Diversity of geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses

Abstract

The abundance, distribution, and phylogenetic diversity of members of the Fe(III)-reducing family Geobacteraceae were studied along a gradient of metal contaminants in Lake Coeur d'Alene, Idaho. Partial 16S rRNA gene fragments were amplified by PCR using primers directed toward conserved regions of the gene within the family Geobacteraceae. Analysis of amplicons separated by denaturing gradient gel electrophoresis (DGGE) suggested within-site variation was as great as between-site variation. Amplicons were cloned and grouped by RFLP type and DGGE migration distance and representatives were sequenced. Grouping clones with 3% or less sequence dissimilarity, 15 distinct phylotypes were identified compared to 16 distinct DGGE bands. Only 1 phylotype was recovered from all sites. This clone, B14, is most closely related to Geobacter metallireducens and constituted a greater portion of the pristine community than of the contaminated communities. A second phylotype, Q2, predominated in the contaminated communities and was notably absent from the pristine libraries. Clone Q2 presents a high degree of sequence similarity to two Geobacter spp. previously isolated from this region of Lake Coeur d'Alene. Six phylotypes were unique to the contaminated sediments, whereas two were found only in the pristine sediments. Indices of diversity (Shannon and Simpson) were consistently higher when calculated with DGGE data than when clone library data were used. Most-probable-number PCR and real-time PCR suggested that the Geobacteraceae phylotypes were spread relatively evenly across all three sites along the gradient. Our data indicate that the Geobacteraceae are diverse and abundant in Lake Coeur d'Alene sediments, regardless of metals content. These results provide insight into the ability of dissimilatory Fe(III)-reducing bacteria to colonize habitats with elevated metal concentrations, and they have important implications for the management and remediation of metal-contaminated sites.

Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths

“…Geobacter spp. have been found in metalpolluted freshwaters (Cummings et al, 2003) and detected in high numbers at sites treated for U(VI) remediation (Holmes et al, 2002;. The metabolic potential of iron-oxidizing and iron-reducing populations could have further implications on the stability of U(VI) immobilization as iron-oxidizing populations can potentially re-oxidize U(IV) and/or oxidize Fe(II) in a nitrate-dependent manner.…”

Wetland restoration and methanogenesis: the activity of microbial populations and competition for substrates at different temperatures

“…Fe-reducing bacteria form a polyphyletic functional group. While a PCR-assay directed against a functional gene common to all Fe-reducing bacteria is not available, the PCR-assay targeting the 16S rRNA gene covers a significant fraction of these organisms (Cummings et al, 2003). Geobacteraceae can use short-chain fatty acids, monoaromatic compounds, and hydrogen as electron donors (Lovley, 2000).…”

“…Only the primer set of Luton et al (2002) yielded sufficient PCR product. Partial 16S rRNA gene sequences of the ironreducing Geobacteraceae were amplified with Geo564F and Geo840R primers (Cummings et al, 2003). For denaturing gradient gel electrophoresis (DGGE) analysis of Geobacteraceae, a GC clamp was added to the 5 end of the Geo840R primer.…”

“…Geobacteraceae-targeting DGGE analysis was performed with a Bio-Rad system following the modified procedure of Cummings et al (2003). The PCR product was loaded onto 1-mm thick 7.5% (wt/vol) polyacrylamide gels containing a 30-60% linear denaturing gradient; 100% of denaturant was defined as 7 M urea and 40% formamide.…”

Developments in Bioremediation of Soils and Sediments Polluted with Metals and Radionuclides – 1. Microbial Processes and Mechanisms Affecting Bioremediation of Metal Contamination and Influencing Metal Toxicity and Transport

“…Both Fe(III)-and sulfate-reducing organisms are known to enzymatically reduce contaminant metals such as U(VI), Cr(VI), Co(III) and Tc(VII) in laboratory cultures (Lovley et al 1991;Lovley & Phillips 1992a, b;Gorby & Lovley 1992;Lovley 1993;Caccavo Jr. et al 1994;Gorby & Bolton 1998;Tebo & Obraztsova 1998; but for remediation purposes it is necessary to demonstrate that the appropriate microorganisms are present within the contaminated subsurface. Members of the Geobacteraceae (d-proteobacteria) are of particular note as these organisms have been identified as a dominant group within sediments upon the stimulation of Fe(III)-reducing conditions (Snoeyenbos-West et al 2000;Finneran et al 2002;Holmes et al 2002;Anderson et al 2003) and in contaminated sediment where Fe(III) reduction is a dominant process (Anderson et al 1998;Ro¨ling et al 2001;Cummings et al 2003). Geobacteraceae were also recently detected within the groundwater of an uraniumcontaminated aquifer during a test of stimulated in situ U(VI) reduction (Anderson et al 2003).…”