Genomic and transcriptomic insights into complex virus–prokaryote interactions in marine biofilms

作者：Kun Zhou, Tin Yan Wong, Lexin Long, Karthik Anantharaman, Weipeng Zhang, Wai Chuen Wong, Rui Zhang, Pei‐Yuan Qian · 发表于：The ISME Journal · 年份：2023 · DOI：10.1038/s41396-023-01546-2 · 被引用次数：35 · 研究领域：Bacteriophages and microbial interactions、Microbial Community Ecology and Physiology、Genomics and Phylogenetic Studies

Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus-prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus-host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction-modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay w...