Summary Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro‐ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate‐active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate‐binding modules. These results demonstrate that virus‐encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.
Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem “phages, prophages, transposable elements, and plasmids”. Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.
Background Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. Results Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. Conclusions The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.