T4-Type phage and host diversities in coastal wetland

Bacteriophages are abundant and diverse in soils, playing a major role in regulating bacterial communities and consequently affecting biogeochemical cycles. Such host-phage interactions may be influenced by fluctuations in soil moisture, as observed in wetlands soils which constitute a key feature of the ongoing climate change. Here, we investigated the spatial and temporal dynamics of both bacteria and T4-type bacteriophage community structures and diversities in soil of a freshwater wetland. Soil was sampled in three sites across a proximal soil transect presenting an increase moisture content at seven dates over an 18 months period with contrasted flooding periods. DNA was extracted and we applied amplicon sequencing of the bacterial 16S rRNA gene and viral g23 gene. Bacterial community composition varied across the proximal soil transect, with Methylomirabilia and Gammaproteobacteria being significantly enriched in the wettest site and comprising ASVs affiliated to methanotroph and denitrifier bacteria, respectively. We identified a large diversity of T4-type phages, among which a fraction was novel, while others were similar to phages previously sequenced from various biomes. These findings suggest that T4-type phages are capable of successfully colonizing diverse niches in the biosphere, contributing to their ubiquity and diversity. Viral community was however dominated by few vASVs, which were highly represented in one or two of the three studied sites supporting the Bank model. All together our results indicate that T4-type phages have broad host ranges and more likely follow bacterial population dynamics. The present study provides new insights into the role of phages in soil, highlighting their interactions with bacterial hosts involved in carbon and nitrogen cycles, interactions that are likely regulated by fluctuations in soil moisture, as observed in wetlands.

噬菌体（Bacteriophages）在土壤中分布广泛且多样性极高，在调控细菌群落结构方面发挥关键作用，进而对生物地球化学循环产生重要影响。此类宿主与噬菌体的互作可能受土壤水分波动的调控，这一现象在湿地土壤中已有观测；而湿地本身正是当前气候变化的核心表征之一。
本研究针对一处淡水湿地的土壤，探究了细菌与T4型噬菌体（T4-type bacteriophage）的群落结构及多样性的时空动态变化。研究团队沿一条土壤水分梯度递增的近岸样带设置3个采样点，并在18个月内的7个时间节点开展土壤采样，覆盖了差异显著的淹水周期。提取土壤总DNA后，分别对细菌16S rRNA基因与病毒g23基因进行扩增子测序。
细菌群落组成沿近岸样带呈现显著分异：甲基孢囊菌门（Methylomirabilia）与γ-变形菌纲（Gammaproteobacteria）在最湿润的采样点显著富集，二者分别包含隶属于甲烷氧化菌与反硝化细菌的扩增子序列变体（Amplicon Sequence Variants，ASVs）。本研究共鉴定出大量T4型噬菌体类群，其中一部分为全新类群，其余则与此前在不同生物群落中测序获得的噬菌体具有较高同源性。上述结果表明，T4型噬菌体可成功定殖于生物圈中的多样生境，这也是其分布广泛且多样性丰富的重要原因。
不过病毒群落仅由少量病毒扩增子序列变体（viral Amplicon Sequence Variants，vASVs）主导，这些vASVs在3个采样点中的1个或2个中占比极高，该结果支持库模型（Bank model）。综合来看，本研究结果表明T4型噬菌体具有广泛的宿主范围，且其种群动态更可能与细菌种群动态同步。
本研究为阐明噬菌体在土壤生态系统中的作用提供了新的视角，重点揭示了噬菌体与参与碳、氮循环的细菌宿主之间的互作关系——正如在湿地中观测到的那样，这类互作很可能受土壤水分波动的调控。