Wu Xingjie, Liu Ye, He Zhibin, Zhou Xi, Liesack Werner, Peng Jingjing
State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany.
ISME Commun. 2025 May 23;5(1):ycaf088. doi: 10.1093/ismeco/ycaf088. eCollection 2025 Jan.
Methanogens play a critical role in global methane (CH) 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 , , , , and . We identified 419 virus-host linkages involving 56 methanogenic host species and 189 viruses, spanning the families , , , , and , 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.
产甲烷菌在稻田生态系统的全球甲烷（CH）排放中起着关键作用。通过宏基因组分析和荟萃分析的整合，我们构建了一个CRISPR间隔区数据库，该数据库包含来自351个产甲烷基因组的14475个间隔区。这使得我们能够鉴定出靶向稻田中普遍存在的关键产甲烷菌科的病毒，包括、、、、和。我们确定了419个病毒-宿主联系，涉及56个产甲烷宿主物种和189种病毒，涵盖了、、、、和科，以及126个未分类的病毒实体。这些发现突出了一种与肠道环境中观察到的病毒群落组成明显不同的病毒群落组成。预测会感染多个密切相关产甲烷菌物种的特定病毒的存在支持了交叉感染模式。在24种编码抗CRISPR蛋白的病毒中观察到了潜在病毒-宿主共同进化的证据，这可能有助于逃避宿主CRISPR介导的免疫。总的来说，这项研究揭示了一个复杂而动态的病毒-宿主相互作用网络，该网络塑造了稻田生态系统中产甲烷菌群落。
