Enumerating soil biodiversity

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(33)

Published: Aug. 7, 2023

Soil is an immense habitat for diverse organisms across the tree of life, but just how many live in soil surprisingly unknown. Previous efforts to enumerate biodiversity consider only certain types (e.g., animals) or report values groups without partitioning species that versus other habitats. Here, we reviewed literature show likely home 59 ± 15% on Earth. We therefore estimate approximately two times greater than previous estimates, and include representatives from simplest (microbial) most complex (mammals) organisms. Enchytraeidae have greatest percentage (98.6%), followed by fungi (90%), Plantae (85.5%), Isoptera (84.2%). Our results demonstrate biodiverse singular habitat. By using this biodiversity, can more accurately quantitatively advocate organismal conservation restoration as a central goal Anthropocene.

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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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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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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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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Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: Oct. 27, 2023

Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral have been identified, with a global distribution seemingly driven by multiple biotic abiotic factors, especially soil temperature moisture. However, our current understanding of the stability across time response to strong seasonal changes in environmental parameters remains limited. Here, we investigated diversity activity DNA RNA viruses, focusing bacteriophages, dynamics' snow-dominated mountainous watershed examining paired metagenomes metatranscriptomes.

Language: Английский

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 20, 2023

Abstract Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland following “wet-up”, when resident microbes both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics viromic analyses indicate holds diverse low biomass reservoir virions, which only subset thrives wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral increases four-fold one week. Though recent hypotheses suggest lysogeny predominates soil, our evidence indicates viruses lytic cycles dominate the response We estimate drive measurable continuous rate cell lysis, with up 46% death driven lysis week Thus, contribute turnover widely reported CO 2 efflux wet-up seasonally soils.

Language: Английский

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Adaptive expression of phage auxiliary metabolic genes in paddy soils and their contribution toward global carbon sequestration

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(49)

Published: Nov. 27, 2024

Habitats with intermittent flooding, such as paddy soils, are crucial reservoirs in the global carbon pool; however, effect of phage–host interactions on biogeochemical cycling soils remains unclear. Hence, this study applied multiomics and datasets integrated validation experiments to investigate community potential phages impact sequestration soils. The results demonstrated that soil harbor a diverse abundant repertoire auxiliary metabolic genes (AMGs) associated fixation, comprising 23.7% identified AMGs. successful annotation protein structures promoters further suggested an elevated expression these within their bacterial hosts. Moreover, environmental stressors, heavy metal contamination, cause genetic variation up-regulate fixation AMGs, by significant enrichment related metabolites ( P < 0.05). Notably, findings indicate lysogenic infecting carbon-fixing hosts increased 10.7% under stress. In addition, situ isotopic labeling induced mitomycin-C revealed increasing concentrations, 13 CO 2 emissions from treatment added phage decreased approximately 17.9%. contrast, C-labeled microbial biomass content average 35.4% compared control. These suggest prominently influence cycle, particularly change conditions. This research enhances our understanding cooperation driving amid evolving

Language: Английский

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Evolutionary diversification and succession of soil huge phages in glacier foreland

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: Jan. 21, 2025

Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy soils remain poorly understood due to the scarcity soil-derived genomes. Here, we conduct size-fractioned (< 0.22 μm) metagenomic analysis across 130-year chronosequence glacier foreland Tibetan Plateau discovered 412 novel viral operational taxonomic units (vOTUs) huge phages. The phylogenomic gene-shared network gained insights into unique evolutionary history compared with smaller Their communities revealed distinct pattern between early (≤ 41 years) late stages (> based on macrodiveristy (interspecies diversity) analysis. A significant increase diversity following retreat were observed according current database. distributed sites within stage demonstrated remarkable higher microdiversity (intraspecies other geographic range such as intra stage, suggesting that glacial is key drivers phage speciation. Alongside shift communities, also noted an functional transition stages. identification abundant CRISPR-Cas12 type IV restriction-modification (RM) systems indicates complex mechanisms for adaptive immunity. Overall, this study unravels importance climate change shaping composition, evolution, function soil further understanding vital broader inclusion ecosystem models.

Language: Английский

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Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109741 - 109741

Published: Feb. 1, 2025

Language: Английский

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