A drop of seawater contains numerous microspatial niches at the scale relevant to microbial activities. Examples are abiotic niches such as detrital particles that show different sizes and organic contents, and biotic niches resulting from bacteria–phage and bacteria–phytoplankton interactions. A common practice to investigate the impact of microenvironments on bacterial evolution is to separate the microenvironments physically and compare the bacterial inhabitants from each. It remains poorly understood, however, which microenvironment primarily drives bacterioplankton evolution in the pelagic ocean. By applying a dilution cultivation approach to an undisturbed coastal water sample, we isolate a bacterial population affiliated with the globally dominant Roseobacter group. Although varying at just a few thousand nucleotide sites across the whole genomes, members of this clonal population are diverging into two genetically separated subspecies. Genes underlying speciation are not unique to subspecies but instead clustered at the shared regions that represent ~6% of the genomic DNA. They are primarily involved in vitamin synthesis, motility, oxidative defense, carbohydrate, and amino acid utilization, consistent with the known strategies that roseobacters take to interact with phytoplankton and particles. Physiological assays corroborate that one subspecies outcompetes the other in these traits. Our results indicate that the microenvironments in the pelagic ocean represented by phytoplankton and organic particles are likely important niches that drive the cryptic speciation of the Roseobacter population, though microhabitats contributed by other less abundant pelagic hosts cannot be ruled out.

一滴海水包含许多与微生物活动相关的微空间生态位。例子是非生物生态位，例如显示不同大小和有机含量的碎屑颗粒，以及由细菌-噬菌体和细菌-浮游植物相互作用产生的生物生态位。研究微环境对细菌进化的影响的一种常见做法是在物理上分离微环境并比较每个微环境中的细菌居民。然而，人们仍然知之甚少，即哪种微环境主要驱动远洋海洋中的浮游细菌进化。通过对未受干扰的沿海水样应用稀释培养方法，我们分离出与全球占主导地位的玫瑰杆菌属相关的细菌种群团体。尽管在整个基因组中只有几千个核苷酸位点有所不同，但这个克隆种群的成员正在分化为两个基因分离的亚种。物种形成的基因不是亚种独有的，而是聚集在代表约 6% 基因组 DNA 的共享区域。它们主要参与维生素合成、运动、氧化防御、碳水化合物和氨基酸利用，这与玫瑰杆菌与浮游植物和颗粒相互作用的已知策略一致。生理分析证实，一个亚种在这些特征上胜过另一个亚种。我们的研究结果表明，以浮游植物和有机颗粒为代表的远洋海洋微环境可能是驱动海洋生物神秘物种形成的重要生态位。Roseobacter种群，尽管不能排除其他较不丰富的远洋宿主贡献的微生境。