Diversity of Dissimilatory Sulfite Reductase Genes ( dsrAB ) in a Salt Marsh Impacted by Long-Term Acid Mine Drainage

Abstract

Sulfate-reducing bacteria (SRB) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. By implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. In this study, we combined DsrAB gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of SRB and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (AMD) for over 100 years. Recovered dsrAB sequences from three sites sampled along an AMD flow path indicated the dominance of a single Desulfovibrio species. Other major sequence clades were related most closely to Desulfosarcina, Desulfococcus, Desulfobulbus, and Desulfosporosinus species. The presence of metal sulfides with low ␦ 34 S values relative to ␦ 34 S values of pore water sulfate showed that sediment SRB populations were actively reducing sulfate under ambient conditions (pH of ϳ2), although possibly within less acidic microenvironments. Interestingly, ␦ 34 S values for pore water sulfate were lower than those for sulfate delivered during tidal inundation of marsh sediments. 16S rRNA gene sequence data from sediments and sulfur isotope data confirmed that sulfur-oxidizing bacteria drove the reoxidation of biogenic sulfide coupled to oxygen or nitrate reduction over a timescale of hours. Collectively, these findings imply a highly dynamic microbially mediated cycling of sulfate and sulfide, and thus the speciation and mobility of chalcophilic contaminant metal(loid)s, in AMD-impacted marsh sediments.Salt marshes exhibit high primary production rates (1, 101) and form biogeochemical "transition zones" for nutrient production, transport, and cycling between terrestrial and coastal marine environments (41, 66, 100). These zones also serve to reduce the flux of potentially toxic metals in contaminated groundwater to estuaries (12,99,106). Both functions depend strongly on microbial activity, especially that of sulfate-reducing bacteria (SRB) (42,62,67). SRB recycle much of the sedimentary organic carbon pool in marsh sediments (42-44) and indirectly inhibit production of the greenhouse gas methane (37, 71). They can restrict the mobility of dissolved contaminant metals by inducing precipitation of poorly soluble metal sulfides, and studies have examined their use in constructed wetlands to bioremediate acid mine drainage (AMD) and other metalliferous waste streams (11,35,40,46,50,76,90,94,104). However, the high acidity and metal concentrations inherent to AMD can inhibit SRB growth (15,88,98), and preferential growth of iron-and sulfur-oxidizing bacteria over SRB has been observed in some treatment wetlands (39).For natural salt marshes, 16S ribosomal nucleic acid-and phospholipid fatty acid (PLFA)-based analyses have shown that SRB commonly comprise a significant fraction of the microbial community (13,24,31,34,51,58). Studies of salt marsh dissimilatory sulfite reductase genes (dsrAB), a highly conserved functional phylogenetic marker of pro...

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…3.14.6 Acidophiles SRP have been repeatedly recognized as members of the microbial community thriving in acid mine drainage sediments with ambient conditions down to pH 2-3 (Giloteaux et al, 2013;Kock & Schippers, 2008;Martins et al, 2009;Moreau, Zierenberg, & Banfield, 2010;Sánchez-Andrea, Rodríguez, Amils, & Sanz, 2011). The moderately acidophilic D. acidiphilus was isolated from a mining site at Chessy-Les-Mines (Beaujolais, France) and was found to grow optimally at pH 5.2, with a lower limit at pH 3.6 (Alazard et al, 2010).…”

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

“…PCR amplification-based approaches have been used to study the abundance, diversity and composition of SRMs from different habitats [101][102][103][104][105][106] . However, highthroughput sequencing and associated metagenomic technologies, such as phylogenetic oligonucleotide arrays and functional gene arrays 107 , are more powerful for providing a comprehensive view of SRM diversity and sulphate reduction processes in natural environments 15,97,[108][109][110][111] .…”

Effects of Iron and Nitrogen Limitation on Sulfur Isotope Fractionation during Microbial Sulfate Reduction

“…Of the four stable isotopes of sulfur in nature ( 32 S, 33 S, 34 S, and 36 S), MSR preferentially utilizes lighter S-isotopes, producing sulfide that is depleted in heavy isotopes relative to the reactant sulfate. This isotope fractionation between sulfate and sulfide has been widely used to trace the biogeochemical cycling of sulfur and carbon (43,48). Numerous studies have characterized S-isotope fractionation in pure and mixed cultures of sulfate-reducing microbes, demonstrating a general correlation between sulfate reduction rates and the magnitude of S-isotope fractionation (6 and 62 and references therein).…”