Wang Yuanyuan, Huang Shanzi, He Jian, Feng Zhengqi, Wu Wenbo, Guo Changjun, He Jianguo
School of Marine Sciences, State Key Laboratory for Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals/Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
School of Marine Sciences, State Key Laboratory for Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals/Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
J Hazard Mater. 2025 Aug 15;494:138594. doi: 10.1016/j.jhazmat.2025.138594. Epub 2025 May 12.
Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.
冷泉是富含甲烷的生态系统，在全球生物地球化学循环中发挥着关键作用，但其病毒群落仍未得到充分研究。我们首次对海马冷泉的发育阶段进行了全面的病毒宏基因组分析。对来自化学自养、成熟和灭绝冷泉沉积物的病毒群落进行特征分析，共鉴定出4272个病毒操作分类单元，其中77%代表新谱系，凸显了冷泉独特的病毒多样性。病毒群落结构和多样性因冷泉阶段而异，在化学自养阶段多样性最高。虽然肌尾噬菌体科和微小噬菌体科占主导地位，但其相对丰度随成熟度而变化。γ-变形菌成为主要的病毒宿主，在不同阶段呈现出不同的相互作用模式。值得注意的是，化学自养阶段拥有最高丰度和多样性的病毒编码辅助代谢基因（AMGs；约450个AMGs），碳水化合物代谢和中心碳途径基因显著富集（分别高出2.2倍和1.8倍，p<0.005），氨基酸代谢（高出1.9倍，p=0.003），以及硫传递系统基因（高出2.0倍，p=0.002）。相比之下，成熟阶段在能量代谢基因（位点间差异高达3.9倍，p<0.001）和外源物质降解途径中表现出明显的富集，表明不同阶段的病毒对生物地球化学循环有特定影响。裂解性生活方式在各个阶段都占主导，表明冷泉发育过程中病毒-宿主相互作用动态变化。这些发现揭示了冷泉中复杂的病毒生态学，对微生物群落结构和生物地球化学过程具有潜在影响。本研究为理解病毒在冷泉生态系统功能和生物地球化学循环中的作用奠定了基础，对海洋微生物生态学和环境生物技术具有重要意义。
