# Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils

## TL;DR

This study explores virus-host interactions in rice paddy soils, revealing complex networks involving methanogens and their viruses.

## Contribution

A CRISPR spacer database was used to identify virus-host linkages and coevolution in methanogens from rice paddies.

## Key findings

- 419 virus–host linkages were identified involving 56 methanogenic species and 189 viruses.
- Evidence of potential virus–host coevolution was found in 24 viruses encoding anti-CRISPR proteins.
- The virome composition in rice paddies differs significantly from gut environments.

## Abstract

Methanogens play a critical role in global methane (CH4) emissions from rice paddy ecosystems. Through the integration of metagenomic analysis and meta-analysis, we constructed a CRISPR spacer database comprising 14 475 spacers derived from 351 methanogenic genomes. This enabled the identification of viruses targeting key methanogenic families prevalent in rice paddies, including Methanosarcinaceae, Methanotrichaceae, Methanobacteriaceae, Methanocellaceae, and Methanomassiliicoccaceae. We identified 419 virus–host linkages involving 56 methanogenic host species and 189 viruses, spanning the families Straboviridae, Salasmaviridae, Kyanoviridae, Herelleviridae, and Demerecviridae, along with 126 unclassified viral entities. These findings highlight a virome composition that is markedly distinct from those observed in gut environments. Cross-infection patterns were supported by the presence of specific viruses predicted to infect multiple closely related methanogenic species. Evidence for potential virus–host coevolution was observed in 24 viruses encoding anti-CRISPR proteins, likely facilitating evasion of host CRISPR-mediated immunity. Collectively, this study reveals a complex and dynamic network of virus–host interactions shaping methanogen communities in rice paddy ecosystems.