On March 27, 2026, Prof. Meng Li’s team from the Institute for Advanced Study (IAS) at Shenzhen University published a research paper titled “Insights into the arms race between prokaryotic hosts and their viruses in mangrove ecosystem” in Environmental Science & Technology. Prof. Meng Li is the corresponding author, and Chengxiang Gu and Jiazheng Gu are co-first authors. Shenzhen University is the sole affiliation.

Prokaryotes and phages (viruses) are engaged in a perpetual coevolutionary arms race, driving the evolution of sophisticated phage counter-defense strategies and diverse host immune mechanisms. Mangrove wetlands, among Earth’s most productive ecosystems, harbor vast microbial diversity. The resource-rich and dynamically changing mangrove ecosystem serves as an ideal model for studying host–virus arms races. This study integrated metagenomic and metatranscriptomic analyses of mangrove habitats in Futian, China, to resolve the dynamics of defense systems across microbial communities and their associated viruses.

A total of 1,334 non-redundant medium- and high-quality prokaryotic metagenome-assembled genomes (MAGs) were recovered from 40 sediment samples. PERMANOVA results showed that the prokaryotic community was significantly influenced by both depth and season, with depth having a greater impact. Among the 149,010 non-redundant viral contigs identified, 6,266 host–virus connections were established.

Within 324 prokaryotic MAGs and 140 viral contigs, 604 and 146 defense systems were detected, respectively, with the restriction-modification (RM) system being the most common (Figure 1). Phylogenetic analysis suggested that viral-encoded RM systems may have originated from lineages distinct from those of their predicted hosts. Notably, the relative abundances of prokaryotes and viruses carrying defense systems were significantly correlated with sediment depth: as depth increased, the relative abundance of defense-containing prokaryotes increased, whereas that of defense-containing viruses decreased.

Metatranscriptomic data revealed that 40% of prokaryotic defense genes and 37% of viral defense genes were transcribed, with expression levels of some defense system genes varying by season or depth. The transcription levels of virus-encoded Abi, RM, and SoFic systems were significantly higher than those of the corresponding systems in prokaryotes. Heterologous expression of bacterial and viral defense systems in E. coli BL21 resulted in distinct anti-phage activities.

This study explores the defense systems encoded by prokaryotes and viruses in mangrove sediments. By integrating metagenomic and metatranscriptomic data, it reveals the distribution patterns and expression profiles of these defense systems and experimentally validates their anti-phage effects, thereby expanding our understanding of the prokaryotic arms race in mangrove sediments.

This work was supported by the National Key Research and Development Program of China, the National Natural Science Foundation of China, the Guangdong Major Project of Basic and Applied Basic Research, the Shenzhen Medical Research Fund, the Shenzhen University 2035 Program for Excellent Research, and the research fund from the Synthetic Biology Research Center and Intelligent Computing Center of Shenzhen University.

Article: https://doi.org/10.1021/acs.est.5c14802

Figure 1. The distribution of defense systems of prokaryotes and viruses in the mangrove habitats.