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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Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(7), P. 1956 - 1970

Published: Feb. 21, 2021

Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at preplanting and harvesting stages a tomato growing season via paired total metagenomes size fraction (viromes). Size fractionation prior to DNA extraction reduced sources nonviral viromes, enabling recovery vaster richness populations (vOTUs), greater taxonomic diversity, broader range predicted hosts, better access rare virosphere, relative metagenomes, which tended recover only most persistent vOTUs. Of 2961 detected vOTUs, 2684 were recovered exclusively from while three alone. Both microbial communities differed significantly over time, suggesting coupled response rhizosphere recruitment processes and/or nitrogen amendments. Viral alone also structured along an 18 m spatial gradient. Overall, our results highlight utility viromics reveal similarities between community dynamics throughout suggest partial decoupling driving their distributions, potentially due differences dispersal, decay rates, sensitivities heterogeneity.

Language: Английский

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Energy use efficiency of soil microorganisms: Driven by carbon recycling and reduction

Global Change Biology, Journal Year: 2023, Volume and Issue: 29(22), P. 6170 - 6187

Published: Aug. 30, 2023

Abstract Carbon use efficiency (CUE) is being intensively applied to quantify carbon (C) cycling processes from microbial cell global scales. Energy (EUE) at least as important the CUE because (i) microorganisms organic C mainly an energy source and not elemental per se, (ii) growth maintenance are limited by energy, but a structural element. We conceptualize review importance of EUE soil focus on content in compounds depending nominal oxidation state (NOSC), approaches assess EUE, (iii) similarities differences between (iv) discuss mechanisms responsible for lower compared CUE. The atom (enthalpy combustion, total stored compound) very closely (R 2 = 0.98) positively related NOSC increases 108 kJ mol −1 one unit. For first time we assessed biomass (−0.52) calculated corresponding −510 C. linked considering element compositions substrates utilized microorganisms. mean (0.32–0.35) 18% than (0.41) using glucose substrate. This definitely indicates that relative Based comparison broad range utilization maintenance, well database experimental various compounds, clearly explained five main factors why two behind versus are: recycling: can be microbially recycled, whereas always only once, chemical reduction inorganic compounds: used reduction, which ongoing without utilization.

Language: Английский

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The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

Environmental Microbiome, Journal Year: 2021, Volume and Issue: 16(1)

Published: Dec. 1, 2021

The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response environmental drivers or host organisms. Their mechanisms employed cope with oxidative stress largely unknown. Here, we utilized genome-resolved metagenomics investigate the adaptive genome repertoire oxic anoxic groundwaters, infer putative ranges.Within six groundwater wells, was most dominant (up 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 0.1 µm filters after sequential filtration. Of reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Patescibacteria. Paceibacteria Microgenomates enriched exclusively fractions, whereas candidate division ABY1 Gracilibacteria fractions. On average, smaller filter fractions had 22% genomes, 13.4% lower replication measures, higher proportion rod-shape determining proteins, genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored rates than downstream characterized by longer water residence time. Except prevalence superoxide dismutase genes groundwaters (83%), no major phylogenetic differences observed. abundant MAG encoded a nitrate transporter, nitrite reductase, F-type ATPase, an alternative energy conservation mechanism. consistently co-occurred one another members phyla Nanoarchaeota, Bacteroidota, Nitrospirota, Omnitrophota. Among fractions,, only 8% showed significant one-to-one correlation, mostly Motility transport related certain similar other (Omnitrophota, Proteobacteria Nanoarchaeota).Other stress, found little evidence for niche adaptation groundwaters. Given that could detect specific preference few MAGs, speculate majority is able attach multiple hosts just long enough loot exchange supplies.

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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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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Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: June 4, 2022

The increased use of metagenomics and single-cell genomics led to the discovery organisms from phyla with no cultivated representatives proposed new microbial lineages such as candidate radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, cell sizes, a general host-associated lifestyle was for radiation. So far, most CPR genomes were obtained groundwaters; however, their diversity, abundance, role in surface freshwaters is largely unexplored. Here, we attempt close these knowledge gaps by deep metagenomic sequencing 119 samples 17 different freshwater lakes located Europe Asia. Moreover, applied Fluorescence situ Hybridization followed Catalyzed Reporter Deposition (CARD-FISH) first visualization distinct samples.A total 174 dereplicated metagenome-assembled (MAGs) diverse recovered investigated lakes, higher prevalence hypolimnion (162 MAGs). They (median size 1 Mbp) generally found low abundances (0.02-14.36 coverage/Gb) estimated slow replication rates. analysis genomic traits CARD-FISH results showed that an eclectic group terms capabilities potential lifestyles, ranging what appear be free-living host- particle-associated groups. Although some complexes electron transport chain present MAGs, together ion-pumping rhodopsins heliorhodopsins, believe they probably adopt fermentative metabolism. Terminal oxidases might function O2 scavenging, while heliorhodopsins could involved mitigation against oxidative stress.A high diversity MAGs recovered, did not seem limited specific trophic states. Their capacities resemble ones described groundwater animal-associated samples, apart Gracilibacteria possesses more complete pathways. Even though this mostly host-associated, also observed clades (ABY1, Paceibacteria, Saccharimonadia) unattached any other associated 'lake snow' particles Gracilibacteria), suggesting broad range life-strategies phylum. Video Abstract.

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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Substantial differences in soil viral community composition within and among four Northern California habitats

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

Published: Oct. 13, 2022

Viruses contribute to food web dynamics and nutrient cycles in diverse ecosystems, yet the biogeographical patterns that underlie these viral are poorly understood, particularly soil. Here, we identified trends soil community composition relation habitat, moisture content, physical distance. We generated 30 viromes from four distinct habitats (wetlands, grasslands, woodlands, chaparral) by selectively capturing virus-sized particles prior DNA extraction, recovered 3432 unique 'species' (dsDNA vOTUs). Viral communities differed significantly with richness generally higher wet compared dry habitats. However, vOTUs were rarely shared between viromes, including replicates <10 m apart, suggesting viruses may not disperse well future sampling strategies need account for extreme differences over small spatial scales. Of 19% of detected more than one virome, 93% same habitat site, greater similarity closer proximity under similar environmental conditions. Within-habitat indicate extensive would be required rigorous cross-habitat comparisons, results highlight emerging paradigms high activity soils heterogeneity.

Language: Английский

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Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: Feb. 17, 2023

Abstract Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) DPANN radiation characterized ultra-small cell genomes sizes, resulting in limited metabolic capacities probable dependency on other organisms to survive. We applied a multi-omics approach characterize the communities over wide range of aquifer groundwater chemistries. Results expand known global these unusual organisms, demonstrate geographical 11,000 subsurface-adapted Patescibacteria, Dependentiae archaea, indicate that prokaryotes with minimalistic metabolism characteristic feature terrestrial subsurface. Community composition activities were largely shaped water oxygen content, while site-specific relative abundance profiles driven combination physicochemistries (pH, nitrate-N, dissolved organic carbon). provide insights into activity evidence they major contributors community transcriptional activity. Ultra-small exhibited genetic flexibility respect transcriptionally distinct responses, proportionally greater transcription invested amino acid lipid signal transduction oxic groundwater, along differences taxa active. Those associated sediments differed from planktonic counterparts species activity, adaptations reflecting surface-associated lifestyle. Finally, results showed groups phylogenetically co-occurred strongly across sites, indicating shared preferences for conditions.

Language: Английский

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