Zheng Qiang, Liu Yanting, Jeanthon Christian, Zhang Rui, Lin Wenxin, Yao Jicheng, Jiao Nianzhi
State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China.
Appl Environ Microbiol. 2016 Nov 21;82(24):7205-7216. doi: 10.1128/AEM.02495-16. Print 2016 Dec 15.
Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus Citromicrobium, widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine Citromicrobium strains isolated from the South China Sea, the Mediterranean Sea, or the tropical South Atlantic Ocean were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs) involved mainly in type IV secretion systems, flagellar biosynthesis, prophage, and integrative conjugative elements, were identified by a fine-scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the coexistence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, to our knowledge, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for Citromicrobium members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, average nucleotide identity [ANI], single-nucleotide polymorphisms [SNPs], and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea versus Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences and allow microbes to evolve through local adaptation. Three Citromicrobium strains isolated from the Mediterranean Sea diverged millions of years ago from other strains and evolved into a novel group.
Aerobic anoxygenic phototrophic bacteria are a widespread functional group in the upper ocean, and their abundance could be up to 15% of the total heterotrophic bacteria. To date, a great number of studies display AAPB biogeographic distribution patterns in the ocean; however, little is understood about the geographic isolation impact on the genome divergence of marine AAPB. In this study, we compare nine Citromicrobium genomes of strains that have identical 16S rRNA sequences but different ocean origins. Our results reveal that strains isolated from the same marine region share a similar evolutionary history that is distinct from that of strains isolated from other regions. These Citromicrobium strains diverged millions of years ago. In addition, the coexistence of two different PGCs is prevalent in the analyzed genomes and in environmental samples.
需氧不产氧光合细菌（AAPB）被认为是海洋真光层碳和能量循环的重要参与者。广泛存在于贫营养海洋中的柠檬酸微菌属是海洋α-变形菌纲AAPB的一员。从南海、地中海或热带南大西洋分离出的9株柠檬酸微菌菌株具有相同的16S rRNA序列。它们的基因组测序显示主要区域具有高度共线性。通过精细比较基因组学分析，鉴定出9个主要参与IV型分泌系统、鞭毛生物合成、原噬菌体和整合性接合元件的基因岛（GI）。这些基因岛在基因组进化和分化中发挥了重要作用。有趣的是，不仅在所分析的基因组中发现了两种不同光合基因簇（PGC）的共存，据我们所知，这也是首次在环境样本中得到证实。两种不同PGC共存的普遍性可能表明柠檬酸微菌属成员在海洋中生存的一种适应机制。对基因组特征（如基因岛、平均核苷酸同一性[ANI]、单核苷酸多态性[SNP]和系统发育）的比较表明，同一海洋区域内的菌株具有相似的进化历史，这与从其他区域（南海与地中海）分离出的菌株不同。地理差异在一定程度上导致了观察到的基因组差异，并使微生物通过局部适应而进化。从地中海分离出的3株柠檬酸微菌菌株在数百万年前就与其他菌株分化，并进化成一个新的类群。
需氧不产氧光合细菌是海洋上层广泛存在的功能菌群，其丰度可达总异养细菌的15%。迄今为止，大量研究展示了需氧不产氧光合细菌在海洋中的生物地理分布模式；然而，对于地理隔离对海洋需氧不产氧光合细菌基因组分化的影响知之甚少。在本研究中，我们比较了9株具有相同16S rRNA序列但海洋来源不同的柠檬酸微菌基因组。我们的结果表明，从同一海洋区域分离出的菌株具有相似的进化历史，这与从其他区域分离出的菌株不同。这些柠檬酸微菌菌株在数百万年前就发生了分化。此外，在所分析的基因组和环境样本中，两种不同PGC的共存很普遍。
