Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues
Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues
复制标题
DOI：
10.1002/mlf2.12088
复制
发表时间：
2023-12
期刊：
影响因子：
--
通讯作者：
K. Konstantinidis
中科院分区：
文献类型：
--
作者：
K. Konstantinidis
抽象的原核生物和其他微生物是否形成可以被认为是物种的不同簇，这是最重要的理论和实际结果，以及在过去十年中识别，调节，调节和交流这些生物的问题，可以比较成千上万的Metagenomes的基因组。的生物但是，识别出的簇之间的中间相关性也经常发现，但是，后者的“中间”生物显示出足够的生态和/或功能独特性，可以被认为是不同的物种。相似的病毒和微生物真核生物的多样性模式也意味着在群集的维持下，这是一个特定的机械过程，这是基础机制的实质性降低。多样性可能是由于生态学分化而导致的，这可能是基因转移的障碍。
Abstract Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence‐discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter “intermediate” organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often—but not always—appears to be around 85%–95% genome‐average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.