University of California, Berkeley, CA 94720, USA.
Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2383-90. doi: 10.1073/pnas.0907041107. Epub 2010 Feb 2.
Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry-based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the approximately 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.
细菌种系概念存在争议。更广泛被接受的是，需要了解基因内容和序列的差异如何导致生态分歧。为了在生态系统背景下解决这种关系，我们调查了两种基因型的 Leptospirillum 组 II 细菌在全面表征的自然嗜酸生物膜群落中的基因型和生态学之间的联系。这些群体在 16S rRNA 基因序列上具有 99.7%的同一性，在直系同源物之间具有 95%的平均氨基酸同一性。一个基因型群体在早期定植时占优势，而另一个群体通常在后续的演替阶段增殖，形成直径数十到数百微米的明显斑块。在早期定植的种群中，我们观察到与晚期定植类型重组程度不同的五个基因型的优势。我们的分析表明，早期定植群体内的特定重组变体是由环境参数（如温度）选择的，这与重组作为生态微调的机制一致。进化特征以及通过基于质谱的蛋白质组学测量的菌株分辨表达模式表明，晚期定植者的钴胺素生物合成、（去）甲基化和甘氨酸裂解增加。这可能表明生物膜在发育过程中发生了环境变化，同时将来自渗透压保护剂的相容溶质重新定向到代谢中。在 27 个群落中，比较蛋白质基因组学分析表明，共享基因的差异调控和每个基因型特有的约 15%基因的一小部分的表达涉及生态位划分。总之，结果表明，微小的遗传变异如何导致不同的生态策略。
