title: Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.
abstract: 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.
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
authors.forename: Dawn E
authors.initials: DE
authors.lastname: Holmes
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Nevin
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D027081:DNA Gyrase / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000737:chemistry / Q000302:isolation & purification; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D020564:Deltaproteobacteria / Q000145:classification* / Q000235:genetics*; D045287:Desulfuromonas / Q000145:classification; D005798:Genes, Bacterial; D020459:Genes, rRNA; D045302:Geobacter / Q000145:classification; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation / Q000235:genetics; D020653:Peptide Elongation Factor G / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D011938:Rec A Recombinases / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D020653:Peptide Elongation Factor G; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D011938:Rec A Recombinases; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D027081:DNA Gyrase