Genome characteristics of a generalist marine bacterial lineage
Genome characteristics of a generalist marine bacterial lineage
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DOI：
10.1038/ismej.2009.150
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发表时间：
2010-06-01
期刊：
影响因子：
11
通讯作者：
Moran, Mary Ann
中科院分区：
文献类型：
--
作者：
Newton, Ryan J.;Griffin, Laura E.;Moran, Mary Ann
海洋玫瑰杆菌谱系的成员被认为是生态通才，这表明在为该分类群分配良好的生态角色和生物地球化学功能方面将面临挑战。为了解决这一问题，研究人员利用系统发育亲缘性、生活方式策略和分离物的环境起源这三个预测框架，分析了32株玫瑰杆菌分离物的基因组序列，分析了基因组特征、基因清单和个体基因/途径分布的模式。对于第一个框架，从70个保守的单拷贝基因串联中获得了包含5个深分支分支的系统发育。令人惊讶的是，系统发育树拓扑结构并不是组织基因组特征或单个基因/途径分布模式的最佳模型，尽管它提供了一些预测能力。根据异养、光异养或自养的证据对分离物进行分组，建立了生活方式框架，解释了该谱系中更多的基因库。环境框架对每个菌株的整体基因组含量的预测能力较弱，但解释了几个单独的基因/途径的分布，包括与磷获取、趋化性和芳香族化合物降解相关的基因/途径。全球海洋采样宏基因组数据中的未组装序列独立验证了某些玫瑰杆菌基因中的全球尺度地理信号。这种比较基因组分析的主要发现是，谱系的成员不能轻易地分解成几个生态分化的集群（也就是说，集群几乎和分离的集群一样多）；预测基因组内容的最强框架是营养策略，但没有一个框架能给出可靠的预测；以及以前未知的H-2氧化、基于变形紫红质的光养、基于黄嘌呤的光养和通过IC型核酮糖-1,5-二磷酸羧化酶/加氧酶（RuBisCO）固定二氧化碳的基因同源物，扩大了这种非常通用的细菌谱系中能量和碳获取的可能机制。ISME Journal (2010) 4,784 -798；doi: 10.1038 / ismej.2009.150;2010年1月14日在线发布
Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there will be challenges in assigning well-delineated ecological roles and biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat surprisingly, phylogenetic tree topology was not the best model for organizing genome characteristics or distribution patterns of individual genes/pathways, although it provided some predictive power. The lifestyle framework, established by grouping isolates according to evidence for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this lineage. The environment framework had a weak predictive power for the overall genome content of each strain, but explained the distribution of several individual genes/pathways, including those related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale geographical signal in some Roseobacter genes. The primary findings emerging from this comparative genome analysis are that members of the lineage cannot be easily collapsed into just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates); the strongest framework for predicting genome content is trophic strategy, but no single framework gives robust predictions; and previously unknown homologs to genes for H-2 oxidation, proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO2 fixation by Form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms for energy and carbon acquisition in this remarkably versatile bacterial lineage. The ISME Journal (2010) 4, 784-798; doi:10.1038/ismej.2009.150; published online 14 January 2010