Polaribacter属细菌适应藻类丰富环境的进化机制研究

Flavobacteria is one of the major decomposers of algal polysaccharides which occupy an important position in marine carbon cycle. Strains in genus Polaribacter of family Flavobacteriaceae are widely found in different environments including particle-associated strains from seaweed-rich environments and free living strains from other environments, these two types of strains are quite distinct in genome. The relationship between this difference and the niche adaptation of strains in seaweed-rich environments and related evolutionary mechanism need further study. In this study, based on the former finding that the differentiation of these two types of strains was probably based on genome streamlining, we use all type strains in genus Polaribacter as the materials and plan to determine their life habits and genomic features using biochemical detection and genome sequencing, to confirm the evolutionary relationship between particle-associated strains and free living strains with the reconstruction of phylogenetic tree, the prediction of most recent common ancestor's genome and the analysis of the gene gain and loss and the differentiation time of different strains, to analyse the genomic and transcriptomic differences of particle-associated strains from different seaweed-rich environments and related mechanisms with the comparison of core genomes, the analysis of foreign fragments, the differences in PUL structures and the transcriptomes of strains in different seaweed-rich environments. With this study, we can illuminate the evolutionary mechanism of strains in genus Polaribacter during the niche adaptation in seaweed-rich environments, increase our understandings about the role of flavobacteria in the marine carbon cycle and provide the research basis for the utilization of algal polysaccharides.

藻类多糖在海洋碳循环中极其重要，黄杆菌科细菌是其最主要的分解者之一。黄杆菌科Polaribacter属细菌分布广泛，包含来自藻类丰富环境的营共附生菌株和来自其他环境的营自由生活菌株，两者基因组差异明显，基因组差异与菌株适应藻类丰富环境的关系及其进化机制有待揭示。本项目在前期发现两类菌株的分化可能基于基因组简化的基础上，拟使用该属模式菌株为研究对象，通过生化检测和基因组测序，明确菌株的生活习性和基因特征；通过构建系统发育树、预测祖先基因组以及分析菌株间基因增减和分化时间，确定营共附生和营自由生活菌株的演化关系；通过比较核心基因组、分析外源片段和PUL结构差异以及检测菌株在不同藻类丰富环境中的转录组，解析处于不同藻类丰富环境中的营共附生菌株间的差异及其形成机制。通过项目实施将阐明该属细菌适应藻类丰富环境的进化机制，进一步认识黄杆菌科细菌在海洋碳循环中的作用，可为开发利用藻类多糖提供理论基础。

藻类多糖在海洋碳循环中极其重要，黄杆菌科细菌是其最主要的分解者之一。黄杆菌科Polaribacter属广泛分布于藻类丰富环境和寡营养环境，不同环境来源菌株间的基因组差异及其适应藻类丰富环境的进化机制有待揭示。本项目采用多学科交叉手段，在该属基因组差异、不同类群演化关系以及环境适应机制方面取得了一系列新认识：（1）获得该属53株菌株的基因组，并根据肽酶/多糖酶比值分为营自由生（FL）和营共附生（PA）两类；（2）构建了基于同源单拷贝蛋白的系统发育树，揭示了该属祖先为营自由生，PA类群来源于较晚分化的同一祖先；构建了基因增减树，发现了该属祖先不存在基因组精简化现象，该属种分化过程早期未发生大规模的水平基因转移事件；完成了两个类群的核心基因组和泛基因组比较，明确了PA类群的主要演化机制为获得藻类多糖降解相关基因；（3）发现了PA类群均具有藻类多糖相关多糖利用位点（PUL），但底物差异较大；明确了PA类群中Sus C/D蛋白等PUL功能组件的演化关系，揭示了其PUL演化过程中存在多次功能组件的丢失和获得；发现了不同藻类多糖相关PUL的结构及分布具明显差异，PUL进化存在垂直遗传和水平基因转移现象，提出藻类多糖结构可能是决定PUL进化方式的主要因素之一；（4）从藻类丰富环境分离了菌株131株，建立了5个细菌新种，分析了菌株ALG8基因组并提出质粒可能导致了近缘菌株间的功能差异；确定了菌株A64和A80是Polaribacter属近缘属的新种，分析了其基因组并提出多次基因重组导致的残缺PUL可能会造成假水平基因转移。项目执行期间，项目负责人以第一作者或通讯作者发表SCI 期刊论文6 篇，2020年职称晋升为副教授，2021年完成在职博士后工作并获优秀出站。本项目基本阐明了Polaribacter属细菌适应藻类丰富环境的进化机制，可以为进一步认识黄杆菌科细菌在海洋碳循环中的作用提供基础。