Department of Marine Sciences, University of Georgia, Athens, GA 30602-3636, USA.
ISME J. 2010 Jun;4(6):784-98. doi: 10.1038/ismej.2009.150. Epub 2010 Jan 14.
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 CO(2) 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.
海洋玫瑰杆菌谱系的成员已被确认为生态广义主义者，这表明将明确的生态角色和生物地球化学功能分配给该分类群将具有挑战性。为了解决这个问题，对 32 个玫瑰杆菌分离物的基因组序列进行了分析，以使用三个预测框架（系统发育关系、生活方式策略和分离物的环境来源）研究基因组特征、基因库和单个基因/途径的分布模式。对于第一个框架，从 70 个保守的单拷贝基因的串联体中获得了一个包含五个深度分支枝的系统发育树。令人有些惊讶的是，尽管系统发育树拓扑结构为组织基因组特征或单个基因/途径的分布模式提供了一些预测能力，但它并不是最佳模型。根据异养、光异养或自养的证据对分离物进行分组而建立的生活方式框架，解释了该谱系中更多的基因库。环境框架对每个菌株的全基因组含量的预测能力较弱，但解释了几个单个基因/途径的分布，包括与磷获取、趋化作用和芳香化合物降解有关的基因。全球海洋取样宏基因组数据中的未组装序列独立地验证了一些玫瑰杆菌基因在全球范围内的地理信号。从比较基因组分析中得出的主要发现是，该谱系的成员不能轻易地归入少数几个具有明显生态差异的聚类（即，聚类的数量几乎与分离物的数量一样多）；预测基因组含量的最强框架是营养策略，但没有单一框架能给出可靠的预测；以前未知的与 H2 氧化、基于蛋白视紫红质的光养、基于黄嘌呤氧化酶的光养以及通过 Form IC 核酮糖-1,5-二磷酸羧化酶/加氧酶（RuBisCO）固定 CO2 的基因同源物扩展了这个非常通用的细菌谱系中能量和碳获取的可能机制。
