A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide DOI Creative Commons
S. Emil Ruff, Isabella Hrabě de Angelis, Megan M. Mullis

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(51)

Published: Dec. 18, 2024

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface subsurface microbiomes. Here, analyzed 478 archaeal 964 bacterial metabarcoding datasets 147 metagenomes from diverse widely environments. Microbial diversity is similar in microbiomes at local global scales. However, community composition greatly differs sea land, corroborating a phylogenetic divide that mirrors patterns plant animal diversity. In contrast, overlaps supporting continuum rather than discrete biosphere. Differences life thus seem greater land subsurface. Diversity of decreases with depth, while distance cultured isolates rivals or exceeds We identify distinct compositions but

Language: Английский

Soil pH influences the composition of bacteriophage communities infecting individual hosts DOI
Sungeun Lee, Graeme W. Nicol, Christina Hazard

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 4, 2024

Abstract Bacteriophages (phages) can infect a range of hosts in highly diverse soil bacterial communities. However, selection host communities across ecological gradients and co-evolutionary processes may influence both the distribution phages susceptibility individual through virus interactions local adaptation within distinct niches. Metagenomic-based analyses have revealed that pH selects for populations community structures phage at global scales. whether contrasting represents selective barrier capable infecting an is unknown. To examine on host-virus interactions, two closely related Bacillus strains were isolated characterized from 7.5 associated with long-term contiguous gradient (pH 4.5 to 7.5). Phages each strain subsequently enriched soils 4.5, 5.5, 6.5 7.5), enumerated using plaque assay, via metagenomic analysis. cultivated all but their composition abundance varied pH. Phage despite close relatedness hosts, indicating relatively narrow ranges virus. These results suggest while vary substantially gradient, alone does not represent host.

Language: Английский

Citations

0
Influence of climate on soil viral communities in Australia on a regional scale DOI Creative Commons
Li Bi,

Zi‐Yang He,

Bảo Anh Nguyễn

et al.

Journal of Sustainable Agriculture and Environment, Journal Year: 2024, Volume and Issue: 3(4)

Published: Oct. 1, 2024

Abstract Viruses play a crucial role in regulating microbial communities and ecosystem functioning. However, the biogeographic patterns of viruses their responses to climate factors remain underexplored. In this study, we performed viral size fraction metagenomes on 108 samples collected along 2600 km transect across Australia, encompassing distinct conditions. A total 14,531 operational taxonomic units were identified. Climate had greater influence than edaphic biotic driving alpha diversity communities. The strongest relationship was observed between mean annual temperature Moreover, factors, particularly aridity index, primary drivers community structure. Overall, these findings underscore pivotal shaping have implications for understanding how change influences soil ecology.

Language: Английский

Citations

0
V- and VL-Scores Uncover Viral Signatures and Origins of Protein Families DOI Creative Commons
Kun Zhou, James C. Kosmopoulos, Eugenia Colón

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 29, 2024

Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much the viral genome, leaving proteins functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score VL-score, designed quantify virus-likeness protein families genomes create an open-access searchable database, V-Score-Search. By applying V- VL-scores public databases (KEGG, Pfam, eggNOG), link 38−77% with viruses, 9−16x increase over current estimates. These metrics outperform existing approaches, enabling precise detection genomes, prophages, host-derived auxiliary (AVGs) from fragmented sequences, significantly improving genome binning. Remarkably, identify up 17x more AVGs, dominated by non-metabolic unknown function. This innovation unlocks new insights into virus signatures host interactions, wide-ranging implications genomics biotechnology.

Language: Английский

Citations

0
Phosphate amendment drives bloom of RNA viruses after soil wet-up DOI Creative Commons
Ella T. Sieradzki, George Allen, Jeffrey A. Kimbrel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 30, 2024

Abstract Soil rewetting after a dry period results in surge of activity and succession both microbial DNA virus communities. Less is known about the response RNA viruses to soil rewetting—while they are highly diverse widely distributed soil, remain understudied. We hypothesized that would show temporal following phosphate amendment influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes amplicon data, 2,190 populations were identified across five phyla, with 37% these predicted infect bacteria (26%) or fungi (11%). Only 1.2% had annotated capsid genes, suggesting most persist via intracellular replication without free virion phase. Phosphate altered community composition within first week amended vs. unamended communities remained distinguishable for up three weeks. While overall host stable, certain bacterial showed reduced abundance phosphate-amended soils, likely due increased lysis, bacteriophages, particularly Leviviricetes , proliferated significantly. Notably, 60% under belonged basal Lenarviricota clades rather than well-known groups like . estimate bacteriophage infections affect 10 7 –10 9 per gram aligning total population (10 g −1 soil), phages significantly post-wet-up, availability modulating this effect. Highlights wet-up influences dynamics over The majority hosts preferentially supports other vOTUs responded from unknown Most be infected by bacteriophages

Language: Английский

Citations

0
A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide DOI Creative Commons
S. Emil Ruff, Isabella Hrabě de Angelis, Megan M. Mullis

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(51)

Published: Dec. 18, 2024

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface subsurface microbiomes. Here, analyzed 478 archaeal 964 bacterial metabarcoding datasets 147 metagenomes from diverse widely environments. Microbial diversity is similar in microbiomes at local global scales. However, community composition greatly differs sea land, corroborating a phylogenetic divide that mirrors patterns plant animal diversity. In contrast, overlaps supporting continuum rather than discrete biosphere. Differences life thus seem greater land subsurface. Diversity of decreases with depth, while distance cultured isolates rivals or exceeds We identify distinct compositions but

Language: Английский

Citations

0