Nested PCR and New Primers for Analysis of Sulfate-Reducing Bacteria in Low-Cell-Biomass Environments

Giloteaux, Ludovic; Goñi-Urriza, Marisol; Duran, Robert

doi:10.1128/aem.02023-09

Cited by 45 publications

(30 citation statements)

References 52 publications

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“…The phylogenetic analysis of dsrAB sequences was performed as described in Giloteaux et al . (). Briefly, after databank query using the blast tools (Altschul et al ., ), ClustalX v1.83 (Thompson et al ., ) and proseq v2.9 (Filatov, ) software were used for alignments.…”

Section: Methodsmentioning

confidence: 97%

Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic

Giloteaux

Duran

Casiot

et al. 2012

FEMS Microbiol Ecol

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A 3-year survey on sulfate-reducing bacteria (SRB) was conducted in the waters of the arsenic-rich acid mine drainage (AMD) located at Carnoulès (France) to determine the influence of environmental parameters on their community structure. The source (S5 station) exhibited most extreme conditions with pH lowering to ~1.2; iron, sulfate, and arsenic concentrations reaching 6843, 29 593, and 638 mg L(-1), respectively. The conditions were less extreme at the downstream stations S1 (pH ~3.7; iron, sulfate, and arsenic concentrations of 1114, 4207, and 167 mg L(-1), respectively) and COWG (pH ~3.4; iron, sulfate, and arsenic concentrations of 854, 3134, and 110 mg L(-1), respectively). SRB community structures were characterized by terminal restriction fragment length polymorphism and library analyses based on dsrAB genes. The predominant dsrAB sequences detected were most similar to the family Desulfobulbaceae. Additionally, certain phylotypes could be related to spatio-temporal fluctuations of pH, iron, and arsenic species. For example, Desulfohalobiaceae-related sequences were detected at the most acidic sample (pH 1.4) with high iron and arsenic concentrations (6379 and 524 mg L(-1), respectively). New dsrAB sequences, with no isolated representatives, were found exclusively in COWG. This study gives new insights on SRB community dynamics in AMD systems.

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Section: Methodsmentioning

confidence: 97%

Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic

Giloteaux

Duran

Casiot

et al. 2012

FEMS Microbiol Ecol

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“…All evolutionary distances were computed with the Poisson correction method with 1000 bootstrap replicates. Homologous coverage calculations and rarefaction analyses of each library were performed as described previously (Giloteaux et al, 2010).…”

Section: Cell Number Estimates From Qpcr Resultsmentioning

confidence: 99%

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

et al. 2013

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The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uraniumcontaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a preypredator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.

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“…The confidence level of the phylogenetic tree topology was evaluated by performing 1000 bootstrap replications. Homologous coverage calculation and rarefaction analysis of each library was performed as previously described (Giloteaux et al, 2010).…”

Section: Methodsmentioning

confidence: 99%

Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation

et al. 2012

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The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the a-subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative reverse transcription-PCR. Most of the arrA (460%) and acr3-1 (490%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (450%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated the transcription of arrA in situ, even though the presence of As(V) increased the transcription of arrA in cultures of Geobacter lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.

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Nested PCR and New Primers for Analysis of Sulfate-Reducing Bacteria in Low-Cell-Biomass Environments

Cited by 45 publications

References 52 publications

Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic

Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation

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