Improved dsrA-based terminal restriction fragment length polymorphism analysis of sulfate-reducing bacteria

Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay

We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0–5 mm) and subsurface (5–10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0–10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment

Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H₂ oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with ¹³C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.

Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

Occurrence and activity of sulphate reducing bacteria in aerobic activated sludge systems

In the sewage or wastewater treatment plant, biological sulphate reduction can occur spontaneously or be applied beneficially for its treatment. The results of this study can be applied to control SRB in the sewage and WWTP. Therefore, population diversity analyses of SRB for nine activated sludge wastewater treatment plants (WWTP) in the Netherlands and the effect of long-term (months) oxygen exposures on the SRB activity were carried out. T-RFLP and clone sequencing analyses of winter and summer samples revealed that (1) all WWTP have a similar SRB population, (2) there is no seasonal impact (10-20 °C) on the SRB population present in the WWTP and (3) Desulfobacter postgatei, Desulfovibrio desulfuricans and Desulfovibrio intestinalis were the most common and dominant SRB species observed in these samples, and origin from the sewage. Short term activity tests demonstrated that SRB were not active in the aerobic WWTP, but while flushed with N2-gas SRB became slightly active after 3 h. In a laboratory reactor at a dissolved oxygen concentration of <2 %, sulphate reduction occurred and 89 % COD removal was achieved. SRB grew in granules, in order to protect themselves for oxygen exposures. SRB are naturally present in aerobic WWTP, which is due to the formation of granules.

Methylation of mercury in earthworms and the effect of mercury on the associated bacterial communities

Methylmercury compounds are very toxic for most organisms. Here, we investigated the potential of earthworms to methylate inorganic-Hg. We hypothesized that the anaerobic and nutrient-rich conditions in the digestive tracts of earthworm's promote the methylation of Hg through the action of their gut bacteria. Earthworms were either grown in sterile soils treated with an inorganic (HgCl₂) or organic (CH₃HgCl) Hg source, or were left untreated. After 30 days of incubation, the total-Hg and methyl-Hg concentrations in the soils, earthworms, and their casts were analyzed. The impact of Hg on the bacterial community compositions in earthworms was also studied. Tissue concentrations of methyl-Hg in earthworms grown in soils treated with inorganic-Hg were about six times higher than in earthworms grown in soils without Hg. Concentrations of methyl-Hg in the soils and earthworm casts remained at significantly lower levels suggesting that Hg was mainly methylated in the earthworms. Bacterial communities in earthworms were mostly affected by methyl-Hg treatment. Terminal-restriction fragments (T-RFs) affiliated to Firmicutes were sensitive to inorganic and methyl-Hg, whereas T-RFs related to Betaproteobacteria were tolerant to the Hg treatments. Sulphate-reducing bacteria were detected in earthworms but not in soils.

Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment

A novel sulfate-reducing bacterium, strain S28bFT, was isolated from tidal flat sediment from Tokyo Bay, Japan. Cells of strain S28bFT were rod-shaped (0.5–0.6×1.7–3.8 µm), motile and Gram-stain-negative. For growth, the optimum pH was pH 6.8–7.3 and the optimum temperature was 34–42 °C. Strain S28bFT used sulfate and thiosulfate as electron acceptors, but not nitrate. The G+C content of the genomic DNA was 56.6 mol%. The fatty acid profile of strain S28bFT was characterized by the presence of anteiso-C15 : 0 and C16 : 0 as the major components. Phylogenetic analyses based on genes for 16S rRNA, the alpha subunit of dissimilatory sulfite reductase (dsrA) and adenosine-5′-phosphosulfate reductase (aprA) revealed that the isolated strain belonged to the class Deltaproteobacteria . Its closest relative was Desulfosarcina cetonica DSM 7267T with a 16S rRNA gene sequence similarity of 93.3 %. Two other strains, S28OL1 and S28OL2 were also isolated from the same sediment. These strains were closely related to S28bFT with 16S rRNA gene sequence similarities of 99 %, and the same physiological characteristics were shared with strain S28bFT. On the basis of phylogenetic and phenotypic characterization, a novel species in a new genus, Desulfatitalea tepidiphila gen. nov., sp. nov., is proposed to accommodate the strains obtained in this study. The type strain is S28bFT ( = NBRC 107166T = DSM 23472T).

Microbial composition affects the functioning of estuarine sediments

Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whether variability in microbial composition affects functional processes in a field setting, by reciprocally transplanting riverbed sediments between low- and high-salinity locations along the Nonesuch River (Maine, USA). We placed the sediments into microbial 'cages' to prevent the migration of microorganisms, while allowing the sediments to experience the abiotic conditions of the surroundings. We performed two experiments, short- (1 week) and long-term (7 weeks) reciprocal transplants, after which we assayed a variety of functional processes in the cages. In both experiments, we examined the composition of bacteria generally (targeting the 16S rDNA gene) and sulfate-reducing bacteria (SRB) specifically (targeting the dsrAB gene) using terminal restriction fragment length polymorphism (T-RFLP). In the short-term experiment, sediment processes (CO2 production, CH4 flux, nitrification and enzyme activities) depended on both the sediment's origin (reflecting differences in microbial composition between salt and freshwater sediments) and the surrounding environment. In the long-term experiment, general bacterial composition (but not SRB composition) shifted in response to their new environment, and this composition was significantly correlated with sediment functioning. Further, sediment origin had a diminished effect, relative to the short-term experiment, on sediment processes. Overall, this study provides direct evidence that microbial composition directly affects functional processes in these sediments.

Isolation and characterization of novel sulfate-reducing bacterium capable of anaerobic degradation of p-xylene

A novel strain of p-xylene-degrading sulfate reducer was isolated in pure culture. Strain PP31 was obtained from a p-xylene-degrading enrichment culture established from polluted marine sediment. Analyses of the 16S rRNA gene and two functional genes involved in sulfate respiration and anaerobic degradation of aromatic compounds revealed that the isolate was closely related to members of the genus Desulfosarcina. Strain PP31 was capable of growing on p-xylene under sulfate-reducing conditions, and the ratio of generated sulfide and consumed p-xylene suggested complete oxidation by the novel isolate. The strain could not grow on benzene, toluene, ethylbenzene, m-xylene o-xylene, or n-hexane as an electron donor. Strain PP31 is the first isolated bacterium that degrades p-xylene anaerobically, and will be useful to understanding the mechanism of anaerobic degradation of p-xylene.