Life and death in the soil microbiome: how ecological processes influence biogeochemistry

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(7), P. 415 - 430

Published: Feb. 28, 2022

Language: Английский

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Diversity in the soil virosphere: to infinity and beyond?

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 30(11), P. 1025 - 1035

Published: May 26, 2022

Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome metatranscriptome analyses offer unprecedented windows into the soil virosphere. Given emerging picture high viral activity, diversity, dynamics over short spatiotemporal scales, then outline eco-evolutionary processes hypothesize major diversity drivers for viruses. We argue a effort is needed to establish 'global virosphere atlas' can be used address roles viruses microbiomes terrestrial biogeochemical cycles across scales.

Language: Английский

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Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(6), P. 916 - 930

Published: April 8, 2023

Abstract While decomposition of organic matter by bacteria plays a major role in nutrient cycling terrestrial ecosystems, the significance viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study mesophilic thermophilic their on during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics activity are tightly coupled, where specific track host densities, triggering microbial community succession via top-down control HTC. Moreover, encoded expressed several auxiliary metabolic genes (AMGs) linked carbon cycling, impacting turnover alongside bacteria. Nutrient correlated positively virus–host ratio, indicative positive relationship between ecosystem functioning, viral abundances, activity. These effects were predominantly driven DNA as most detected RNA associated eukaryotes not phase composting. findings suggest could drive HTC recycling bacterial biomass through cell lysis expressing key AMGs. Viruses hence potentially be used indicators functioning optimize productivity biotechnological agricultural systems.

Language: Английский

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Extreme summers impact cropland and grassland soil microbiomes

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(10), P. 1589 - 1600

Published: July 7, 2023

The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond such disturbances. Here, metagenomics was used investigate effects future climate scenarios (+0.6 °C warming and altered precipitation) on during summers 2014-2019. Unexpectedly, Central Europe experienced heatwaves droughts 2018-2019, causing significant impacts structure, assembly, function microbiomes. Specifically, relative abundance Actinobacteria (bacteria), Eurotiales (fungi), Vilmaviridae (viruses) significantly increased in both cropland grassland. contribution homogeneous selection bacterial community assembly from 40.0% normal 51.9% summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), sporulation (spoIID, spoVK) were identified as potential contributors drought-enriched taxa, their expressions confirmed by metatranscriptomics 2022. impact further evident taxonomic profiles 721 recovered metagenome-assembled genomes (MAGs). Annotation contigs MAGs suggested that may have a competitive advantage due geosmin 2-methylisoborneol. Future caused similar pattern changes communities summers, but much lesser extent. Soil grassland showed greater resilience change than those cropland. Overall, this study provides comprehensive framework for understanding response

Language: Английский

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A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(7), P. 1873 - 1883

Published: June 20, 2024

Historically neglected by microbial ecologists, soil viruses are now thought to be critical global biogeochemical cycles. However, our understanding of their distribution, activities and interactions with the microbiome remains limited. Here we present Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced metagenomes composed 616,935 uncultivated viral genomes 38,508 unique operational taxonomic units. Rarefaction curves Atlas indicate that most diversity unexplored, further underscored high spatial turnover low rates shared units across samples. By examining genes associated functions, also demonstrate potential impact carbon nutrient cycling. This study represents an extensive characterization provides foundation for developing testable hypotheses regarding role virosphere in biogeochemistry.

Language: Английский

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Unravelling viral ecology and evolution over 20 years in a freshwater lake

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Language: Английский

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Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems

Annual Review of Virology, Journal Year: 2022, Volume and Issue: 9(1), P. 57 - 78

Published: May 19, 2022

Viruses of bacteria (bacteriophages or phage) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape diversity, influence nutrient cycling ecosystem function. The unrelenting impact phages within the realm is result, large part, their ability to rapidly evolve response host dynamics. knowledge gained from laboratory systems, typically using pairwise interactions between single-host single-phage has made clear coevolve with hosts rapidly, somewhat predictably, primarily by counteradapting resistance. Recent advancement metagenomics approaches, as well a shifting focus toward natural communities host-associated microbiomes, beginning uncover full picture phage more complex settings. As these data reach potential, it will be critical ask when how insights studies vitro can meaningfully applied understanding bacteria-phage nature. In this review, we explore myriad ways phagesshape are themselves shaped populations communities, particular observed predicted differences communities.

Language: Английский

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Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(45)

Published: Nov. 2, 2022

Viruses shape microbial communities, food web dynamics, and carbon nutrient cycling in diverse ecosystems. However, little is known about the patterns drivers of viral community composition, particularly soil, precluding a predictive understanding impacts on terrestrial habitats. To investigate soil assembly processes, here we analyzed 43 viromes from rainfall manipulation experiment Mediterranean grassland California. We identified 5,315 populations (viral operational taxonomic units [vOTUs] with representative sequence ≥10 kbp) found that composition exhibited highly significant distance–decay relationship within 200-m 2 field site. This pattern was recapitulated by intrapopulation microheterogeneity trends prevalent vOTUs (detected ≥90% viromes), which tended to exhibit negative correlations between spatial distance genomic similarity their predominant allelic variants. Although structuring also observed bacterial archaeal signal dampened relative viromes, suggesting differences local for viruses prokaryotes and/or temporal scales captured total DNA. Despite overwhelming signal, evidence environmental filtering revealed protein-sharing network analysis, wherein group related predicted infect actinobacteria shown be significantly enriched low-moisture samples distributed throughout field. Overall, our results indicate diverse, dynamic, active, spatially structured virosphere capable rapid responses changing conditions.

Language: Английский

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Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition

ISME Communications, Journal Year: 2022, Volume and Issue: 2(1)

Published: March 16, 2022

To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from correlational evidence, such as virus-driven changes microbial abundances, auxiliary metabolic genes, and links with physiochemical properties. more directly test viruses carbon cycling during plant litter decomposition, we added concentrated community suspensions to complex decomposer 40-day microcosm experiments. Microbial two New Mexico alpine soils, Pajarito (PJ) Santa Fe (SF), were inoculated onto grass sand, three treatments applied triplicate each set microcosms: addition buffer (no virus), live virus (+virus), or killed-virus (+killed-virus) fractions extracted same soil. Significant differences respiration observed between +virus +killed-virus PJ, but not SF microcosms. Bacterial fungal composition differed significantly by treatment both PJ Combining data across altered bacterial diversity, dissolved organic total nitrogen. Overall, demonstrate that increasing pressure can terrestrial is context-dependent.

Language: Английский

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Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(11), P. 1809 - 1822

Published: Sept. 28, 2023

Language: Английский

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