical ; Nitrogen/metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Root Nodules, Plant/*physiology ; Symbiosis ; },
abstract = {Root nodules are agricultural-important symbiotic plant-microbe composites in which microorganisms receive energy from plants and reduce dinitrogen (N2) into fertilizers. Mimicking root nodules using artificial devices can enable renewable energy-driven fertilizer production. This task is challenging due to the necessity of a microscopic dioxygen (O2) concentration gradient, which reconciles anaerobic N2 fixation with O2-rich atmosphere. Here we report our designed electricity-powered biological|inorganic hybrid system that possesses the function of root nodules. We construct silicon-based microwire array electrodes and replicate the O2 gradient of root nodules in the array. The wire array compatibly accommodates N2-fixing symbiotic bacteria, which receive energy and reducing equivalents from inorganic catalysts on microwires, and fix N2 in the air into biomass and free ammonia. A N2 reduction rate up to 6.5 mg N2 per gram dry biomass per hour is observed in the device, about two orders of magnitude higher than the natural counterparts.},
}

Ammonia
Biomass
*Electricity
Electrochemistry/*methods
Fertilizers
Models, Theoretical
Nitrogen/metabolism
Nitrogen Cycle
Nitrogen Fixation
Root Nodules, Plant/*physiology
Symbiosis

@article {pmid32015497,
year = {2020},
author = {Ansari, I and Raddatz, G and Gutekunst, J and Ridnik, M and Cohen, D and Abu-Remaileh, M and Tuganbaev, T and Shapiro, H and Pikarsky, E and Elinav, E and Lyko, F and Bergman, Y},
title = {The microbiota programs DNA methylation to control intestinal homeostasis and inflammation.},
journal = {Nature microbiology},
volume = {5},
number = {4},
pages = {610-619},
doi = {10.1038/s41564-019-0659-3},
pmid = {32015497},
issn = {2058-5276},
mesh = {Animals ; Colitis/chemically induced/*genetics/microbiology/pathology ; Colon/metabolism/microbiology ; DNA/*genetics/metabolism ; DNA Methylation ; Dextran Sulfate/administration & dosage ; *Epigenesis, Genetic ; Gastrointestinal Microbiome/*physiology ; *Genome ; Germ-Free Life ; Homeostasis/genetics ; Inflammation ; Male ; Mice ; Mice, Inbred C57BL ; Symbiosis/*genetics ; Whole Genome Sequencing ; },
abstract = {Although much research has been done on the diversity of the gut microbiome, little is known about how it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested to operate at the interface between the microbiota and the intestinal epithelium. We performed whole-genome bisulfite sequencing on conventionally raised and germ-free mice, and discovered that exposure to commensal microbiota induced localized DNA methylation changes at regulatory elements, which are TET2/3-dependent. This culminated in the activation of a set of 'early sentinel' response genes to maintain intestinal homeostasis. Furthermore, we demonstrated that exposure to the microbiota in dextran sodium sulfate-induced acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements, leading to alterations in gene expression programs enriched in colitis- and colon-cancer-associated functions. Finally, by employing genetic interventions, we show that microbiota-induced epigenetic programming is necessary for proper intestinal homeostasis in vivo.},
}

Animals
Colitis/chemically induced/*genetics/microbiology/pathology
Colon/metabolism/microbiology
DNA/*genetics/metabolism
DNA Methylation
Dextran Sulfate/administration & dosage
*Epigenesis, Genetic
Gastrointestinal Microbiome/*physiology
*Genome
Germ-Free Life
Homeostasis/genetics
Inflammation
Male
Mice
Mice, Inbred C57BL
Symbiosis/*genetics
Whole Genome Sequencing

@article {pmid31959970,
year = {2020},
author = {Thanh Duy, P and Thi Nguyen, TN and Vu Thuy, D and Chung The, H and Alcock, F and Boinett, C and Dan Thanh, HN and Thanh Tuyen, H and Thwaites, GE and Rabaa, MA and Baker, S},
title = {Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei.},
journal = {Nature microbiology},
volume = {5},
number = {2},
pages = {256-264},
doi = {10.1038/s41564-019-0645-9},
pmid = {31959970},
issn = {2058-5276},
support = {100087/WT_/Wellcome Trust/United Kingdom ; 100087/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Child ; Ciprofloxacin/pharmacology ; Digestive System/microbiology ; Disease Reservoirs/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Dysentery, Bacillary/drug therapy/epidemiology/microbiology ; Epidemics ; Escherichia coli/*genetics/isolation & purification ; Fluoroquinolones/*pharmacology ; Genes, Bacterial ; Humans ; Phylogeny ; R Factors/*genetics ; Shigella sonnei/classification/*drug effects/*genetics ; Symbiosis/genetics ; Vietnam/epidemiology ; },
abstract = {Despite the sporadic detection of fluoroquinolone-resistant Shigella in Asia in the early 2000s and the subsequent global spread of ciprofloxacin-resistant (cipR) Shigella sonnei from 2010, fluoroquinolones remain the recommended therapy for shigellosis1-7. The potential for cipR S. sonnei to develop resistance to alternative second-line drugs may further limit future treatment options8. Here, we aim to understand the evolution of novel antimicrobial resistant (AMR) S. sonnei variants after introduction into Vietnam. We found that cipR S. sonnei displaced the resident ciprofloxacin-susceptible (cipS) lineage while rapidly acquiring additional resistance to multiple alternative antimicrobial classes. We identified several independent acquisitions of extensively drug-resistant/multidrug-resistant-inducing plasmids, probably facilitated by horizontal transfer from commensals in the human gut. By characterizing commensal Escherichia coli from Shigella-infected and healthy children, we identified an extensive array of AMR genes and plasmids, including an identical multidrug-resistant plasmid isolated from both S. sonnei and E. coli in the gut of a single child. We additionally found that antimicrobial usage may impact plasmid transfer between commensal E. coli and S. sonnei. These results suggest that, in a setting with high antimicrobial use and a high prevalence of AMR commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines.},
}

Child
Ciprofloxacin/pharmacology
Digestive System/microbiology
Disease Reservoirs/microbiology
Drug Resistance, Multiple, Bacterial/*genetics
Dysentery, Bacillary/drug therapy/epidemiology/microbiology
Epidemics
Escherichia coli/*genetics/isolation & purification
Fluoroquinolones/*pharmacology
Genes, Bacterial
Humans
Phylogeny
R Factors/*genetics
Shigella sonnei/classification/*drug effects/*genetics
Symbiosis/genetics
Vietnam/epidemiology

@article {pmid31959968,
year = {2020},
author = {Oliveira, RA and Ng, KM and Correia, MB and Cabral, V and Shi, H and Sonnenburg, JL and Huang, KC and Xavier, KB},
title = {Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition.},
journal = {Nature microbiology},
volume = {5},
number = {4},
pages = {630-641},
doi = {10.1038/s41564-019-0658-4},
pmid = {31959968},
issn = {2058-5276},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteroidetes/classification/isolation & purification ; Ciprofloxacin/pharmacology ; Colony Count, Microbial ; Dysbiosis/chemically induced/*microbiology ; Escherichia coli/drug effects/growth & development/pathogenicity ; Firmicutes/classification/isolation & purification ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Klebsiella/drug effects/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; *Microbial Interactions ; Salmonella typhimurium/drug effects/growth & development/pathogenicity ; Streptomycin/pharmacology ; Symbiosis/*physiology ; Verrucomicrobia/classification/isolation & purification ; },
abstract = {Intestinal microbiotas contain beneficial microorganisms that protect against pathogen colonization; treatment with antibiotics disrupts the microbiota and compromises colonization resistance. Here, we determine the impact of exchanging microorganisms between hosts on resilience to the colonization of invaders after antibiotic-induced dysbiosis. We assess the functional consequences of dysbiosis using a mouse model of colonization resistance against Escherichia coli. Antibiotics caused stochastic loss of members of the microbiota, but the microbiotas of co-housed mice remained more similar to each other compared with the microbiotas among singly housed animals. Strikingly, co-housed mice maintained colonization resistance after treatment with antibiotics, whereas most singly housed mice were susceptible to E. coli. The ability to retain or share the commensal Klebsiella michiganensis, a member of the Enterobacteriaceae family, was sufficient for colonization resistance after treatment with antibiotics. K. michiganensis generally outcompeted E. coli in vitro, but in vivo administration of galactitol-a nutrient that supports the growth of only E. coli-to bi-colonized gnotobiotic mice abolished the colonization-resistance capacity of K. michiganensis against E. coli, supporting the idea that nutrient competition is the primary interaction mechanism. K. michiganensis also hampered colonization of the pathogen Salmonella, prolonging host survival. Our results address functional consequences of the stochastic effects of microbiota perturbations, whereby microbial transmission through host interactions can facilitate reacquisition of beneficial commensals, minimizing the negative impact of antibiotics.},
}

Animals
Anti-Bacterial Agents/pharmacology
Bacteroidetes/classification/isolation & purification
Ciprofloxacin/pharmacology
Colony Count, Microbial
Dysbiosis/chemically induced/*microbiology
Escherichia coli/drug effects/growth & development/pathogenicity
Firmicutes/classification/isolation & purification
Gastrointestinal Microbiome/*physiology
Germ-Free Life
Klebsiella/drug effects/*physiology
Male
Mice
Mice, Inbred C57BL
*Microbial Interactions
Salmonella typhimurium/drug effects/growth & development/pathogenicity
Streptomycin/pharmacology
Symbiosis/*physiology
Verrucomicrobia/classification/isolation & purification

@article {pmid31844298,
year = {2020},
author = {Ryu, MH and Zhang, J and Toth, T and Khokhani, D and Geddes, BA and Mus, F and Garcia-Costas, A and Peters, JW and Poole, PS and Ané, JM and Voigt, CA},
title = {Control of nitrogen fixation in bacteria that associate with cereals.},
journal = {Nature microbiology},
volume = {5},
number = {2},
pages = {314-330},
doi = {10.1038/s41564-019-0631-2},
pmid = {31844298},
issn = {2058-5276},
mesh = {Azorhizobium caulinodans/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Edible Grain/*metabolism/*microbiology ; Escherichia coli/genetics/metabolism ; Genes, Bacterial ; Metabolic Engineering ; Multigene Family ; *Nitrogen Fixation/genetics ; Nitrogenase/genetics/metabolism ; Plant Root Nodulation/genetics ; Pseudomonas/genetics/metabolism ; Rhizobium/genetics/metabolism ; Symbiosis/genetics ; },
abstract = {Legumes obtain nitrogen from air through rhizobia residing in root nodules. Some species of rhizobia can colonize cereals but do not fix nitrogen on them. Disabling native regulation can turn on nitrogenase expression, even in the presence of nitrogenous fertilizer and low oxygen, but continuous nitrogenase production confers an energy burden. Here, we engineer inducible nitrogenase activity in two cereal endophytes (Azorhizobium caulinodans ORS571 and Rhizobium sp. IRBG74) and the well-characterized plant epiphyte Pseudomonas protegens Pf-5, a maize seed inoculant. For each organism, different strategies were taken to eliminate ammonium repression and place nitrogenase expression under the control of agriculturally relevant signals, including root exudates, biocontrol agents and phytohormones. We demonstrate that R. sp. IRBG74 can be engineered to result in nitrogenase activity under free-living conditions by transferring a nif cluster from either Rhodobacter sphaeroides or Klebsiella oxytoca. For P. protegens Pf-5, the transfer of an inducible cluster from Pseudomonas stutzeri and Azotobacter vinelandii yields ammonium tolerance and higher oxygen tolerance of nitrogenase activity than that from K. oxytoca. Collectively, the data from the transfer of 12 nif gene clusters between 15 diverse species (including Escherichia coli and 12 rhizobia) help identify the barriers that must be overcome to engineer a bacterium to deliver a high nitrogen flux to a cereal crop.},
}

Azorhizobium caulinodans/genetics/metabolism
Bacterial Proteins/genetics/metabolism
Edible Grain/*metabolism/*microbiology
Escherichia coli/genetics/metabolism
Genes, Bacterial
Metabolic Engineering
Multigene Family
*Nitrogen Fixation/genetics
Nitrogenase/genetics/metabolism
Plant Root Nodulation/genetics
Pseudomonas/genetics/metabolism
Rhizobium/genetics/metabolism
Symbiosis/genetics

@article {pmid31219733,
year = {2019},
author = {Scoffield, J and Michalek, S and Harber, G and Eipers, P and Morrow, C and Wu, H},
title = {Dietary Nitrite Drives Disease Outcomes in Oral Polymicrobial Infections.},
journal = {Journal of dental research},
volume = {98},
number = {9},
pages = {1020-1026},
pmid = {31219733},
issn = {1544-0591},
support = {R00 DE025913/DE/NIDCR NIH HHS/United States ; R01 DE028329/DE/NIDCR NIH HHS/United States ; K99 DE025913/DE/NIDCR NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; R01 DE022350/DE/NIDCR NIH HHS/United States ; R01 DE017954/DE/NIDCR NIH HHS/United States ; },
mesh = {Animals ; Biofilms/*growth & development ; Coinfection ; Dental Caries/*prevention & control ; *Diet ; Microbiota ; Nitrites/*administration & dosage ; Random Allocation ; Rats ; Rats, Inbred F344 ; Streptococcus/physiology ; Streptococcus mutans/growth & development/pathogenicity ; Symbiosis ; },
abstract = {Streptococcus mutans resides in the oral polymicrobial biofilm and is a major contributor to the development of dental caries. Interestingly, high salivary nitrite concentrations have been associated with a decreased prevalence of dental caries. Moreover, the combination of hydrogen peroxide-producing oral commensal streptococci and nitrite has been shown to mediate the generation of reactive nitrogen species, which have antimicrobial activity. The goal of this study was to examine whether nitrite affects S. mutans virulence during polymicrobial infections with the commensal Streptococcus parasanguinis. Here, we report that the combination of S. parasanguinis and nitrite inhibited S. mutans growth and biofilm formation in vitro. Glucan production, which is critical for S. mutans biofilm formation, was also inhibited in 2-species biofilms with S. parasanguinis containing nitrite as compared with biofilms that contained no nitrite. In the in vivo caries model, enamel and dentin carious lesions were significantly reduced in rats that were colonized with S. parasanguinis prior to infection with S. mutans and received nitrite in the drinking water, as compared with animals that had a single S. mutans infection or were co-colonized with both bacteria and received no nitrite. Last, we report that S. mutans LiaS, a sensor kinase of the LiaFSR 3-component system, mediates resistance to nitrosative stress. In summary, our data demonstrate that commensal streptococci and nitrite provide protection against S. mutans pathogenesis. Modulating nitrite concentrations in the oral cavity could be a useful strategy to combat the prevalence of dental caries.},
}

Animals
Biofilms/*growth & development
Coinfection
Dental Caries/*prevention & control
*Diet
Microbiota
Nitrites/*administration & dosage
Random Allocation
Rats
Rats, Inbred F344
Streptococcus/physiology
Streptococcus mutans/growth & development/pathogenicity
Symbiosis

@article {pmid32668507,
year = {2020},
author = {Ghirardo, A and Fochi, V and Lange, B and Witting, M and Schnitzler, JP and Perotto, S and Balestrini, R},
title = {Metabolomic adjustments in the orchid mycorrhizal fungus Tulasnella calospora during symbiosis with Serapias vomeracea.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.16812},
pmid = {32668507},
issn = {1469-8137},
abstract = {All orchids rely on mycorrhizal fungi for organic carbon, at least during early development. Orchid seed germination leads in fact to the formation of a protocorm, a heterotrophic postembryonic structure colonized by intracellular fungal coils, thought to be the site for nutrients transfer. The molecular mechanisms underlying mycorrhizal interactions and metabolic changes induced by this symbiosis in both partners remain mostly unknown. We studied plant-fungus interactions in the mycorrhizal association between the Mediterranean orchid Serapias vomeracea and the basidiomycete Tulasnella calospora using non-targeted metabolomics. Plant and fungal metabolomes obtained from symbiotic structures were compared with those obtained under asymbiotic conditions. Symbiosis induced strong metabolomic alterations in both partners. In particular, structural and signaling lipid compounds remarkably increased in the external fungal mycelium growing near the symbiotic protocorms, whereas chito-oligosaccharides were identified uniquely in symbiotic protocorms. This work represents the first description of metabolic changes occurring in orchid mycorrhiza. These results - combined with previous transcriptomic data - provide novel insights on the mechanisms underlying the orchid mycorrhizal association and open intriguing questions on the role of fungal lipids in this symbiosis.},
}