Department of Molecular Ecology, Max-Planck-Institute for Marine Microbiology, D-28359 Bremen, Germany; Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), E-07190 Esporles, Balearic Islands, Spain.
Department of Molecular Ecology, Max-Planck-Institute for Marine Microbiology, D-28359 Bremen, Germany.
Syst Appl Microbiol. 2020 Mar;43(2):126065. doi: 10.1016/j.syapm.2020.126065. Epub 2020 Jan 27.
To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caaCOX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caaCOX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.
迄今为止，厚壁菌门包含了超过 1500 种具有不同生态作用的描述物种。然而，对于细菌门的典型特征在基因组水平上的了解甚少。在本研究中，我们编译了一组具有代表性的 89 个厚壁菌门基因组，并进行了两两最佳匹配基因比较和基因同线性分析，以鉴定允许厚壁菌门进化和适应性辐射的共同特征。所有研究的厚壁菌门都高度保守的存在着 9 型分泌系统（T9SS）。在纲水平的比较中进一步表明，ACIII-caaCOX 超级复合物是在有氧细菌的祖先谱系中进化而来的，并且在现存的无氧厚壁菌门中被二次丢失。另一个厚壁菌门特有的呼吸链适应是钠泵 Nqr 复合物 I，它取代了海洋物种中祖先的质子泵复合物 I。T9SS 在滑行运动和获取复杂的大分子有机化合物中发挥作用，而 ACIII-caaCOX 超级复合物允许在呼吸过程中有效控制电子通量。这种组合可能为原始厚壁菌门提供了一个决定性的竞争优势，有效地掠夺、吸收和降解复杂的有机分子，因此在该门成功的适应性辐射中发挥了关键作用。
