Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden

The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were diluted and treated by mild sonication. A 10-ml aliquot of a 1:40 dilution was filtered onto a 0.2-mm-pore-size type GTTP polycarbonate filter (Millipore, Eschborn, Germany). Hybridization and microscopic counting of hybridized and 49,69-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Details of probes and formamide concentrations which were used are listed in futher details.. Means were calculated by using 10 to 20 randomly chosen fields for each filter section, which corresponded to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with probe NON338. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected.

A preliminary characterization of mercury uptake by the sulfate-reducing bacteria Desulfovibrio desulfuricans

The focus of this research is to determine if a relationship exists between the stability constant and the initial uptake rate of a mercury species by bacteria. Cultures of the sulfate-reducing bacteria (SRB) strain Desulfovibrio desulfuricans G20 were washed with a bicarbonate buffer solution containing either lactate and sulfate or pyruvate and fumarate. The washed cell solutions were then spiked with either mercury bound to natural organic matter (Hg-NOM) or neutral mercury chloride (HgCl2), followed by sampling over time to provide kinetic data. Despite the significantly different stability constants for Hg-NOM and HgCl2, the calculated initial rate constants for mercury uptake for these two types of complexes appeared to be comparable. Uptake of mercury sulfide species was inconclusive due to possible formation of cinnabar. A simple model that is based on assumptions of passive diffusion and facilitated uptake of mercury by bacteria was evaluated for its potential to simulate the uptake. The model results only agreed with experimental data for HgCl2 uptake.

Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments

The distribution and activity of communities of sulfate-reducing bacteria (SRB) and methanogenic archaea in two contrasting Antarctic sediments were investigated. Methanogenesis dominated in freshwater Lake Heywood, while sulfate reduction dominated in marine Shallow Bay. Slurry experiments indicated that 90% of the methanogenesis in Lake Heywood was acetoclastic. This finding was supported by the limited diversity of clones detected in a Lake Heywood archaeal clone library, in which most clones were closely related to the obligate acetate-utilizing Methanosaeta concilii. The Shallow Bay archaeal clone library contained clones related to the C-1-utilizing Methanolobus and Methanococcoides and the H-2-utilizing Methanogenium. Oligonucleotide probing of RNA extracted directly from sediment indicated that archaea represented 34% of the total prokaryotic signal in Lake Heywood and that Methanosaeta was a major component (13.2%) of this signal. Archaea represented only 0.2% of the total prokaryotic signal in RNA extracted from Shallow Bay sediments. In the Shallow Bay bacterial clone library, 10.3% of the clones were SRB-like, related to Desulfotalea/Desulforhopalus, Desulfofaba, Desulfosarcina, and Desulfobacter as well as to the sulfur and metal oxidizers comprising the Desulfuromonas cluster. Oligonucleotide probes for specific SRB clusters indicated that SRB represented 14.7% of the total prokaryotic signal, with Desulfotalea/Desulforhopalus being the dominant SRB group (10.7% of the total prokaryotic signal) in the Shallow Bay sediments; these results support previous results obtained for Arctic sediments. Methanosaeta and Desulfotalea/Desulforhopalus appear to be important in Lake Heywood and Shallow Bay, respectively, and may be globally important in permanently low-temperature sediments.

Real-time PCR quantification and diversity analysis of the functional genes aprA and dsrA of sulfate-reducing prokaryotes in marine sediments of the Peru continental margin and the Black Sea

Sulfate-reducing prokaryotes (SRP) are ubiquitous and quantitatively important members in many ecosystems, especially in marine sediments. However their abundance and diversity in subsurface marine sediments is poorly understood. In this study, the abundance and diversity of the functional genes for the enzymes adenosine 5'-phosphosulfate reductase (aprA) and dissimilatory sulfite reductase (dsrA) of SRP in marine sediments of the Peru continental margin and the Black Sea were analyzed, including samples from the deep biosphere (ODP site 1227). For aprA quantification a Q-PCR assay was designed and evaluated. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 10(8)/g sediment close to the sediment surface to less than 10(5)/g sediment at 5 mbsf. The 16S rRNA gene copy numbers of total bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRP to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5-1% of the 16S rRNA gene copy numbers of total bacteria in the sediments up to a depth of ca. 40 mbsf. In the zone without detectable sulfate in the pore water from about 40-121 mbsf (Peru margin ODP site 1227), only dsrA (but not aprA) was detected with copy numbers of less than 10(4)/g sediment, comprising ca. 14% of the 16S rRNA gene copy numbers of total bacteria. In this zone, sulfate might be provided for SRP by anaerobic sulfide oxidation. Clone libraries of aprA showed that all isolated sequences originate from SRP showing a close relationship to aprA of characterized species or form a new cluster with only distant relation to aprA of isolated SRP. For dsrA a high diversity was detected, even up to 121 m sediment depth in the deep biosphere.

Controls on suppression of methane flux from a peat bog subjected to simulated acid rain sulfate deposition

The effect of acid rain SO42− deposition on peatland CH4 emissions was examined by manipulating SO42− inputs to a pristine raised peat bog in northern Scotland. Weekly pulses of dissolved Na2SO4 were applied to the bog over two years in doses of 25, 50, and 100 kg S ha−1 yr−1, reflecting the range of pollutant S deposition loads experienced in acid rain-impacted regions of the world. CH4 fluxes were measured at regular intervals using a static chamber/gas chromatographic flame ionization detector method. Total emissions of CH4 were reduced by between 21 and 42% relative to controls, although no significant differences were observed between treatments. Estimated total annual fluxes during the second year of the experiment were 16.6 g m−2 from the controls and (in order of increasing SO42− dose size) 10.7, 13.2, and 9.8 g m−2 from the three SO42− treatments, respectively. The relative extent of CH4 flux suppression varied with changes in both peat temperature and peat water table with the largest suppression during cool periods and episodes of falling water table. Our findings suggest that low doses of SO42− at deposition rates commonly experienced in areas impacted by acid rain, may significantly affect CH4 emissions from wetlands in affected areas. We propose that SO42− from acid rain can stimulate sulfate-reducing bacteria into a population capable of outcompeting methanogens for substrates. We further propose that this microbially mediated interaction may have a significant current and future effect on the contribution of northern peatlands to the global methane budget.