Sulfuriferula nivalis sp. nov., a sulfur oxidizer isolated from snow and emended description of Sulfuriferula plumbiphila

A chemolithoautotrophic sulfur-oxidizing bacterium, strain SGTM^T was isolated from snow collected in Japan. As electron donors for growth, SGTM^T oxidized thiosulfate, tetrathionate and elemental sulfur. Heterotrophic growth was not observed. Growth of the novel isolate was observed at a temperature range of 5-28 °C, with optimum growth at 18 °C. SGTM^T grew at a pH range of 4.3-7.4, with optimum growth at pH 6.1-7.1. Major components in the cellular fatty acid profile were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c) and C_16 : 0. The complete genome of SGTM^T consisted of a circular chromosome of approximately 3.4 Mbp and two plasmids. Phylogenetic analysis based on the 16S rRNA gene indicated that SGTM^T represented a member of the genus Sulfuriferula, and its closest relative is Sulfuriferula thiophila mst6^T with a sequence identity of 98 %. A comparative genome analysis showed dissimilarity between the genomes of SGTM^T and S. thiophila mst6^T, as low values of average nucleotide identity (74.9 %) and digital DNA-DNA hybridization (20.4%). On the basis of its genomic and phenotypic properties, SGTM^T (=DSM 109609^T=BCRC 81185^T) is proposed as the type strain of a novel species, Sulfuriferula nivalis sp. nov. Some characteristics of another species in the same genus, Sulfuriferula plumbiphila, were also investigated to revise and supplement its description. The type strain of S. plumbiphila can grow on thiosulfate, tetrathionate and elemental sulfur. The strain showed optimum growth at pH 6.3-7.0 and shared major cellular fatty acids with the other species of the genus Sulfuriferula.

Effects of Planted Versus Naturally Growing Vallisneria natans on the Sediment Microbial Community in West Lake, China

Submerged macrophytes play an important role in aquatic ecosystems, which has led to an increase in studies on vegetation recovery in polluted lakes from which submerged macrophytes have disappeared. The comparison of microbial communities in sediment cloned with planted and naturally growing submerged macrophytes is an interesting but rarely studied topic. In this investigation, Maojiabu and Xilihu, two adjacent sublakes of West Lake (Hangzhou, China), were selected as aquatic areas with planted and naturally growing macrophytes, respectively. Sediment samples from sites with/without Vallisneria natans were collected from both sublakes. The results showed that sediment total nitrogen and organic matter were significantly lower in the plant-covered sites than that in the non-plant sites in Maojiabu. Additionally, the sediment microbial community characterized by 16S ribosomal RNA (rRNA) sequencing differed more significantly for Maojiabu than for Xilihu. The relative abundances of microbes involved in C, N, and S elemental cycling were significantly higher in the sediments with plants than in those without. Results from both fatty acid methyl ester analysis and 16S rRNA sequencing indicated that vegetation significantly influenced the sulfate-reducing bacteria (SRB). Thus, the gene copies and composition of SRB were explored further. The relative gene abundance of SRB was 66% higher with natural vegetation colonization but was not influenced by artificial colonization. An increase in dominant SRB members from the families Syntrophobacteraceae and Thermodesulfovibrionaceae contributed to the increase of total SRB. Thus, macrophyte planting influences sediment nutrient levels and microbial community more than natural growth does, whereas the latter is more beneficial to sediment SRB.

Bacterial periphytic communities related to mercury methylation within aquatic plant roots from a temperate freshwater lake (South-Western France)

Macrophyte floating roots are considered as hotspots for methylmercury (MeHg) production in aquatic ecosystems through microbial activity. Nevertheless, very little is known about periphyton bacterial communities and mercury (Hg) methylators in such ecological niches. The ability to methylate inorganic Hg is broadly distributed among prokaryotes; however, sulfate-reducers have been reported to be the most important MeHg producers in macrophyte floating roots. In the present work, the periphyton bacterial communities colonizing Ludwigia sp. floating roots were investigated through molecular methods. Among the 244 clones investigated, anaerobic microorganisms associated with the sulfur biogeochemical cycle were identified. Notably, members of the sulfur-oxidizing prokaryotes and the anoxygenic, purple non-sulfur bacteria (Rhodobacteraceae, Comamonadaceae, Rhodocyclaceae, Hyphomicrobiaceae) and the sulfate reducers (Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae) were detected. In addition, 15 sulfate-reducing strains related to the Desulfovibrionaceae family were isolated and their Hg-methylation capacity was tested using a biosensor. The overall results confirmed that Hg methylation is a strain-specific process since the four strains identified as new Hg-methylators were closely related to non-methylating isolates. This study highlights the potential involvement of periphytic bacteria in Hg methylation when favorable environmental conditions are present in such ecological micro-niches.

Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan

Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.

Efficacy and role of inulin in mitigation of enteric sulfur-containing odor in pigs

BACKGROUND

The efficacy and role of inulin in the mitigation of enteric sulfur-containing odor gases hydrogen sulfide (H₂ S) and methyl mercaptan (CH₃ SH) in pigs were examined in this study. Twelve Duroc × Landrace × Yorkshire male finisher pigs (60.7 ± 1.9 kg), housed individually in open-circuit respiration chambers, were randomly assigned to two dietary groups, namely basal diet (control) and basal diet supplemented with 1% (w/w) inulin. At the end of the 45 day experiment, pigs were slaughtered and volatile fatty acid (VFA) concentration, sulfate radical (SO₄^2- ) concentration, population of sulfate-reducing bacteria (SRB) and expression of methionine gamma-lyase (MGL) gene were determined in contents from the caecum, colon (two segments) and rectum. Metabonomic analysis was used to compare differences in biochemical composition, and the Illumina MiSeq procedure to investigate differences in bacterial components, in the different parts of the large intestine between inulin-supplemented and inulin-free (control) groups.

RESULTS

Inulin decreased (P < 0.05) the average daily enteric H₂ S and CH₃ SH production by 12.4 and 12.1% respectively. The concentrations of acetate, propionate and butyrate in the large intestinal content were significantly increased (P < 0.05) with inulin treatment, whereas valerate concentration and MGL mRNA expression decreased (P < 0.05). The growth of Lactobacillus, Butyrivibrio, Pseudobutyrivibrio, Bifidobacterium and Clostridium butyricum was stimulated, while that of Desulfovibrio, the dominant SRB, was inhibited, and there was an accumulation of SO₄^2- in the large intestinal content of the inulin-supplemented pigs, suggesting that inulin mitigates H₂ S generation from the SO₄^2- reduction pathway by reducing the growth of SRB.

CONCLUSION

The results showed that inulin mitigates CH₃ SH generation via three methionine degradation metabolic pathways and H₂ S generation from two cysteine degradation metabolic pathways, thus resulting in increased synthesis of these two sulfur-containing amino acids in the pig large intestine. © 2016 Society of Chemical Industry.

Sulfate Reduction and Inorganic Carbon Assimilation in Acidic Thermal Springs of the Kamchatka Peninsula

Thermoacidophilic sulfate reduction remains a poorly studied process, which was investigated in the present work. Radioisotope analysis with 35S-Iabeled sulfate was used to determine the rates of dissimilatory sulfate reduction in acidic thermal springs of Kamchatka, Russia. Sulfate reduction rates were found to vary from 0.054 to 12.9 nmol S04/(cm3 day). The Neftyanaya ploshchadka spring (Uzon caldera, 60'C, pH 4.2) and Oreshek spring (Mutnovskii volcano, 91'C, pH 3.5) exhibited the highest activity of sulfate-reducing prokaryotes. Stable enrich- ment'cultures reducing sulfate at pH and temperature values close to'the environmental ones were obtained from these springs. Analysis of the 16S rRNA gene sequences revealed that'a chemolithoautotrophic bacterium Ther- modesufobium sp. 3127-1 was responsible for sulfate reduction in the enrichment from the Oil Site spring. A chemoorganoheterotrophic archaeon Vulcanisaeta sp. 3102-1 (phylum Crenarchaeota) was identified in the en- richment from Oreshek spring. Thus, dissimilatory sulfate reduction under thermoacidophilic conditions was demonstrated and the agents responsible for this process were revealed.

[Achievement of Sulfate-Reducing Anaerobic Ammonium Oxidation Reactor Started with Nitrate-Reducting Anaerobic Ammonium Oxidation]

The transformation of nitrite-reducing anaerobic ammonium oxidation to sulfate-reducing anaerobic ammonium oxidation in an UASB was performed and the changes in microbial community were studied. The result showed that the sulfate reducing anaerobic ammonium oxidation process was successfully accomplished after 177 days' operation. The removal rate of ammonium nitrogen and sulfate were up to 58. 9% and 15. 7%, the removing load of ammonium nitrogen and sulfate were 74. 3 mg.(L.d)-1 and 77. 5 mg.(L.d)-1 while concentration of ammonium nitrogen and sulfate of influent were 130 mg.(L.d)-1 and 500 mg.(L.d)-1, respectively. The lost nitrogen and sulphur was around 2 in molar ratio. The pH value of the effluent was lower than that of the influent. Instead of Candidatus brocadia in nitrite reducing anaerobic ammonium oxidation granular sludge, Bacillus benzoevorans became the dominant species in sulfate reducing anaerobic ammonium oxidation sludge. The dominant bacterium in the two kinds of anaerobic ammonium oxidation process is different. Our results imply that the two anaerobic ammonium oxidation processes are carried out by different kind of bacterium.

[Sulfate-Reducing Bacterial Communities in the Water Column of the Gdansk Deep (Baltic Sea)]

Biodiversity of sulfate-reducing bacterial communities in the water column of the Gdansk Deep, Baltic Sea, where H2S had been detected in near-bottom layers, was analyzed by PCR with primers for the 16S rRNA genes of six major phylogenetic subgroups of sulfate-reducing bacteria (SRB). Using denaturing gradient gel electrophoresis followed by sequencing, the nucleotide sequences of reamplified dsrB gene fragments from investigated water samples were determined. For the first time the presence of nucleotide sequences of the dsrB gene was detected by PCR in the water samples from all hydrochemical layers, including subsurface oxic waters. The presence of the 16S rRNA genes of representatives of Desulfotomaculum, Desulfococcus-Desulfonema-Desulfosarcina, and Desulfovibrio-Desulfomicrobium SRB subgroups was also revealed throughout the water column of the Gdansk Deep. Analysis of translated amino acid sequences encoded by the dsrB gene demonstrated the highest homology with the relevant sequences of uncultured SRB from various marine habitats.

Desulfosporosinus acididurans sp. nov.: an acidophilic sulfate-reducing bacterium isolated from acidic sediments

Three strains of sulfate-reducing bacteria (M1(T), D, and E) were isolated from acidic sediments (White river and Tinto river) and characterized phylogenetically and physiologically. All three strains were obligately anaerobic, mesophilic, spore-forming straight rods, stained Gram-negative and displayed variable motility during active growth. The pH range for growth was 3.8-7.0, with an optimum at pH 5.5. The temperature range for growth was 15-40 °C, with an optimum at 30 °C. Strains M1(T), D, and E used a wide range of electron donors and acceptors, with certain variability within the different strains. The nominated type strain (M1(T)) used ferric iron, nitrate, sulfate, elemental sulfur, and thiosulfate (but not arsenate, sulfite, or fumarate) as electron acceptors, and organic acids (formate, lactate, butyrate, fumarate, malate, and pyruvate), alcohols (glycerol, methanol, and ethanol), yeast extract, and sugars (xylose, glucose, and fructose) as electron donors. It also fermented some substrates such as pyruvate and formate. Strain M1(T) tolerated up to 50 mM ferrous iron and 10 mM aluminum, but was inhibited by 1 mM copper. On the basis of phenotypic, phylogenetic, and genetic characteristics, strains M1(T), D, and E represent a novel species within the genus Desulfosporosinus, for which the name Desulfosporosinus acididurans sp. nov. is proposed. The type strain is M1(T) (=DSM 27692(T) = JCM 19471(T)). Strain M1(T) was the first acidophilic SRB isolated, and it is the third described species of acidophilic SRB besides Desulfosporosinus acidiphilus and Thermodesulfobium narugense.

Phylogenetic and functional diversity within toluene-degrading, sulphate-reducing consortia enriched from a contaminated aquifer

Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.

[Biodiversity of sulfate-reducing bacteria growing on objects of heating systems]

It was shown that sulfate-reducing bacteria developed on the sections of Kyiv municipal heating systems, which are exploited in conditions of different temperatures. The bacteria were different as to their morphological and physiological properties. The bacteria of Desulfovibrio genus were revealed on the sections, which were exploited at a temperature of 35-40 degrees C and bacteria of Desulfomicrobium and Desulfotomaculum genera were revealed on the sections with a higher temperature such as 60 degrees C. Based on of the 16S rRNA gene analysis data, it was demonstrated that sequences of TC2, TC3 and TC4 clones related to Desulfovibrio sp. DSM 12803 (100% sequence similarity), Desulfotomaculum sp. ECP-C-5 (92% sequence similarity) and Desulfomicrobium baculatum strain DSM 2555 (99% sequence similarity), respectively. The identified bacteria are potentially dangerous for heating systems and can be the agents of microbial corrosion.

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology.

Linkage between community diversity of sulfate-reducing microorganisms and methylmercury concentration in paddy soil

Sulfate-reducing microorganisms (SRM) have been thought to play a key role in mercury (Hg) methylation in anoxic environments. The current study examined the linkage between SRM abundance and diversity and contents of methylmercury (MeHg) in paddy soils collected from a historical Hg mining area in China. Soil profile samples were collected from four sites over a distance gradient downstream the Hg mining operation. Results showed that MeHg content in the soil of each site significantly decreased with the extending distance away from Hg mine. Soil MeHg content was correlated positively with abundance of SRM and the contents of organic matter (OM), NH4(+), SO4(2-), and Hg. The abundances of SRM based on dissimilatory (bi) sulfite reductase (dsrAB) gene at 0-40 cm depths were higher than those at 40-80 cm depth at all sites. The SRM community composition varied in the soils of different sampling sites following terminal restriction fragment length polymorphism (T-RFLP) and phylogenetic analyses, which appeared to be correlated with contents of MeHg, OM, NH4(+), and SO4(2-) through canonical correspondence analysis. The dominant groups of SRM in the soils examined belonged to Deltaproteobacteria and some unknown SRM clusters that could have potential for Hg methylation. These results advance our understanding of the relationship between SRM and methylmercury concentration in paddy soil.

Detection of sulphate-reducing bacteria in human saliva

OBJECTIVE

The aim of the current study was to investigate the presence of sulphate-reducing bacteria (SRB) in human saliva and correlate with oral and systemic conditions.

METHODS

Saliva samples were collected from 118 patients and inoculated in 2 ml of modified Postgate's E medium culture. After 28 days of incubation at 30°C the presence of SRB was identified by the production of sulphide.

RESULTS

Of 118 saliva samples collected, 35 were positive for the presence of SRB. Three positive samples were randomly chosen to identify the species of SRB by PCR and sequenced. The three selected samples were identified as Desulfovibrio fairfieldensis, Desulfovibrio desulfuricans and Raoultella ornithinolytica. Gastritis (14.4%) was the most prevalent systemic disease, followed by diabetes (3.4%), while periodontitis (11%) and traumatic fibroma (4.2%) were the oral manifestations most frequently found. A bivariate analysis was performed to examine for the presence of SRB and the most prevalent systemic and oral manifestations. Only periodontitis showed a statistically significant association (p = 0.0003).

CONCLUSIONS

The results showed SRB can be found in oral microbiota of healthy patients. Regarding the several conditions studied, there was a higher prevalence of SRB in patients with gastritis and patients with periodontal disease, with a possible correlation between the presence of SRB in the oral microbiota and periodontal disease.

Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade

Bacteria from the uncultured SUP05/Arctic96BD-19 clade of gamma proteobacterial sulfur oxidizers (GSOs) have the genetic potential to oxidize reduced sulfur and fix carbon in the tissues of clams and mussels, in oxygen minimum zones and throughout the deep ocean (>200 m). Here, we report isolation of the first cultured representative from this GSO clade. Closely related cultures were obtained from surface waters in Puget Sound and from the deep chlorophyll maximum in the North Pacific gyre. Pure cultures grow aerobically on natural seawater media, oxidize sulfur, and reach higher final cell densities when glucose and thiosulfate are added to the media. This suggests that aerobic sulfur oxidation enhances organic carbon utilization in the oceans. The first isolate from the SUP05/Arctic96BD-19 clade was given the provisional taxonomic assignment 'Candidatus: Thioglobus singularis', alluding to the clade's known role in sulfur oxidation and the isolate's planktonic lifestyle.

Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.

Influence of season and plant species on the abundance and diversity of sulfate reducing bacteria and ammonia oxidizing bacteria in constructed wetland microcosms

Constructed wetlands offer an effective means for treatment of wastewater from a variety of sources. An understanding of the microbial ecology controlling nitrogen, carbon and sulfur cycles in constructed wetlands has been identified as the greatest gap for optimizing performance of these promising treatment systems. It is suspected that operational factors such as plant types and hydraulic operation influence the subsurface wetland environment, especially redox, and that the observed variation in effluent quality is due to shifts in the microbial populations and/or their activity. This study investigated the biofilm associated sulfate reducing bacteria and ammonia oxidizing bacteria (using the dsrB and amoA genes, respectively) by examining a variety of surfaces within a model wetland (gravel, thick roots, fine roots, effluent), and the changes in activity (gene abundance) of these functional groups as influenced by plant species and season. Molecular techniques were used including quantitative PCR and denaturing gradient gel electrophoresis (DGGE), both with and without propidium monoazide (PMA) treatment. PMA treatment is a method for excluding from further analysis those cells with compromised membranes. Rigorous statistical analysis showed an interaction between the abundance of these two functional groups with the type of plant and season (p < 0.05). The richness of the sulfate reducing bacterial community, as indicated by DGGE profiles, increased in planted vs. unplanted microcosms. For ammonia oxidizing bacteria, season had the greatest impact on gene abundance and diversity (higher in summer than in winter). Overall, the primary influence of plant presence is believed to be related to root oxygen loss and its effect on rhizosphere redox.

Impact of copper on the abundance and diversity of sulfate-reducing prokaryotes in two chilean marine sediments

We studied the abundance and diversity of the sulfate-reducing prokaryotes (SRPs) in two 30-cm marine chilean sediment cores, one with a long-term exposure to copper-mining residues, the other being a non-exposed reference sediment. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and showed that SRPs are sensitive to high copper concentrations, as the mean number of SRPs all along the contaminated sediment was two orders of magnitude lower than in the reference sediment. SRP diversity was analyzed by using the dsrB-sequences-based PCR-DGGE method and constructing gene libraries for dsrB-sequences. Surprisingly, the diversity was comparable in both sediments, with dsrB sequences belonging to Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae, SRP families previously described in marine sediments, and to a deep branching dsrAB lineage. The hypothesis of the presence of horizontal transfer of copper resistance genes in the microbial population of the polluted sediment is discussed.

Effects of sulfate reducing bacteria and sulfate concentrations on mercury methylation in freshwater sediments

Methylmercury (MeHg) is the most poisonous form of mercury (Hg) and it enters the human body primarily through consumption of Hg contaminated fish. Sulfate reducing bacteria (SRB) are major producers of MeHg in anoxic sediments. The dsrAB gene was isolated from freshwater fish pond sediments. Sequence analyses showed that the SRB in sediments was mainly composed of Desulfobulbus propionicus and Desulfovibrio vulgaris. The two species of SRB were cultured from freshwater sediments. The addition of inorganic Hg to these freshwater sediments caused an increase in MeHg concentrations at 30 days incubation. MeHg levels were sensitive to sulfate concentrations; a medium sulfate level (0.11 mg/g) produced higher levels than treatments lacking sulfate addition or when amended with 0.55 mg/g. Assessment of bacterial levels by PCR measurements of microbial DNA indicated that the MeHg levels were correlated with cell growth.

Thiofractor thiocaminus gen. nov., sp. nov., a novel hydrogen-oxidizing, sulfur-reducing epsilonproteobacterium isolated from a deep-sea hydrothermal vent chimney in the Nikko Seamount field of the northern Mariana Arc

A novel chemolithoautotrophic hydrogen-oxidizing and sulfur-reducing bacterium, strain 496Chim(T), was isolated from a deep-sea hydrothermal vent chimney collected from the hydrothermal field at the summit of Nikko Seamount field, in the Mariana Arc. Cells were rods or curved rods, motile by means of a single polar flagellum. Growth was observed between 15 and 45 °C (optimum 37 °C; doubling time, 2.1 h) and between pH 5.3 and 8.0 (optimum pH 6.0). The isolate was a strictly anaerobic, obligate chemolithoautotroph capable of growth using molecular hydrogen as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source, and elemental sulfur as the electron acceptor. The G+C content of genomic DNA was 35 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate belonged to the class Epsilonproteobacteria, but the isolate was distantly related to the previously described Epsilonproteobacteria species potentially at the genus level (<90 %). On the basis of its physiological and molecular characteristics, strain 496Chim(T) (=DSM 22050(Τ) = JCM 15747(Τ) = NBRC 105224(Τ)) represents the sole species of a new genus, Thiofractor, for which the name Thiofractor thiocaminus is proposed.

Microbial fouling community analysis of the cooling water system of a nuclear test reactor with emphasis on sulphate reducing bacteria

Culture and molecular-based techniques were used to characterize bacterial diversity in the cooling water system of a fast breeder test reactor (FBTR). Techniques were selected for special emphasis on sulphate-reducing bacteria (SRB). Water samples from different locations of the FBTR cooling water system, in addition to biofilm scrapings from carbon steel coupons and a control SRB sample were characterized. Whole genome extraction of the water samples and SRB diversity by group specific primers were analysed using nested PCR and denaturing gradient gel electrophoresis (DGGE). The results of the bacterial assay in the cooling water showed that the total culturable bacteria (TCB) ranged from 10(3) to 10(5) cfu ml(-1); iron-reducing bacteria, 10(3) to 10(5) cfu ml(-1); iron oxidizing bacteria, 10(2) to 10(3) cfu ml(-1) and SRB, 2-29 cfu ml(-1). However, the counts of the various bacterial types in the biofilm sample were 2-3 orders of magnitude higher. SRB diversity by the nested PCR-DGGE approach showed the presence of groups 1, 5 and 6 in the FBTR cooling water system; however, groups 2, 3 and 4 were not detected. The study demonstrated that the PCR protocol influenced the results of the diversity analysis. The paper further discusses the microbiota of the cooling water system and its relevance in biofouling.

[Diversity analysis of desulfuration bacterium from the oxidation ditch of city sewage treatment plant with SO2 gas]

A group of removing SO2 bacterium was obtained from the oxidation ditch of city sewage treatment plant by inductive domestication over 6 d with low concentration SO2 gas, and they have an ability with biodegradation rate of 888 mg x (L x h)(-1) and a degradation efficiency of 85% during 1.5 h for SO2 dissolved in water with their synergy. The clone library and two phylogenetic trees of the removing SO2 bacterium communities were obtained based on 16S rRNA DNA comparison by DNA extraction of the sample and in situ polymerase chain reaction (PCR). The phylogenetic analysis showed that 8 dominant desulfuration bacterium occupy about 69% of all removing SO2 bacterium, and some of them have a kindred with discovered desulfuration bacterium but not homogeneity, and there are four belong to alpha-Proteobacteria, another four belong to beta-Proteobacteria in them. The gene information about 16S rRNA sequence of the dominant desulfuration bacteria and domestication method provide a basic of looking for or domesticating removing SO2 bacterium for development microbial desulfurization technology of contained SO2 tail gas.

Evidence of methylmercury production and modification of the microbial community structure in estuary sediments contaminated with wastewater treatment plant effluents

The Seine's estuary (France) waters are the receptacle of effluents originating from wastewater treatment plants (WWTP). In this estuary, mudflats are deposition zones for sediments and their associated contaminants, and play an essential role in the mercury (Hg) biogeochemical cycle mainly due to indigenous microorganisms. Microcosms were used to assess the impact of WWTP-effluents on mercury methylation by monitoring Hg species (total dissolved Hg in porewater, methylmercury and total mercury) and on microbial communities in sediments. After effluent amendment, methylmercury (MeHg) concentrations increased in relation with the total Hg and organic matter content of the WWTP-effluents. A correlation was observed between MeHg and acid-volatile-sulfides concentrations. Quantification of sulfate-reducing microorganisms involved in Hg methylation showed no increase of their abundance but their activity was probably enhanced by the organic matter supplied with the effluents. WWTP-effluent spiking modified the bacterial community fingerprint, mainly influenced by Hg contamination and the organic matter amendment.

Structure of microbial communities and hydrocarbon-dependent sulfate reduction in the anoxic layer of a polluted microbial mat

The bacterial communities in the anoxic layer of a heavily polluted microbial mat and their growth on hydrocarbons under sulfate-reducing conditions were investigated. Microbial communities were dominated by members of Alphaproteobacteria (27% of the total rRNA), Planctomycetes (21.1%) and sulfate-reducing bacteria (SRB: 17.5%). 16S rRNA cloning revealed sequences beloning to the same bacterial groups with SRB affiliated to the genera Desulfobulbus, Desulfocapsa, Desulfomicrobium, Desulfobacterium and Desulfosarcina/Desulfococcus. The derived enrichment cultures on crude oil, hexadecane and toluene were dominated by SRB. While most SRB sequences of the toluene and hexadecane cultures were related to the sequence of Desulfotignum toluolica, the crude oil enrichment showed a more diverse bacterial community with sequences from the genera Desulfotignum, Desulfobacter, Desulfatibacillus, Desulfosalina, and Desulfococcus. We conclude that the anoxic layer of the studied mats contains a diverse community of anaerobic bacteria, dominated by SRB, some of which are able to grow on hydrocarbons.

Abundance and diversity of biofilms in natural and artificial aquifers of the Äspö Hard Rock Laboratory, Sweden

Six cores were drilled and retrieved from 186-m depth in the Äspö Hard Rock Laboratory (HRL) tunnel to investigate whether indigenous biofilms develop on fracture surfaces in groundwater-conducting aquifers in granitic rock. A clone library was constructed from fracture surface material (FSM), for community composition analysis. Quantitative polymerase chain reaction (qPCR) was applied to quantify gene copies using the 16S rRNA gene for domain Bacteria and the adenosine-phosphosulfate reductase gene (apsA) for sulfate-reducing bacteria (SRB). Results were compared with three groundwater systems with biofilms in laminar flow reactors (LFRs) at 450-m depth in the Äspö HRL. The total number of cells, counted microscopically, was approximately 2 × 10(5) cells cm(-2) in the LFR systems, consistent with the obtained qPCR 16S rRNA gene copies. qPCR analysis reported ∼1 × 10(2) up to ∼1 × 10(4) gene copies cm(-2) on the FSM from the drill cores. In the FSM biofilms, 33% of the sequenced clones were related to the iron-reducing bacterium Stenotrophomonas maltophilia, while in the LFR biofilms, 41% of the sequenced clones were affiliated with the genera Desulfovibrio, Desulforhopalus, Desulfomicrobium, and Desulfobulbus. The community composition of the FSM biofilms differed from the drill water community, excluding drill water contamination. This work reports significant numbers of microorganisms on natural hard rock aquifer fracture surfaces with site-specific community compositions. The probability that biofilms are generally present in groundwater-conducting aquifers in deep granitic rock is consequently great.

Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers

Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.

Biogeochemical interactions among the arsenic, iron, humic substances, and microbes in mud volcanoes in southern Taiwan

Fluid and mud samples collected from Hsiaokunshui (HKS), Wushanting (WST), Yenshuikeng (YSK), Kunshuiping (KSP), Liyushan (LYS), and Sinyangnyuhu (SYNH) mud volcanoes of southwestern Taiwan were characterized for major ions, humic substances (HS) and trace elements concentrations. The relationship between the release of arsenic (As) and activities of sulfate-reducing bacteria has been assessed to understand relevant geochemical processes in the mud volcanoes. Arsenic (0.02-0.06 mg/L) and humic substances (4.13 × 10(-4) to 1.64 × 10(-3) mM) in the fluids of mud volcanoes showed a positive correlation (r = 0.99, p < 0.05) except in Liyushan mud volcano. Arsenic and iron in mud sediments formed two separate groups i) high As, but low Fe in HKS, WST, and SYNH; and ii) low As, but high Fe in the YSK, KSP, and LYS mud volcanoes. The Eh(S.H.E.) values of the mud volcano liquids were characterized by mild to strongly reducing conditions. The HKS, SYNH, and WST mud volcanoes (near the Chishan Fault) belongs to strong reducing environment (-33 to -116 mV), whereas the LYS, YSK, and KSP mud volcanoes located near the coastal plain are under mild reducing environment (-11 to 172 mV). At low Eh values mud volcanoes, saturation index (SI) values of poorly crystalline phases such as amorphous ferric hydroxide indicate understaturation, whereas saturation is reached in relatively high Eh(S.H.E.) values mud volcanoes. Arsenic contents in sediments are low, presumably due to its release to fluids (As/Fe ratio in YSK, KSP, and LYS sediment: 4.86 × 10(-4)-6.20 × 10(-4)). At low Eh(S.H.E.) values (mild to strong reducing environment), arsenic may co-precipitate with sulfides as a consequence of sulfate reduction (As/Fe ratios in WST, HKS, and SYNH sediments: 0.42-0.69).

Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes

Seafloor iron oxide deposits are a common feature of submarine hydrothermal systems. Morphological study of these deposits has led investigators to suggest a microbiological role in their formation, through the oxidation of reduced Fe in hydrothermal fluids. Fe-oxidizing bacteria, including the recently described Zetaproteobacteria, have been isolated from a few of these deposits but generally little is known about the microbial diversity associated with this habitat. In this study, we characterized bacterial diversity in two Fe oxide samples collected on the seafloor of Volcanoes 1 and 19 on the South Tonga Arc. We were particularly interested in confirming the presence of Zetaproteobacteria at these two sites and in documenting the diversity of groups other than Fe oxidizers. Our results (small subunit rRNA gene sequence data) showed a surprisingly high bacterial diversity, with 150 operational taxonomic units belonging to 19 distinct taxonomic groups. Both samples were dominated by Zetaproteobacteria Fe oxidizers. This group was most abundant at Volcano 1, where sediments were richer in Fe and contained more crystalline forms of Fe oxides. Other groups of bacteria found at these two sites include known S- and a few N-metabolizing bacteria, all ubiquitous in marine environments. The low similarity of our clones with the GenBank database suggests that new species and perhaps new families were recovered. The results of this study suggest that Fe-rich hydrothermal sediments, while dominated by Fe oxidizers, can be exploited by a variety of autotrophic and heterotrophic micro-organisms.

[Distribution and diversity of sulfate-reducing bacteria in a crude oil gathering and transferring system]

The distribution of sulfureted hydrogen (H2S) as well as sulfate-reducing bacteria (SRB) distribution and diversity in crude oil and oilfield production water samples from a oil gathering and transferring system in Changqing Oilfield of China were investigated by methylene blue colorimetric method, the most probable number technique and sequence analysis of the 16S rRNA gene, respectively. At the oil gathering and transferring system which from oil well through oil flowstation and then to oil comprehensive treatment station, the results showed that in oil samples, the content of H2S were 105.80, 99.70, and 24.57 mg x L(-1), respectively; and the count of SRB were 98, 300, and 680 CFU x100 mL(-1), respectively. In water samples, the content of H2S were 1.13, 2.80, and 3.49 mg x L(-1), respectively; and the count of SRB were 9 500, 40 000, and 76 000 CFU x 100 mL(-1), respectively. The abundance of SRB in the water samples is about 100 times than that in the crude-oil samples. High concentration of H2S in oil well inhibited the growth of SRB, thereby the count of SRB in oil well were small. With the reduction of H2S concentration, the actions of inhibition weakened and disappeared, then the number of SRB were gradual increase in the gathering and transferring system. For the initial concentration of H2S in water samples was low, and the number of SRB were large, then the content of H2S increased gradually with the number of SRB were increased. Sequence analysis of the 16S rRNA gene indicated that SRB related to Desulfovibrionaceae sp. and Desulfococcus sp. were detected in the water and crude oil samples, simultaneously. However, SRB related to Desulfomonile sp., Desulfotomaculum sp. and Desulfosarcina sp. were detected in the water samples but not in crude-oil samples. Abundance of SRB was increased due to the variation of environmental condition during the period of oil gathering and transferring process.

[Taxonomic position of certain representatives of sulphate-reducing corrosive microbial community]

Sulfate-reducing bacteria and their heterotrophic satellites have been isolated from the biofilm formed on steel by sulfidogenic corrosive microbial community. Bacteria were characterized according to phenotypical features and investigated by the methods of molecular-genetic analysis. In accordance with the phenotypical features the studied strain of sulfate-reducing bacteria were related to Desulfovibrio genus, Gram-positive strains of heterotrophic satellites were related to Bacillus genus, B. firmus and B. subtilis species. Gram-negative strains, as to their physiological-biochemical characteristics were related to Pseudomonas genus, P. aeruginosa species, Stenotrophomonas genus, S. maltophilia species, and Aeromonas genus, A. hydrophila/caviae species. Taxonomic position of certain representatives of the community is confirmed by the molecular-genetic methods. A comparative analysis of the sequencing results has evidenced for the identity of sequences of 16S rRNA of the studied bacteria with analogous sequence of strains from the GenBank database. Nucleotide sequence of strain 27 has a 99% homology with the sequence of Pseudomonas aeruginosa, strain 36 deposited at GenBank to nucleotide sequence of Bacillus subtilis. As to sulfate-reducing bacteria, only their belonging to Desulfovibrio genus has been confirmed. Thus the results of sequence-analysis of 16S rRNA genes are in agreement with the data obtained from studying the phenotypical features.

[Isolation and characterization of a sulfate reducing Citrobacter sp. strain SR3]

A sulfate reducing bacterium, designated strain 'SR3', was isolated from sludge of a sulfate-reducing up-flow anaerobic sludge bed (UASB) reactor for treating high concentration sulfate wastewater. It was identified as Citrobacter sp. based upon the phenotypic-characteristics and physiological properties as well as the analysis of the sequence of 16S rDNA. The strain could reduce sulfate under anaerobic and micro-aerobic conditions. The dissimilatory sulphite reductase gene (dsr) was also amplified from this strain's genomic DNA using specific dsr gene primers. In aerobic conditions, the strain couldn't reduce sulfate, but exhibited a highest growth rate. In anaerobic conditions, the optimal growth conditions for this stain were temperature 37 degrees C and initial pH 8.0. Under this conditions,the strain could reduced both SO4(2-) and Cr(VI) at initial Cr(VI) concentrations of 0.4-0.8 mmol synchronously. Its tolerance ability to Cr(VI) concentrations reaches 1.0 mmol. This is the first report about an facultative anaerobe with sulfate reducing function and dissimilatory sulphite reductase gene (dsr).

Biocorrosion and biofilm formation in a nutrient limited heating system subjected to alternating microaerophilic conditions

Severe biofilm formation and biocorrosion have been observed in heating systems even when the water quality complied with existing standards. The coupling between water chemistry, biofilm formation, species composition, and biocorrosion in a heating system was investigated by adding low concentrations of nutrients and oxygen under continuous and alternating dosing regimes. Molecular analysis of 16S rRNA gene fragments demonstrated that the amendments did not cause changes in the overall bacterial community composition. The combined alternating dosing of nutrients and oxygen caused increased rates of pitting (bio-) corrosion. Detection of bacteria involved in sulfide production and oxidation by retrieval of the functional dsrAB and apsA genes revealed the presence of Gram-positive sulfate- and sulfite-reducers and an unknown sulfur-oxidizer. Therefore, to control biocorrosion, sources of oxygen and nutrients must be limited, since the effect of the alternating operational conditions apparently is more important than the presence of potentially corrosive biofilm bacteria.

Biofouling and microbial corrosion problem in the thermo-fluid heat exchanger and cooling water system of a nuclear test reactor

This article discusses aspects of biofouling and corrosion in the thermo-fluid heat exchanger (TFHX) and in the cooling water system of a nuclear test reactor. During inspection, it was observed that >90% of the TFHX tube bundle was clogged with thick fouling deposits. Both X-ray diffraction and Mossbauer analyses of the fouling deposit demonstrated iron corrosion products. The exterior of the tubercle showed the presence of a calcium and magnesium carbonate mixture along with iron oxides. Raman spectroscopy analysis confirmed the presence of calcium carbonate scale in the calcite phase. The interior of the tubercle contained significant iron sulphide, magnetite and iron-oxy-hydroxide. A microbiological assay showed a considerable population of iron oxidizing bacteria and sulphate reducing bacteria (10(5) to 10(6) cfu g(-1) of deposit). As the temperature of the TFHX is in the range of 45-50 degrees C, the microbiota isolated/assayed from the fouling deposit are designated as thermo-tolerant bacteria. The mean corrosion rate of the CS coupons exposed online was approximately 2.0 mpy and the microbial counts of various corrosion causing bacteria were in the range 10(3) to 10(5) cfu ml(-1) in the cooling water and 10(6) to 10(8) cfu ml(-1) in the biofilm.

Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent

A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T)).

Importance of different physiological groups of iron reducing microorganisms in an acidic mining lake remediation experiment

Iron- and sulfate-reducing microorganisms play an important role for alkalinity-generating processes in mining lakes with low pH. In the acidic mining lake 111 in Lusatia, Germany, a passive in situ remediation method was tested in a large scale experiment, in which microbial iron and sulfate reduction are stimulated by addition of Carbokalk (a mixture of the nonsugar compounds of sugar beets and lime) and straw. The treated surface sediment consisted of three layers of different pH and geochemical composition. The top layer was acidic and rich in Fe(III), the second and third layer both showed moderately acidic to circum-neutral pH values, but only the second was rich in organics, strongly reduced and sulfidic. Aim of the study was to elucidate the relative importance of neutrophilic heterotrophic, acidophilic heterotrophic, and acidophilic autotrophic iron-reducing microorganisms in each of the three layers. In order to distinguish between them, the effect of their respective characteristic electron donors acetate, glucose, and elemental sulfur on potential iron reduction rates was investigated. Limitation of iron reduction by the availability of Fe(III) was revealed by the addition of Fe(OH)(3). The three groups of iron-reducing microorganisms were quantified by most probable number (MPN) technique and their community composition was analyzed by cloning and sequencing of 16S rRNA genes. In the acidic surface layer, none of the three electron donors stimulated iron reduction; acetate even had an inhibiting effect. In agreement with this, no decrease of the added electron donors was observed. Iron reduction rates were low in comparison to the other layers. Iron reduction in layers 2 and 3 was enhanced by glucose and acetate, accompanied by a decrease of these electron donors. Addition of elemental sulfur did not enhance iron reduction in either layer. Layer 2 exhibited the highest iron reduction rate (4.08 mmol dm(-3) d(-1)) and the highest cell numbers in MPN media. In MPN enrichments from all layers, Acidithiobacillus-like sequences were frequent. In addition to these, sequences related to Fulvimonas and Clostridium dominated in layer 1. MPN enrichments of layer 2 were diverse, containing Rhodocyclaceae-related sequences and surprisingly low numbers of Geobacteraceae. In layer 3, Sulfobacillus and Trichococcus spp. were also important. It was concluded that in the surface layer mainly acidophilic, probably autotrophic and heterotrophic, iron reducers were active, whereas in layers 2 and 3 mainly neutrophilic heterotrophs were important for iron reduction. These differ from well-studied Fe(III) reducers in other environments, so they deserve further study. The potential for acid-producing sulfur-driven Fe(III) reduction seemed not to be critical for in situ remediation.

Diversity of sulfate-reducing genes (dsrAB) in sediments from Puget Sound

The aims of this study were to characterize the population structure and diversity of sulfate-reducing bacteria (SRB) from three distinct sites at Puget Sound, and relate the biogeochemical properties of the sediments to the sulfate-reducer communities. The population composition and diversity of sulfate-reducing bacteria carrying dsrAB genes from surface Puget Sound sediments was investigated using a polymerase chain reaction-based cloning approach. Sediment cores were collected from three different locations: Carr Inlet (C1A), Shallow Bud Inlet (S1A), and Turning Basin (T1A). A total of 498 dsrAB clones were sequenced from the three sites. Ecological indices indicated that T1A had the highest diversity and evenness values and C1A had the lowest. Correlations were also found between diversity indices and geochemical parameters. The diversity of the SRB decreased with decreasing carbon concentrations and sulfate reduction rates, and increasing levels of oxygen. A phylogenetic comparison revealed that the majority of the dsrAB sequences were associated with the delta-proteobacterial phylotypes Desulfonema, Desulfococcus and Desulfosarcina, suggesting that complete oxidizers with high substrate versatility dominate in the sediments. The environmental conditions and energy sources available in the sediments may have dictated microbial community structure and diversity of SRBs. Distinctive community structures of SRBs in Puget Sound sediments were found to vary at different sites with different redox profiles. The dominance of the Desulfobacteraceae-like sequences may be due to the presence of a diverse spectrum of substrates in the sediments. This study represents one of the first efforts to characterize the population of sulfate-reducing microbes in the oxygenated regions of Puget Sound sediments. The phylogenetic identification of dsrAB genes in the sediment samples allows the composition of sulfate-reducing prokaryotic communities to be inferred, and working hypotheses about their likely carbon substrates to be formed.

Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach

The community structure of sulfate-reducing bacteria (SRB) associated with reed (Phragmites australis) rhizosphere in Lake Velencei (Hungary) was investigated by using cultivation-based and molecular methods. The cultivation methods were restricted to recover lactate-utilizing species with the exclusion of Desulfobacter and some Desulfobacterium species presumably not being dominant members of the examined community. The most-probable-number (MPN) estimations of lactate-utilizing SRB showed that the cell counts in reed rhizosphere were at least one order of magnitude higher than that in the bulk sediment. The number of endospores was low compared to the total SRB counts. From the highest positive dilution of MPN series, 47 strains were isolated and grouped by restriction fragment length polymorphism (RFLP) analysis of the amplified 16S ribosomal RNA (rRNA) and dsrAB (dissimilatory sulfite reductase) genes. Contrary to the physiological diversity of the isolates, the combined results of RFLP analysis revealed higher diversity at species as well as at subspecies level. Based on the partial 16S rRNA sequences, the representative strains were closely affiliated with the genera Desulfovibrio and Desulfotomaculum. The partial dsrAB sequences of the clones, recovered after isolation and PCR amplification of the community DNA, were related to hitherto uncultured species of the genera Desulfovibrio and Desulfobulbus. Nevertheless, the representative of the second largest clone group was shown to be closely affiliated with the sequenced dsrAB gene of a strain isolated from the same environment and identified as Desulfovibrio alcoholivorans. Another clone sequence was closely related to a possible novel species also isolated within the scope of this work.

Molecular analysis of the spatio-temporal distribution of sulfate-reducing bacteria (SRB) in Camargue (France) hypersaline microbial mat

The spatio-temporal distribution of sulfate-reducing bacteria (SRB) in the microbial mat of Camargue (Salins-de-Giraud, France) was investigated by molecular approaches at both microscale spatial resolution and different taxonomic organization levels. The vertical distribution of the SRB populations was correlated with oxygen and sulfide microgradient fluctuations. Comparisons of Terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed distinct locations of some operational taxonomic units at daytime and at night (4:00 or 15:00 hours) revealing important differences on the structures of the bacterial communities. When oxygen penetrates the mat, SRB migration was observed either downward to reach deeper anoxic zones to escape oxygen or upward to reach oxic surface zones. When no migration was observed, both metabolism switches and aggregate formations were suspected. These behaviors allowed the aerotolerant SRB to deal with oxygen. The analysis of the Desulfococcus-Desulfonema-Desulfosarcina T-RFLP profiles revealed up-migrating populations related to both Desulfonema sp. and Desulfosarcina variabilis. T-RFLP profiles combined with 16S ribosomal ribonucleic acid gene library analysis of the Desulfobacter group revealed two distinct populations: a population related to the recently described Desulfotignum genus migrating upward during the night and a population of a new species of the Desulfobacter uniformly located throughout the mat independent of the period. Thus, the identification of the new oxygen-tolerant SRB will provide the basis for understanding the physiological adaptations to oxygen.

Spatial and temporal changes in sulphate-reducing groundwater bacterial community structure in response to Managed Aquifer Recharge

The population dynamics of bacterial able to be cultured under sulphate reducing condition was studied in conjunction with changes in aquifer geochemistry using multivariate statistics for two contrasting Managed Aquifer Recharge (MAR) techniques at two different geographical locations (Perth, Western Australia and Adelaide, South Australia). Principal component analysis (PCA) was used to investigate spatial and temporal changes in the overall chemical signature of the aquifers using an array of chemical analytes which demonstrated a migrating geochemical plume. Denaturing Gradient Gel Electrophoresis (DGGE) using DNA from sulphate-reducing bacteria cultures was used to detect spatial and temporal changes in population dynamics. Bacterial and geochemical evidence suggested that groundwater at greatest distance from the nutrient source was least affected by treated effluent recharge. The results suggested that bacterial populations that were able to be cultured in sulphate reducing media responded to the migrating chemical gradient and to the changes in aquifer geochemistry. Most noticeably, sulphate-reducing bacterial populations associated with the infiltration galleries were stable in community structure over time. Additionally, the biodiversity of these culturable bacteria was restored when aquifer geochemistry returned to ambient conditions during the recovery phase at the Adelaide Aquifer Storage and Recovery site.

Phosphate removal and sulfate reduction in a denitrification reactor packed with iron and wood as electron donors

Phosphorus removal and denitrification using iron and wood as electron donors were examined in a laboratory-scale biological filter reactor. Phosphorus removal and denitrification using iron and wood continued for 1,200 days of operation. Wood degradation by heterotrophic denitrification and iron oxidation by hydrogenotrophic denitrification occurred simultaneously. In the biofilm inside the wood, not only heterotrophic denitrification activity but also sulfate reduction and sulfur denitrification activities were recognized inside the wood, indicating that a sulfur oxidation-reduction cycle was established. Sulfate reduction and denitrification were accelerated with the addition of cellulose. Microbial communities of sulfate-reducing bacteria by PCR primer sets could be amplified in the biofilm in the reactors. The dissimilatory sulfite reductase gene and the 16S rRNA gene of six phylogenetic groups of SRB in the reactors were analyzed. Some SRB group-specific primers-amplification products were obtained inside the wood and around iron.

Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oilcontamination and very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such deep subsurface environment.

Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene

The dissimilatory adenosine-5'-phosphosulfate reductase is a key enzyme of the microbial sulfate reduction and sulfur oxidation processes. Because the alpha- and beta-subunit-encoding genes, aprBA, are highly conserved among sulfate-reducing and sulfur-oxidizing prokaryotes, they are most suitable for molecular profiling of the microbial community structure of the sulfur cycle in environment. In this study, a new aprA gene-targeting assay using a combination of PCR and denaturing gradient gel electrophoresis is presented. The screening of sulfate-reducing and sulfur-oxidizing reference strains as well as the analyses of environmental DNA from diverse habitats (e.g., microbial mats, invertebrate tissue, marine and estuarine sediments, and filtered hydrothermal water) by the new primer pair revealed an improved microbial diversity coverage and less-pronounced template-to-PCR product bias in direct comparison to those of the previously published primer set (B. Deplancke, K. R. Hristova, H. A. Oakley, V. J. McCracken, R. Aminov, R. I. Mackie, and H. R. Gaskins, Appl. Environ. Microbiol. 66:2166-2174, 2000). The concomitant molecular detection of sulfate-reducing and sulfur-oxidizing prokaryotes was confirmed. The new assay was applied in comparison with the 16S rRNA gene-based analysis to investigate the microbial diversity of the sulfur cycle in sediment, seawater, and manganese crust samples from four study sites in the area of the Lesser Antilles volcanic arc, Caribbean Sea (Caribflux project). The aprA gene-based approach revealed putative sulfur-oxidizing Alphaproteobacteria of chemolithoheterotrophic lifestyle to have been abundant in the nonhydrothermal sediment and water column. In contrast, the sulfur-based microbial community that inhabited the surface of the volcanic manganese crust was more complex, consisting predominantly of putative chemolithoautotrophic sulfur oxidizers of the Betaproteobacteria and Gammaproteobacteria.

Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes--origin and evolution of the dissimilatory sulfate-reduction pathway

Newly developed PCR assays were used to PCR-amplify and sequence fragments of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase genes (aprBA) comprising nearly the entire gene locus (2.2-2.4 kb, equal to 92-94 % of the protein coding sequence) from 75 sulfate-reducing prokaryotes (SRP) of a taxonomically wide range. Comparative phylogenetic analysis included all determined and publicly available AprBA sequences from SRP and selected homologous sequences of sulfur-oxidizing bacteria (SOB). The almost identical AprB and AprA tree topologies indicated a shared evolutionary path for the aprBA among the investigated SRP by vertical inheritance and concomitant lateral gene transfer (LGT). The topological comparison of AprB/A- and 16S rRNA gene-based phylogenetic trees revealed novel LGT events across the SRP divisions. Compositional gene analysis confirmed Thermacetogenium phaeum to be the first validated strain affected by a recent lateral transfer of aprBA as a putative effect of long-term co-cultivation with a Thermodesulfovibrio species. Interestingly, the Apr proteins of SRP and SOB diverged into two phylogenetic lineages, with the SRP affiliated with the green sulfur bacteria, e.g. Chlorobaculum tepidum, while the Allochromatium vinosum-related sequences formed a distinct group. Analysis of genome data indicated that this phylogenetic separation is also reflected in the differing presence of the putative proteins functionally associated with Apr, QmoABC complex (quinone-interacting membrane-bound oxidoreductase) and AprM (transmembrane protein). Scenarios for the origin and evolution of the dissimilatory APS reductase are discussed within the context of the dissimilatory sulfite reductase (DsrAB) phylogeny, the appearance of QmoABC and AprM in the SRP and SOB genomes, and the geochemical setting of Archean Earth.

Sulfurospirillum cavolei sp. nov., a facultatively anaerobic sulfur-reducing bacterium isolated from an underground crude oil storage cavity

A novel facultatively anaerobic sulfur-reducing bacterium, designated strain Phe91(T), was isolated from petroleum-contaminated groundwater in an underground crude oil storage cavity at Kuji in Iwate, Japan. Cells of strain Phe91(T) were slightly curved rods with single polar flagella. Optimum growth was observed at pH 7.0 and 30 degrees C. The novel strain utilized elemental sulfur, thiosulfate, sulfite, dithionite, arsenate, nitrate and DMSO as electron acceptors with lactate as an energy and carbon source, but nitrite was not utilized. Microaerophilic growth was also observed. Fumarate, pyruvate, lactate, malate, succinate, hydrogen (with acetate as a carbon source) and formate (with acetate) could serve as electron donors. Fumarate, pyruvate and malate were fermented. The DNA G+C content was 42.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Phe91(T) was affiliated with the genus Sulfurospirillum in the class Epsilonproteobacteria and was most closely related to Sulfurospirillum deleyianum (sequence similarity 97 %). However, the DNA-DNA hybridization value between strain Phe91(T) and S. deleyianum was only 14 %. Based on the physiological and phylogenetic data, Phe91(T) should be classified as a representative of a novel species in the genus Sulfurospirillum; the name Sulfurospirillum cavolei sp. nov. is proposed, with Phe91(T) (=JCM 13918(T)=DSM 18149(T)) as the type strain.

Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan

Two strictly anaerobic, mesophilic, sulfate-reducing bacterial strains, Pro1(T) and Pro16, were isolated from an estuarine sediment in the Sea of Japan of the Japanese islands and were characterized by phenotypic and phylogenetic methods. Strains Pro1(T) and Pro16 had almost the same physiological and chemotaxonomic characteristics. Cells of both strains were Gram-negative, motile, non-spore-forming rods. Catalase activity was not detected. The optimum NaCl concentration for growth was 3.0 % (w/v). The optimum temperature for growth was 35 degrees C and the optimum pH was 6.7. Both strains used formate, propionate, pyruvate, lactate, fumarate, malate, ethanol, propanol, butanol, glycerol, alanine, glucose, fructose and H(2) as electron donors for sulfate reduction and did not use acetate, butyrate, succinate, methanol, glycine, serine, aspartate, glutamate, cellobiose or sucrose. Organic electron donors were incompletely oxidized mainly to acetate. Both strains also used thiosulfate as an electron acceptor. Without electron acceptors, both strains fermented pyruvate and lactate. The genomic DNA G+C contents of strains Pro1(T) and Pro16 were 48.6 and 46.0 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-5(H(2)). Major cellular fatty acids of both strains were C(15 : 0), C(16 : 0), C(17 : 1)omega6 and C(18 : 1)omega7. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the class Deltaproteobacteria. The closest recognized relative of strains Pro1(T) and Pro16 was Desulfobulbus mediterraneus with sequence similarities of 95.2 and 94.8 %, respectively. Based on phylogenetic, physiological and chemotaxonomic characteristics, strains Pro1(T) and Pro16 represent a novel species of the genus Desulfobulbus, for which the name Desulfobulbus japonicus is proposed. The type strain is Pro1(T)(=JCM 14043(T)=DSM 18378(T)) and strain Pro16 (=JCM 14044=DSM 18379) is a reference strain.

Quantification of sulfate-reducing bacteria in industrial wastewater, by real-time polymerase chain reaction (PCR) using dsrA and apsA genes

Real-time polymerase chain reaction (PCR) is considered a highly sensitive method for the quantification of microbial organisms in environmental samples. This study was conducted to evaluate real-time PCR with SybrGreen detection as a quantification method for sulfate-reducing bacteria (SRB) in industrial wastewater produced by several chemical industries. We designed four sets of primers and developed standard curves based on genomic DNA of Desulfovibrio vulgaris from pure culture and on plasmids containing dissimilatory sulfate reductase (dsrA) or adenosine-5'-phosphosulfate reductase (apsA) genes of SRB. All the standard curves, two for dsrA and two for apsA genes, had a linear range between 0.95 x 10(2) and 9.5 x 10(6) copies/microL and between 1.2 x 10(3) and 1.2 x 10(7) copies/microL, respectively. The theoretical copy numbers of the tenfold dilutions of D. vulgaris genomic DNA were best estimated (between 2.7 to 10.5 times higher than theoretical numbers) by the standard curve with DSR1F and RH3-dsr-R primers. To mimic the effect of foreign DNA in environmental samples, serial dilutions of D. vulgaris genomic DNA were mixed with Escherichia coli chromosomal DNA (40 ng per assay). This influenced neither PCR amplification nor the quantification of target DNA. Industrial wastewater was sampled during a 15-month period and analyzed for the presence of SRB, based on dsrA gene amplification. SRB displayed a higher abundance during the summer (about 10(7)-10(8) targets mL(-1)) and lower during the winter (about 10(4)-10(5) targets mL(-1)). The results indicate that our real-time PCR approach can be used for detection of uncultured SRB and will provide valuable information related to the abundance of SRB in durable environmental samples, such as complex and saline industrial wastewaters.