Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
Microbiome. 2021 Jun 28;9(1):150. doi: 10.1186/s40168-021-01074-1.
Microbe-virus interactions have broad implications on the composition, function, and evolution of microbiomes. Elucidating the effects of environmental stresses on these interactions is critical to identify the ecological function of viral communities and understand microbiome environmental adaptation. Heavy metal-contaminated soils represent a relevant ecosystem to study the interplay between microbes, viruses, and environmental stressors.
Metagenomic analysis revealed that Cr pollution adversely altered the abundance, diversity, and composition of viral and bacterial communities. Host-phage linkage based on CRISPR indicated that, in soils with high Cr contamination, the abundance of phages associated with heavy metal-tolerant hosts increased, as did the relative abundance of phages with broad host ranges (identified as host-phage linkages across genera), which would facilitate transfection and broader distribution of heavy metal resistance genes in the bacterial community. Examining variations along the pollutant gradient, enhanced mutualistic phage-bacterium interactions were observed in the face of greater environmental stresses. Specifically, the fractions of lysogens in bacterial communities (identified by integrase genes within bacterial genomes and prophage induction assay by mitomycin-C) were positively correlated with Cr contamination levels. Furthermore, viral genomic analysis demonstrated that lysogenic phages under higher Cr-induced stresses carried more auxiliary metabolic genes regulating microbial heavy metal detoxification.
With the intensification of Cr-induced environmental stresses, the composition, replication strategy, and ecological function of the phage community all evolve alongside the bacterial community to adapt to extreme habitats. These result in a transformation of the phage-bacterium interaction from parasitism to mutualism in extreme environments and underscore the influential role of phages in bacterial adaptation to pollution-related stress and in related biogeochemical processes. Video Abstract.
微生物-病毒相互作用对微生物组的组成、功能和进化具有广泛的影响。阐明环境胁迫对这些相互作用的影响对于确定病毒群落的生态功能和理解微生物组环境适应至关重要。重金属污染土壤是研究微生物、病毒和环境胁迫因子相互作用的相关生态系统。
宏基因组分析表明，Cr 污染会对病毒和细菌群落的丰度、多样性和组成产生不利影响。基于 CRISPR 的宿主-噬菌体联系表明，在 Cr 污染较高的土壤中，与重金属耐受宿主相关的噬菌体丰度增加，宿主范围较广的噬菌体（鉴定为跨属的宿主-噬菌体联系）的相对丰度也增加，这将促进转染和重金属抗性基因在细菌群落中的更广泛分布。沿着污染物梯度考察变化，在面临更大环境胁迫时，观察到增强的互利噬菌体-细菌相互作用。具体而言，细菌群落中溶原菌的分数（通过细菌基因组中的整合酶基因和丝裂霉素 C诱导的前噬菌体试验鉴定）与 Cr 污染水平呈正相关。此外，病毒基因组分析表明，在较高 Cr 诱导胁迫下，携带更多辅助代谢基因以调节微生物重金属解毒的溶原噬菌体。
随着 Cr 诱导环境胁迫的加剧，噬菌体群落的组成、复制策略和生态功能都与细菌群落一起进化，以适应极端生境。这导致噬菌体-细菌相互作用从寄生转变为互利，在极端环境中突显噬菌体在细菌适应污染相关胁迫和相关生物地球化学过程中的重要作用。视频摘要。
