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

Microbiome

Research

Clement Coclet¹  Emiley A. Eloe-Fadrosh¹  Simon Roux¹  Ulas Karaoz²  Shi Wang²  Patrick O. Sorensen²  Eoin L. Brodie³ 

[1] DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA;

关键词: Phages;    Viruses;    Metagenomics and metatranscriptomics;    Virus activity;    Virus-host interactions;    Mountainous watershed;    Soils;    Seasonal dynamics;   

DOI  :  10.1186/s40168-023-01666-z

 received in 2023-03-15, accepted in 2023-09-07,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundViruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes.ResultsWe identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth.ConclusionTaken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.2RJdjcjTGzDNGfvgvrWr_YVideo Abstract

【 授权许可】

CC BY   
© © Lawrence Berkeley National Laboratory 2023

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