Interactions between bacterial and phage communities in natural environments

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(1), P. 49 - 62

Published: Aug. 9, 2021

Language: Английский

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iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

PLoS Biology, Journal Year: 2023, Volume and Issue: 21(4), P. e3002083 - e3002083

Published: April 21, 2023

The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available predict host(s) uncultivated based on their genome sequences, but thus far individual limited either precision or recall, i.e., for a number they yield erroneous predictions no prediction at all. Here, we describe iPHoP, two-step framework that integrates multiple methods reliably taxonomy genus rank broad range archaea, while retaining low false discovery rate. Based large dataset virus genomes from IMG/VR database, illustrate how iPHoP can provide extensive guide further characterization viruses.

Language: Английский

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Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

Cell, Journal Year: 2022, Volume and Issue: 185(9), P. 1471 - 1486.e19

Published: April 1, 2022

Argonaute proteins use single-stranded RNA or DNA guides to target complementary nucleic acids. This allows eukaryotic mediate interference and long prokaryotic interfere with invading The function mechanisms of the phylogenetically distinct short remain poorly understood. We demonstrate that associated TIR-APAZ (SPARTA) form heterodimeric complexes. Upon guide RNA-mediated binding, four SPARTA heterodimers oligomers in which TIR domain-mediated NAD(P)ase activity is unleashed. When expressed Escherichia coli, activated presence highly transcribed multicopy plasmid DNA, causes cell death through NAD(P)+ depletion. results removal plasmid-invaded cells from bacterial cultures. Furthermore, we show can be repurposed for programmable detection sequences. In conclusion, our work identifies as a immune system reduces viability upon RNA-guided DNA.

Language: Английский

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Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e15023 - e15023

Published: May 2, 2023

Within microeukaryotes, genetic variation and functional sometimes accumulate more quickly than morphological differences. To understand the evolutionary history ecology of such lineages, it is key to examine diversity at multiple levels organization. In dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians ( e.g ., corals, octocorals, sea anemones, jellyfish), other marine invertebrates e.g. , sponges, molluscs, flatworms), protists foraminifera), molecular data have been used extensively over past three decades describe phenotypes make ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack consensus among researchers respect interpreting has slowed progress field acted as barrier reconciling observations. Here, we identify challenges regarding assessment interpretation across levels: species, populations, communities. We summarize areas agreement highlight techniques approaches that are broadly accepted. where debate remains, unresolved issues discuss technologies help fill knowledge gaps related phenotypic diversity. also ways stimulate progress, particular by fostering inclusive collaborative research community. hope this perspective will inspire accelerate coral reef science serving resource those designing experiments, publishing research, applying for funding their symbiotic partnerships.

Language: Английский

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Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 21, 2025

The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized a hotspot pathogenic and antibiotic-resistant bacteria. However, interactions between bacteria phages facilitated by well their impact on risks to public health, remain unclear. Here, we analyzed metagenomic data from 180 plastisphere environmental samples, stemming four different habitats two types (biodegradable nonbiodegradable plastics) obtained 611 nonredundant metagenome-assembled genomes (MAGs) 4061 phage contigs. community exhibited decreased diversity virulent proportion compared those found in environments. Indexes phage-host interaction networks indicated significant associations with (ARB), particularly biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved nutrient metabolism, antibiotic production, quorum sensing, biofilm formation which contributed enhanced competition survival pathogens ARB hosts. Phages also carried transcriptionally active virulence factor (VFGs) resistance (ARGs), could mediate horizontal transfer communities. Overall, these discoveries suggest that form symbiotic relationships hosts, encoding AMGs mediating gene (HGT) increase source plastisphere.

Language: Английский

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Phages in the infant gut: a framework for virome development during early life

The ISME Journal, Journal Year: 2021, Volume and Issue: 16(2), P. 323 - 330

Published: Aug. 20, 2021

Language: Английский

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Response of soil viral communities to land use changes

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Oct. 12, 2022

Soil viruses remain understudied when compared to virus found in aquatic ecosystems. Here, we investigate the ecological patterns of soil viral communities across various land use types encompassing forest, agricultural, and urban Xiamen, China. We recovered 59,626 operational taxonomic units (vOTUs) via size-fractioned viromic approach with additional mitomycin C treatment induce release from bacterial fraction. Our results show that are significantly different amongst considered. A microdiversity analysis indicates selection act on vOTUs, resulting disparities between associated communities. pH is one major determinants community structure, changes in-silico predicted host compositions vOTUs. Habitat disturbance variation moisture potentially contribute dynamics putative lysogenic These findings provide mechanistic understandings ecology evolution changing environments.

Language: Английский

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A framework for integrating microbial dispersal modes into soil ecosystem ecology

iScience, Journal Year: 2022, Volume and Issue: 25(3), P. 103887 - 103887

Published: Feb. 10, 2022

Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function largely unpredictable. unique in it contributes to both ecological evolutionary processes shaped by deterministic stochastic forces. The ecosystem-level ramifications outcomes are further compounded dormancy dynamics environmental selection. Here we review knowledge gaps challenges remain defining how dispersal, filtering, interact influence relationship between structure soils. We propose classification into three categories, through vegetative or active cells, dormant acellular each with spatiotemporal trait associations. This conceptual framework should improve integration structure-function relationships.

Language: Английский

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Auxiliary Metabolic Gene Functions in Pelagic and Benthic Viruses of the Baltic Sea

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: July 7, 2022

Marine microbial communities are facing various ecosystem fluctuations (e.g., temperature, organic matter concentration, salinity, or redox regimes) and thus have to be highly adaptive. This might supported by the acquisition of auxiliary metabolic genes (AMGs) originating from virus infections. bacteriophages frequently contain AMGs, which allow them augment their host's metabolism enhance fitness. These encode proteins for same functions as similar host homologs. In present study, we analyzed diversity, distribution, composition marine viruses, focusing on AMGs identify putative ecologic role. We viruses assemblies 212 publicly available metagenomes obtained sediment water samples across Baltic Sea. general, in both compartments differed compositionally. While predominant viral lifestyle was found lytic, lysogeny more prevalent sediments than pelagic samples. The highest proportion identified genomes Myoviridae. Overall, most abundantly occurring encoded that protect degradation hosts, such methylases. Additionally, some detected known involved photosynthesis, 7-cyano-7-deazaguanine synthesis, cobalamin biosynthesis among other functions. Several were this study previously a large-scale analysis including origins, i.e., different sites, wastewater, human gut. supports theory globally conserved core spread over genomes, regardless environment.

Language: Английский

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Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(7), P. 1004 - 1014

Published: April 17, 2023

The earthworm gut virome influences the structure and function of microbiome, which in turn worm health ecological functions. However, despite its soil quality implications, it remains elusive how intestinal phages respond to different environmental stress, such as pollution. Here we used metagenomics metatranscriptomics investigate interactions between their bacteria under benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg-1) stress stimulated microbial metabolism (1.74-fold control), enhanced antiphage defense system (n = 75) against infection (8 phage-host pairs). exposure resulted highest proportion lysogenic (88%), prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level (200 disrupted suppressed systems 29), leading increase phage-bacterium association (37 pairs) conversion lytic (lysogenic ratio declined 43%). Despite fluctuating interactions, phage-encoded AMGs related antioxidant pollutant degradation were enriched, apparently alleviate pollution stress. Overall, these findings expand our knowledge complex pollution-stressed guts, deepen understanding evolutionary roles phages.

Language: Английский

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