Bhaya Devaki, Grossman Arthur R, Steunou Anne-Soisig, Khuri Natalia, Cohan Frederick M, Hamamura Natsuko, Melendrez Melanie C, Bateson Mary M, Ward David M, Heidelberg John F
Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA.
ISME J. 2007 Dec;1(8):703-13. doi: 10.1038/ismej.2007.46. Epub 2007 Oct 25.
In microbial mat communities of Yellowstone hot springs, ribosomal RNA (rRNA) sequence diversity patterns indicate the presence of closely related bacterial populations along environmental gradients of temperature and light. To identify the functional bases for adaptation, we sequenced the genomes of two cyanobacterial (Synechococcus OS-A and OS-B') isolates representing ecologically distinct populations that dominate at different temperatures and are major primary producers in the mat. There was a marked lack of conserved large-scale gene order between the two Synechococcus genomes, indicative of extensive genomic rearrangements. Comparative genomic analyses showed that the isolates shared a large fraction of their gene content at high identity, yet, differences in phosphate and nitrogen utilization pathways indicated that they have adapted differentially to nutrient fluxes, possibly by the acquisition of genes by lateral gene transfer or their loss in certain populations. Comparisons of the Synechococcus genomes to metagenomic sequences derived from mats where these Synechococcus stains were originally isolated, revealed new facets of microbial diversity. First, Synechococcus populations at the lower temperature regions of the mat showed greater sequence diversity than those at high temperatures, consistent with a greater number of ecologically distinct populations at the lower temperature. Second, we found evidence of a specialized population that is apparently very closely related to Synechococcus OS-B', but contains genes that function in the uptake of reduced ferrous iron. In situ expression studies demonstrated that these genes are differentially expressed over the diel cycle, with highest expression when the mats are anoxic and iron may be in the reduced state. Genomic information from these mat-specific isolates and metagenomic information can be coupled to detect naturally occurring populations that are associated with different functionalities, not always represented by isolates, but which may nevertheless be important for niche partitioning and the establishment of microbial community structure.
在黄石温泉的微生物席群落中，核糖体RNA（rRNA）序列多样性模式表明，在温度和光照的环境梯度中存在密切相关的细菌种群。为了确定适应的功能基础，我们对两种蓝藻（聚球藻OS-A和OS-B'）分离株的基因组进行了测序，这两种分离株代表了生态上不同的种群，它们在不同温度下占主导地位，并且是微生物席中的主要初级生产者。两种聚球藻基因组之间明显缺乏保守的大规模基因顺序，这表明存在广泛的基因组重排。比较基因组分析表明，这些分离株在高同一性水平上共享了很大一部分基因内容，然而，磷酸盐和氮利用途径的差异表明它们对养分通量有不同的适应性，可能是通过横向基因转移获得基因或在某些种群中丢失基因。将聚球藻基因组与源自最初分离出这些聚球藻菌株的微生物席的宏基因组序列进行比较，揭示了微生物多样性的新方面。首先，微生物席低温区域的聚球藻种群比高温区域的种群表现出更大的序列多样性，这与低温下存在更多生态上不同的种群一致。其次，我们发现了一个特殊种群的证据，该种群显然与聚球藻OS-B'非常密切相关，但含有在还原亚铁铁摄取中起作用的基因。原位表达研究表明，这些基因在昼夜循环中差异表达，在微生物席缺氧且铁可能处于还原状态时表达最高。来自这些微生物席特异性分离株的基因组信息和宏基因组信息可以结合起来，以检测与不同功能相关的自然种群，这些功能并不总是由分离株代表，但对生态位划分和微生物群落结构的建立可能仍然很重要。
