Zhao Jianshu, Pachiadaki Maria, Conrad Roth E, Hatt Janet K, Bristow Laura A, Rodriguez-R Luis M, Rossello-Mora Ramon, Stewart Frank J, Konstantinidis Konstantinos T
Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, United States.
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, United States.
ISME J. 2025 Jan 2;19(1). doi: 10.1093/ismejo/wraf072.
Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% average nucleotide identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83% and 95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes, and companion metagenomes from an oxygen minimum zone in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86% and 91%, with intra-species ANI ranging between 91% and 100%. Measuring recent gene exchange among these genomes based on a recently developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spread of adaptive mutations within the species (gene sweeps), further promoting the high intraspecies diversity observed. Collectively, these results implicate rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species.
对微生物群落（宏基因组学）或分离的基因组进行的调查揭示了序列离散的物种。也就是说，同一物种的成员之间共享基因的平均核苷酸同一性（ANI）>95%，而与其他物种成员的ANI<83%，而ANI在83%至95%之间的基因组对相对较少。在这些调查中，无处不在的SAR11进化枝（α-变形菌纲）的水生细菌是一个例外，它们通常不表现出离散的物种界限，这表明存在遗传分化的替代模式的可能性。为了探索SAR11的进化，我们分析了来自东热带太平洋低氧区的高质量单细胞扩增基因组和配套的宏基因组，在那里SAR11占微生物群落总数的约20%。我们的结果表明，SAR11确实形成了几个序列离散的物种，但其离散的ANI范围转移到了较低的同一性，即86%至91%之间，种内ANI范围在91%至100%之间。基于最近开发的方法测量这些基因组之间最近的基因交换，结果显示种内同源重组的频率高于种间，其对序列进化的影响至少是全基因组多样化点突变的两倍。与其他原核生物物种相比，SAR11中的重组似乎更为杂乱，这可能是由于参与错配修复的通用基因的缺失，并促进了适应性突变在物种内的传播（基因扫描），进一步促进了观察到的高种内多样性。总的来说，这些结果表明全基因组范围内猖獗的同源重组是不同SAR11物种凝聚的机制。
