Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.
Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.
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DOI：
10.1038/ismej.2016.198
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发表时间：
2017-06
期刊：
影响因子：
--
通讯作者：
Göker M
中科院分区：
文献类型：
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作者：
Simon M;Scheuner C;Meier-Kolthoff JP;Brinkhoff T;Wagner-Döbler I;Ulbrich M;Klenk HP;Schomburg D;Petersen J;Göker M
海洋红球藻科（Rhodoproteaceae，Alphaproteobacteria）是海洋地球化学循环的重要参与者，占海洋细菌群落的30%，是真核生物的共生菌。作为“蔷薇属分支”，这些“蔷薇杆菌”被认为是单系的，但非海洋杜鹃花科尚未被包括在基因组分析。因此，我们分析了106个基因组序列，特别强调基因采样及其对系统发育稳定性的影响，并调查了海洋与非海洋栖息地，进化起源和基因组适应之间的关系。我们的分析，roseobacters的单系性没有提供明确的证据，表明海洋和非海洋栖息地之间的几个转变，独立发生，并伴随着直系同源物，酶和代谢途径的基因组含量的特征变化。非海洋杜鹃花科获得了高亲和力的运输，以科普低得多的硫酸盐浓度和失去相关的基因减少氯化钠和有机卤素浓度在其栖息地。海洋杜鹃花科获得了岩藻依聚糖合成所需的基因，并合成了植物激素吲哚3-乙酸和相容性溶质依克多因和肉素。然而，无论是质粒组合物，即使是典型的家庭，也没有程度的寡营养海洋和非海洋杜鹃花科之间的系统差异。我们建议的操作术语'玫瑰组'的海洋杜鹃科菌株。
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As ‘Roseobacter clade', these ‘roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term ‘Roseobacter group' for the marine Rhodobacteraceae strains.