Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel lake, Azerbaijan

The distribution and activity of sulfate-reducing bacteria (SRB) in the water column of the alpine meromictic Gek-Gel lake were studied. Apart from traditional microbiological methods based on cultivation and on measuring the process rates with radioactive labels, in situ fluorescent hybridization (FISH) was used, which enables identification and quantification without cultivating organisms. The peak rate of sulfate reduction, 0.486 μg S 1⁻¹ day⁻¹, was found in the chemocline at 33 m. The peak SRB number of 2.5×10⁶ cells/ml, as determined by the most probable number method on selective media, was found at the same depth. The phylogenetic affiliation of the SRB, as determined by FISH, revealed the predominance of the Desulfovibrio spp., Desulfobulbus spp., and Desulfoarculus spp./Desulfomonile spp. groups. The numbers of spore-forming Desulfotomaculum spp. increased with depth. The low measured rates of sulfate reduction accompanied by high SRB numbers and the predominance of the groups capable of reducing a wide range of substrates permit us to assume utilization of electron acceptors other than sulfate as the main activity of the SRB in the water column. Original Russian Text ? O.V. Karnachuk, N.V. Pimenov, S.K. Yusupov, Yu.A. Frank, Ya.A. Puhakka, M.V. Ivanov, 2006, published in Mikrobiologiya, 2006, Vol. 75, No. 1, pp. 101–109.     

Anoxygenic phototrophic bacteria of the high-altitude meromictic Lake Gek-Gel,Azerbaijan

The anoxygenic phototrophic bacterial community of the high-altitude meromictic Lake Gek-Gel (Azerbaijan) was investigated in September 2003. The highest concentration of bacteriochlorophyll e (48 μg/l) was detected at a depth of 30 m; the peak of bacteriochlorophyll a (4.5 μg/l) occurred at 29 m. Phylogenetic analysis revealed that brown-colored green sulfur bacteria Chlorobium phaeobacteroides predominated in the lake. Nonsulfur purple bacteria phylogenetically close to Blastochloris sulfoviridis were found in insignificant amounts; these organisms have not been previously reported in Lake Gek-Gel.     

Methane formation and oxidation in the meromictic oligotrophic Lake Gek-Gel (Azerbaijan)

The production and oxidation of methane and diversity of culturable aerobic methanotrophic bacteria in the water column and upper sediments of the meromictic oligotrophic Lake Gek-Gel (Azerbaijan) were studied by radioisotope, molecular, and microbiological techniques. The rate of methane oxidation was low in the aerobic mixolimnion, increased in the chemocline, and peaked at the depth where oxygen was detected in the water column. Aerobic methanotrophic bacteria of type II belonging to the genus Methylocystis were identified in enrichment cultures obtained from the chemocline. Methane oxidation in the anaerobic water of the monimolimnion was much more intense than in the aerobic zone. However, below 29–30 m methane concentration increased and reached 68 μM at the bottom. The highest rate of methane oxidation under anaerobic conditions was revealed in the upper layer of bottom sediments. The rate of methane oxidation significantly exceeding that of methane production suggests a deep source of methane in this lake.     

Inorganic carbon fixation by sulfate-reducing bacteria in the Black Sea water column

The Black Sea is the largest anoxic water basin on Earth and its stratified water column comprises an upper oxic, middle suboxic and a lower permanently anoxic, sulfidic zone. The abundance of sulfate-reducing bacteria (SRB) in water samples was determined by quantifying the copy number of the dsrA gene coding for the alpha subunit of the dissimilatory (bi)sulfite reductase using real-time polymerase chain reaction. The dsrA gene was detected throughout the whole suboxic and anoxic zones. The maximum dsrA copy numbers were 5 x 10(2) and 6.3 x 10(2) copies ml(-1) at 95 m in the suboxic and at 150 m in the upper anoxic zone, respectively. The proportion of SRB to total Bacteria was 0.1% in the oxic, 0.8-1.9% in the suboxic and 1.2-4.7% in the anoxic zone. A phylogenetic analysis of 16S rDNA clones showed that most clones from the anoxic zone formed a coherent cluster within the Desulfonema-Desulfosarcina group. A similar depth profile as for dsrA copy numbers was obtained for the concentration of non-isoprenoidal dialkyl glycerol diethers (DGDs), which are most likely SRB-specific lipid biomarkers. Three different DGDs were found to be major components of the total lipid fractions from the anoxic zone. The DGDs were depleted in (13)C relative to the delta(13)C values of dissolved CO(2) (delta(13)C(CO2)) by 14-19 per thousand. Their delta(13)C values [delta(13)C(DGD(II-III))] co-varied with depth showing the least (13)C-depleted values in the top of the sulfidic, anoxic zone and the most (13)C-depleted values in the deep anoxic waters at 1500 m. This co-variation provides evidence for CO(2) incorporation by the DGD(II-III)-producing SRB, while the 1:2 relationship between delta(13)C(CO2) and delta(13)C(DGD(II-III)) indicates the use of an additional organic carbon source.     

Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO(4)(2-) reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day(-1) for sulfate reduction and from 0.13 to 0.60 day(-1) for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.     

Antigenic diversity of cytochromes c3 from the anaerobic,sulfate-reducing bacteria,Desulfovibrio

An indirect enzyme-linked immunoadsorption assay (ELISA) was developed for cytochrome c₃ using antisera to the cytochromes fromDesulfovibrio africanus Benghazi, Desulfovibrio vulgaris Hildenborough andDesulfovibrio salexigens British Guiana. The ELISA system was used to test for cross-reactions between these antisera and the heterologous antigens. In contrast to previous experiments using the Ouchterlony technique, all of the cytochromes c₃ tested exhibited some degree of cross-reaction. Considerable variation was seen in cross-reactions for cytochromes c₃ from differing strains ofD. desulfuricans. This observation raises questions about the taxonomic relatedness of these strains. No cross-reaction was seen with eukaryotic cytochrome c or withD. vulgaris cytochrome c₅₅₃. The data demonstrate that cytochrome c₃ is capable of undergoing nonprecipitating cross-reactions, and thus may not be as immunologically unique as was once thought.Abbreviations ELISA Enzyme-linked immunoadsorption assay     

Comparison of the diversity of sulfate-reducing bacterial communities in the water column and the surface sediments of a Japanese meromictic lake

The diversity and abundance of sulfate-reducing bacteria (SRB) were investigated in Lake Suigetsu, a meromictic lake in Japan characterized by a permanent oxycline at a depth between 3 and 8 m separating the aerobic freshwater epilimnion from the anaerobic, saline, sulfidogenic hypolimnion. A quantitative competitive PCR targeting the gene coding for a portion of the α-subunit of dissimilatory sulfite reductase (dsrA) was used to assess the distribution of the SRB in the stratified water column and the surface sediments. The diversity of the SRB communities was assessed using a sequence analysis of the differing dsrA isomers. The dsrA gene copy numbers of SRB in the hypolimnic waters were from 9.6 × 10³ to 7.5 × 10⁵ copies ml⁻¹, whereas higher dsrA copy numbers of SRB were observed in surface sediments, ranging from 1.8–8.1 × 10⁷ copies ml⁻¹ as estimated by competitive PCR. Phylogenetic analysis of the dsrA sequences retrieved from the surface sediments shows most belong to a deeply branching lineage of diverse dsrA sequences not related to any cultured SRB group. In contrast, dsrA sequences found in the oxycline waters were related to sequences of members of the genera Desulfonema, Desulfosarcina, and Dusulfococcus and to sequences of the incomplete oxidizers from the Desulfobulbaceae family. Diversity and abundance of dsrA genes significantly differed between the samples from the oxycline waters and the surface sediments of Lake Suigetsu, indicating habitat-specific SRB communities may contribute to the biogeochemical cycling of carbon and sulfur.     

Diversity and distribution of sulfate-reducing bacteria in permanently frozen Lake Fryxell, McMurdo Dry Valleys, Antarctica

The permanently frozen freshwater Lake Fryxell, located in the Dry Valleys of Antarctica, exhibits an ideal geochemistry for microbial sulfate reduction. To investigate the population of sulfate-reducing bacteria in Lake Fryxell, both 16S rRNA gene and metabolic primer sets targeting the dsrA gene for the dissimilatory sulfite reductase alpha subunit were employed to analyze environmental DNA obtained from the water column and sediments of Lake Fryxell. In addition, enrichment cultures of sulfate-reducing bacteria established at 4 degrees C from Lake Fryxell water were also screened using the dsrA primer set. The sequence information obtained showed that a diverse group of sulfate-reducing prokaryotes of the domain Bacteria inhabit Lake Fryxell. With one exception, the enrichment culture sequences were not represented within the environmental sequences. Sequence data were compared with the geochemical profile of Lake Fryxell to identify possible connections between the diversity of sulfate-reducing bacteria and limnological conditions. Several clone groups were highly localized with respect to lake depth and, therefore, experienced specific physiochemical conditions. However, all sulfate-reducing bacteria inhabiting Lake Fryxell must function under the constantly cold conditions characteristic of this extreme environment.     

Distribution, diversity and ecology of aerobic CO-oxidizing bacteria

Numerous studies indicate that carbon monoxide (CO) participates in a broader range of processes than any other single molecule, ranging from subcellular to planetary scales. Despite its toxicity to many organisms, a diverse group of bacteria that span multiple phylogenetic lineages metabolize CO. These bacteria are globally distributed and include pathogens, plant symbionts and biogeochemically important lineages in soils and the oceans. New molecular and isolation techniques, as well as genome sequencing, have greatly expanded our knowledge of the diversity of CO oxidizers. Here, we present a newly emerging picture of the distribution, diversity and ecology of aerobic CO-oxidizing bacteria.     

Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats

This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin. Dissimilatory (bi)sulfite reductase gene sequences (dsrAB) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State. A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis. The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems. Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones. Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class Proteobacteria (Desulfobulbus propionicus, Desulfosarcina variabilis) and the Bacillus-Clostridium (Desulfotomaculum putei) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison. This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability.     

Phytoplankton dynamics in the stratified water column of Lake Bonney,Antarctica

Phytoplankton populations in perennially ice-covered Lake Bonney, Antarctica grow in a unique non-turbulent environment. The absence of turbulence generated by winds or major streams, combined with strong vertical gradients in temperature and nutrients, create vertically stratified environmental conditions that support three discrete phytoplankton populations in the east lobe of this lake. Phytoplankton biomass and photosynthesis were measured in the east lobe of Lake Bonney during the winter-spring transicion (September) to mid-summer (January). During this period, irradiance beneath the ice increased from 0.03 to 1.9 mol quanta m⁻² d⁻¹. Chlorophylla concentrations ranged from 0.03 to 3.8 μl⁻¹ within the trophogenic zone (just beneath the permanent ice cover to 20 m) and photosynthesis ranged from below detection to 3.2 μg Cl⁻¹ d⁻¹. Our results indicate: (1) phytoplankton photosynthesis began in late winter (before 9 September, our earliest sampling date); (2) maxima for phytoplankton biomass and production developed sequentially in time from the top to the bottom of the trophogenic zone, following the seasoral increase in irradiance; and (3) the highest photosynthetic efficiencies occurred in early spring, then decreased over the remainder of the phytoplankton growth season. The spring decrease in photosynthetic rates for shallower phytoplankton appeared to be related to nutrient availability, while photosynthesis in the deeper populations was solely lightdependent.     

Sulfur cycling in the water column of Little Rock Lake, Wisconsin

The S cycle in the water column of a small, soft-water lake was studied for 9 years as part of an experimental study of the effects of acid rain on lakes. The two basins of the lake were artificially separated, and one basin was experimentally acidified with sulfuric acid while the other served as a reference or control. Spatial and seasonal patterns of sulfate uptake by plankton (53–70 mmol m^–2 yr^–1), deposition of sulfur to sediments in settling seston (53 mmol m^–2 yr^–1), and sulfate diffusion (0–39 mmol m^–2 yr^–1) into sediments were examined. Measurements of inputs (12–108 mmol m^–2 yr^–1) and outputs (5.5–25 mmol m^–2 yr^–1) allowed construction of a mass balance that was then compared with rates of S accumulation in sediments cores (10–28 mmol m^–2 yr^–1) and measured fluxes of S into the sediments. Because of the low SO₄ ^2– concentrations (µmole L^–1) in the lake, annual uptake by plankton (53–70 mmol m^–2 yr^–1) represented a large fraction (>50%) of the SO₄ ^2– inventory in the lake. Despite this large flux through the plankton, only small seasonal fluctuations in SO₄ ^2– concentrations (µmole L^–1) were observed; rapid mineralization of organic matter (half-life <3 months) prevented sulfate depletion in the water column. The turnover time for sulfate in the water column is only 1.4 yr; much less than the 11-yr turnover time of a conservative ion in this seepage lake. Sulfate diffusion into and reduction in the sediments (0–160 µmole m^–2 d^–1) caused SO₄ ^2– depletion in the hypolimnion. Modeling of seasonal changes in lake-water SO₄ ^2– concentrations indicated that only 30–50% of the diffusive flux of sulfate to the sediments was permanently incorporated in solid phases, and about 15% of sulfur in settling seston was buried in the sediments. The utility of sulfur mass balances for seepage lakes would be enhanced if uncertainty about the deposition velocity for both sulfate aerosols and SO₂, uncertainty in calculation of a lake-wide rate of S accumulation in sediments, and uncertainty in the measured diffusive fluxes could be further constrained.     

Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno,Switzerland

Primary production in the meromictic Lake Cadagno, Switzerland, is dominated by anoxygenic photosynthesis. The green sulfur bacterium Chlorobium clathratiforme is the dominant phototrophic organism in the lake, comprising more than half of the bacterial population, and its biomass increases 3.8‐fold over the summer. Cells from four positions in the water column were used for comparative analysis of the Chl. clathratiforme proteome in order to investigate changes in protein composition in response to the chemical and physical gradient in their environment, with special focus on how the bacteria survive in the dark. Although metagenomic data are not available for Lake Cadagno, proteome analysis was possible based on the completely sequenced genome of an isolated strain of Chl. clathratiforme. Using LC‐MS/MS we identified 1321 Chl. clathratiforme proteins in Lake Cadagno and quantitatively compared 621 of these in the four samples. Our results showed that compared with cells obtained from the photic zone, cells collected from the dark part of the water column had the same expression level of key enzymes involved in carbon metabolism and photosynthetic light harvesting. However, most proteins participating in nitrogen and sulfur metabolism were twofold less abundant in the dark. From the proteome analysis we were able to show that Chl. clathratiforme in the photic zone contains enzymes for fixation of N₂ and the complete oxidation of sulfide to sulfate while these processes are probably not active in the dark. Instead we propose that Chl. clathratiforme cells in the dark part of the water column obtain energy for maintenance from the fermentation of polyglucose. Based on the observed protein compositions we have constructed possible pathways for C, N and S metabolism in Chl. clathratiforme.     

Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments

The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected and up to 70% of the SRB rRNA 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 comparison of the two methods used for quantification showed that FISH and rRNA slot blot hybridization gave comparable results. Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile. The rRNA contents of Desulfosarcina-Desulfococcus cells were highest in the first 5 mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface. Based on SRB cell numbers, cellular sulfate reduction rates were calculated. The rates were highest in the surface layer (0.14 fmol cell(-1) day(-1)), decreased by a factor of 3 within the first 2 cm, and were relatively constant in deeper layers.