Enrichment of Members of the Family Geobacteraceae Associated with Stimulation of Dissimilatory Metal Reduction in Uranium-Contaminated Aquifer Sediments

Abstract

Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)-and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetateamended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.

Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.

“…It is likely that the influx of organic carbon into these otherwise nutrient-poor subsurface environments resulted in a limitation of fixed nitrogen relative to the availability of carbon substrates. In a similar manner, geobacteraceae became the predominant dissimilatory metalreducing micro-organisms when acetate, but no fixed nitrogen, was added to uranium-contaminated subsurface sediments to promote the reductive precipitation of uranium (Anderson et al, 2003;Holmes et al, 2002). The results suggest that the ability to adapt to such nitrogenlimited environments is typically found in geobacteraceae.…”

“…Although a wide diversity of bacteria and archaea are capable of dissimilatory Fe(III) reduction (Lovley, 2000a, b), most of these organisms do not appear to be important in Fe(III) reduction in typical subsurface environments, which are at circumneutral pH, freshwater or marine salinities and temperatures of about 10-20 u C. This finding, coupled with the fact that it is possible to recover geobacteraceae in culture, provides the rare potential opportunity to apply knowledge gained from pure culture physiology studies to the subsurface. Furthermore, the finding that geobacteraceae can account for about 40-90 % of the total microbial community under Fe(III)-reducing conditions in some subsurface environments (Anderson et al, 2003;Holmes et al, 2002) suggests that subsurface Fe(III)-reducing communities may provide the type of low-diversity community that is most amenable to environmental genomics studies. This is also true for the surface of electrodes harvesting energy from aquatic sediments, in which geobacteraceae typically comprise about half of the microbial community Holmes et al, 2004;Tender et al, 2002).…”

“…nov. are the predominant Fe(III)-reducing microorganisms in a diversity of subsurface environments in which Fe(III) reduction is important (Anderson et al, 2003;Holmes et al, 2002;Roling et al, 2001;Snoeyenbos-West et al, 2000;Stein et al, 2001). Although a wide diversity of bacteria and archaea are capable of dissimilatory Fe(III) reduction (Lovley, 2000a, b), most of these organisms do not appear to be important in Fe(III) reduction in typical subsurface environments, which are at circumneutral pH, freshwater or marine salinities and temperatures of about 10-20 u C. This finding, coupled with the fact that it is possible to recover geobacteraceae in culture, provides the rare potential opportunity to apply knowledge gained from pure culture physiology studies to the subsurface.…”

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).…”

16S rRNA Gene Microarray Analysis of Microbial Communities in Ethanol-Stimulated Subsurface Sediment

“…Information on the status of microbial communities involved in U(VI) reduction and other electron-accepting pathways is important to understand the spatial/temporal dynamics and overall efficacy of in situ uranium bioremediation (1). Although 16S rRNA clone libraries and/or microarrays have been applied to various U(VI) reduction systems (2,4,7,17,28,29,40,41,44), knowledge remains scant of the quantitative coverage of these techniques, particularly in situations where multiple groups of organisms are active.…”