Data_Sheet_1_Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes.pdf

It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their “host”. However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.

已有研究提出，与浮游动物（zooplankton）共生的微生物可为其“宿主”提供诸多有益服务。然而，目前学界仍未充分理解温度对浮游动物微生物组（microbiome）的影响。此外，学界尚不清楚浮游动物微生物组与自由生活型、颗粒附着型（particle-associated, PA）微生物的差异程度。本研究通过两项实验明确解决了上述问题：(1) 对比自由生活型、颗粒附着型与浮游动物共生微生物的差异；(2) 探究温度对两座发电厂人工加温的一系列湖泊水柱中上述微生物的影响。对16S rRNA基因的高通量扩增子测序结果显示，与浮游动物、颗粒附着型微生物及浮游细菌（bacterioplankton）共生的细菌群落，其多样性与组成均存在显著差异，各自聚为独立类群，这表明浮游微生物存在生境分化现象。在所测定的非生物参数中，温度对所有分析的微生物组的多样性与组成均产生了显著影响。浮游动物微生物组以变形菌门（Proteobacteria）和拟杆菌门（Bacteroidetes）两大菌门为主，而浮游细菌的优势菌门则为放线菌门（Actinobacteria）。相较于浮游细菌与颗粒附着型微生物，浮游动物的微生物物种丰富度与多样性均更低。值得注意的是，甲烷氧化菌、甲基营养菌及硝化菌（如硝化杆菌属Nitrobacter）的类群与浮游动物及颗粒附着型微生物组存在显著关联。本研究明确证实了浮游微生物的生境分化现象，及其与淡水生态系统生物地球化学循环的潜在关联。