Fu Xiaoteng, Gong Linfeng, Liu Yang, Lai Qiliang, Li Guangyu, Shao Zongze
Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.
Front Microbiol. 2021 May 7;12:571212. doi: 10.3389/fmicb.2021.571212. eCollection 2021.
Members of the group (abbreviated as the group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation.
Phylogenomic analysis revealed that the marine group strains were grouped into three species: , and . All the three share a common ancestor. However, members of were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair.
Our results indicated that the isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
该菌群（简称为该菌群）成员在海洋环境中种类繁多且分布广泛，但对其与陆地同类菌群的相关性了解甚少。在本研究中，我们对之前分离的16株海洋菌株进行了测序，并与总共52株该菌群菌株进行了比较基因组分析。分析包括20株海洋分离株（其中包括16株新菌株）和32株陆地分离株，以及它们的进化关系、分化和环境适应性。
系统基因组分析表明，海洋该菌群菌株分为三个物种：、和。这三个物种都有一个共同的祖先。然而，观察到的成员独立聚类，与其他两个物种分离，因此与其他物种不同。与翻译机制功能相关基因的普遍性一致，与翻译相关的基因在核心基因组中富集。功能基因组分析表明，海洋来源菌株和陆地菌株在某些假设蛋白、转录调节因子、钾转运蛋白（TrK）和ABC转运蛋白方面存在差异。然而，物种差异显示环境适应性差异占主导地位。在每个物种中，都发现了具有可能促进在不同陆地生态位中生存功能的陆地特异性基因，而海洋细菌则富含功能未知的基因以及与转录、噬菌体防御、DNA重组和修复相关的基因。
我们的结果表明，该菌群分离株即使共享一个共同核心，也表现出明显的基因组特征。海洋和陆地分离株并非独立进化；海洋和非海洋栖息地之间的转变可能发生过多次。该谱系在驱动其扩散方面对生态位具有优先效应。某些种内生态位特异性基因可能与菌株对其各自海洋或陆地环境的适应性有关。总之，本报告描述了52株该菌群菌株的系统进化，将有助于未来研究了解它们的生态作用以及对海洋和/或陆地环境的适应性。
