Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
ISME J. 2023 Jun;17(6):813-822. doi: 10.1038/s41396-023-01390-4. Epub 2023 Mar 4.
Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species' divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species' pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.
鉴定细菌物种进化和维持基因组多样性的机制对于主导海洋表面的未培养谱系来说特别具有挑战性。对沿海浮游植物繁殖期间细菌基因、基因组和转录本进行的纵向分析揭示了两个共生的、高度相关的红杆菌科物种，它们来自分支很深且尚未培养的 NAC11-7 谱系。这些物种具有相同的 16S rRNA 基因扩增子序列，但从宏基因组和单细胞中组装的基因组内容表明存在种间差异。此外，在 7 周的动态繁殖条件下，物种相对优势的变化证实了这两个同域物种在同一时间对同一微环境的不同反应。每个物种特有的基因和在每个细胞的 mRNA 库存中共享但有差异的基因占物种全基因组内容的 5%。这些分析揭示了区分物种的生理和生态特征，包括有机碳利用能力、细胞表面特性、金属需求和维生素生物合成。这种对高度相关且生态相似的细菌物种在其共同自然栖息地中共存的深入了解很少见。
