Land Resources and Environmental Science, Montana State University, Bozeman, Montana, USA.
Appl Environ Microbiol. 2011 Feb;77(4):1359-67. doi: 10.1128/AEM.02032-10. Epub 2010 Dec 17.
Previous research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all ecologically distinct Synechococcus populations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the ecotype simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more putative ecotypes were predicted from variation in protein-encoding locus sequences than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, suggesting different adaptations to temperature or other parameters that vary along the flow channel.
先前的研究表明，16S rRNA 基因序列和 16S-23S rRNA 内部转录间隔区序列可能没有足够的遗传分辨率来定义栖息在碱性硅质温泉微生物垫中的所有生态独特的聚球藻种群（生态型）。为了获得更高的分子分辨率，我们研究了从蘑菇泉垫（怀俄明州黄石国家公园）的 60°C 和 65°C 位点通过 PCR 采样的三个蛋白编码基因座的序列变异。使用生态型模拟（ES）和 AdaptML 算法分析序列，以鉴定可能的生态型。与 16S rRNA 和 16S-23S rRNA 内部转录间隔区序列的变异相比，从蛋白编码基因座序列的变异中预测到的可能生态型的数量多 4 到 14 倍。预测的可能生态型的数量取决于采样的序列数量和基因座的分子分辨率。Chao 多样性估计表明，很少有稀有生态型被遗漏。序列分析假设的许多生态型在其栖息地特异性方面不同，这表明它们对温度或沿流道变化的其他参数有不同的适应。
