Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.
Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.
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DOI：
10.1099/ijs.0.02958-0
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发表时间：
2004-09-01
影响因子：
2.8
通讯作者：
Lovley, DR
中科院分区：
文献类型：
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作者：
Holmes, DE;Nevin, KP;Lovley, DR
除了16S rRNA基因，5个保守基因的序列进行了研究，在30个成员的土杆菌科。所有成员的Geobacteraceae检查含有nifD，这表明他们能够固氮，这可以解释他们的竞争能力，有效地在氮贫地下环境进行石油或金属污染的补救。根据rpoB、gyrB、fusA、recA和nifD基因序列预测的基因型与根据16SrRNA基因序列预测的基因型基本一致。此外，从所有5个蛋白质编码基因构建的多联体的系统发育分析与16S rRNA基因为基础的同源性密切相关。这项研究表明，Geobacteraceae是变形菌门的δ亚类中的一个遗传上连贯的家族，由三个不同的系统发育簇组成：Geobacterium，Desulfuronas和Desulfuromusa。这里提供的序列数据将使得有可能更好地区分地质杆菌科的生理上不同的成员，如丙酸粪杆菌和地芽孢杆菌属物种，在地质杆菌科为主的微生物群落，并大大扩展了潜在的识别地质杆菌科序列的环境基因组DNA库。
The sequences of five conserved genes, in addition to the 16S rRNA gene, were investigated in 30 members of the Geobacteraceae fam. nov. All members of the Geobacteraceae examined contained nifD, suggesting that they are capable of nitrogen fixation, which may explain their ability to compete effectively in nitrogen-poor subsurface environments undergoing remediation for petroleum or metal contamination. The phylogenies predicted from rpoB, gyrB, fusA, recA and nifD were generally in agreement with the phylogeny predicted from 16S rRNA gene sequences. Furthermore, phylogenetic analysis of concatemers constructed from all five protein-coding genes corresponded closely with the 16S rRNA gene-based phylogeny. This study demonstrated that the Geobacteraceae is a phylogenetically coherent family within the delta-subclass of the Proteobacteria that is composed of three distinct phylogenetic clusters: Geobacter, Desulfuromonas and Desulfuromusa. The sequence data provided here will make it possible to discriminate better between physiologically distinct members of the Geobacteraceae, such as Pelobacter propionicus and Geobacter species, in geobacteraceae-dominated microbial communities and greatly expands the potential to identify geobacteraceae sequences in libraries of environmental genomic DNA.