Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean
Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean
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DOI：
10.1111/j.1462-2920.2011.02555.x
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发表时间：
2012-01-01
影响因子：
5.1
通讯作者：
Amann, Rudolf
中科院分区：
文献类型：
--
作者：
Gomez-Pereira, Paola R.;Schueler, Margarete;Amann, Rudolf
拟杆菌广泛存在于海洋系统中，在有机物降解中发挥着至关重要的作用。几个菌株的全基因组分析揭示了广泛的糖酵解和蛋白水解潜力。在这项研究中，我们使用有针对性的宏基因组方法来研究来自北大西洋极地生物群落（BPLR）和北大西洋亚热带（NAST）两个对比区域的不同拟杆菌分支的降解能力。我们在此介绍了 76 种拟杆菌 fosmid 的分析，其中 28 种编码 16S rRNA 基因作为系统发育标记，以及它们与完整拟杆菌基因组的比较。几乎所有含有 fosmids 的 16S rRNA 都属于我们之前在 BPLR 和 NAST 中鉴定的进化枝。大多数测序的 fosmids 可以归属于隶属于黄杆菌纲的拟杆菌门。我们还提供了有关噬细胞菌和鞘氨醇杆菌类的新基因组信息，表明后者具有附着在藻类表面的能力。在我们的 fosmid 组中，我们发现富含浮游植物的 BPLR 具有更大的多糖降解和细胞表面附着潜力。特别是，两种黄细菌fosmids（一种属于Polaribacter属）显示出一整套酶，这些酶可能在降解已知为浮游植物细胞壁主要成分的硫酸多糖方面发挥作用。参与蛋白质和肽聚糖降解的基因虽然存在于两个 fosmid 组中，但似乎在 NAST 中略有优势。这项研究为海洋拟杆菌对某些类型聚合物的降解具有独特的专业化的假设提供了支持。
Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as phylogenetic marker, and their comparison to complete Bacteroidetes genomes. Almost all of the 16S rRNA harbouring fosmids belonged to clades that we previously identified in BPLR and NAST. The majority of sequenced fosmids could be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also present novel genomic information on the classes Cytophagia and Sphingobacteria, suggesting a capability of the latter for attachment to algal surfaces. In our fosmid set we identified a larger potential for polysaccharide degradation and cell surface attachment in the phytoplankton-rich BPLR. Particularly, two flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a whole armoury of enzymes that likely function in degradation of sulfated polysaccharides known to be major constituents of phytoplankton cell walls. Genes involved in protein and peptidoglycan degradation, although present in both fosmid sets, seemed to have a slight preponderance in NAST. This study provides support for the hypothesis of a distinct specialization among marine Bacteroidetes for the degradation of certain types of polymers.