Vertical distribution of sulfate-reducing bacteria at the oxic-anoxic interface in sediments of the oligotrophic Lake Stechlin

Successional development of sulfate-reducing bacterial populations and their activities in a wastewater biofilm growing under microaerophilic conditions

A combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA fragments, and 16S rRNA gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 microM) and in the presence of nitrate. Microelectrode measurements showed that oxygen penetrated 200 microm from the surface during all stages of biofilm development. The first sulfide production of 0.32 micromol of H(2)S m(-2) s(-1) was detected below ca. 500 microm in the 3rd week and then gradually increased to 0.70 micromol H(2)S m(-2) s(-1) in the 8th week. The most active sulfide production zone moved upward to the oxic-anoxic interface and intensified with time. This result coincided with an increase in SRB populations in the surface layer of the biofilm. The numbers of the probe SRB385- and 660-hybridized SRB populations significantly increased to 7.9 x 10(9) cells cm(-3) and 3.6 x 10(9) cells cm(-3), respectively, in the surface 400 microm during an 8-week cultivation, while those populations were relatively unchanged in the deeper part of the biofilm, probably due to substrate transport limitation. Based on 16S rRNA gene cloning analysis data, clone sequences that related to Desulfomicrobium hypogeium (99% sequence similarity) and Desulfobulbus elongatus (95% sequence similarity) were most frequently found. Different molecular analyses confirmed that Desulfobulbus, Desulfovibrio, and Desulfomicrobium were found to be the numerically important members of SRB in this wastewater biofilm.

Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization

We simultaneously determined the phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria (SRB) inhabiting a sewer biofilm with oxygen, nitrate, or sulfate as an electron acceptor by combining microautoradiography and fluorescent in situ hybridization (MAR-FISH) with family- and genus-specific 16S rRNA probes. The MAR-FISH analysis revealed that Desulfobulbus hybridized with probe 660 was a dominant SRB subgroup in this sewer biofilm, accounting for 23% of the total SRB. Approximately 9 and 27% of Desulfobulbus cells detected with probe 660 could take up [(14)C]propionate with oxygen and nitrate, respectively, as an electron acceptor, which might explain the high abundance of this species in various oxic environments. Furthermore, more than 40% of Desulfobulbus cells incorporated acetate under anoxic conditions. SRB were also numerically important members of H(2)-utilizing and (14)CO(2)-fixing microbial populations in this sewer biofilm, accounting for roughly 42% of total H(2)-utilizing bacteria hybridized with probe EUB338. A comparative 16S ribosomal DNA analysis revealed that two SRB populations, related to the Desulfomicrobium hypogeium and the Desulfovibrio desulfuricans MB lineages, were found to be important H(2) utilizers in this biofilm. The substrate uptake characteristics of different phylogenetic SRB subgroups were compared with the characteristics described to date. These results provide further insight into the correlation between the 16S rRNA phylogenetic diversity and the physiological diversity of SRB populations inhabiting sewer biofilms.

Composition and Activity of Marine Alkane-Degrading Bacterial Communities in the Transition from Suboxic to Anoxic Conditions

The impact of the oxygen supply rate (OSR) on the metabolic activity and on the composition of hexadecane-degrading bacterial communities in a quasi-anoxic milieu (nominal DOT = 0%) was studied in continuous cultures containing intertidal sediment. The dilution rate was kept constant at 0.035 h-1. The OSR was stepwise reduced from 3.5 mmol O2 L-1 h-1 to 0.06 mmol O2 L-1 h-1. Activity was determined by analyzing the respiration quotient (RQ) and the rates of hexadecane degradation (QHex), of hexadecane mineralization, and of protein production (PPR). The community composition and size were investigated by fluorescence in situ hybridization (FISH), by dilution plating (colony forming units or CFU), and by most probable number (MPN). The culture showed an aerobic hexadecane metabolism down to an OSR of 0.35 mmol O2 L-1 h-1. Below this OSR, anaerobic metabolism was initiated. The relationship among the RQ, PPR, QHex, and the OSR can be approximated by hyperbola (Michaelis-Menten kinetics). We suggest that the metabolic adaptation of the culture to low OSRs is due to regulation of protein expression and enzyme activity. Reducing the OSR resulted in minor but significant changes in the concentration of different physiological and phylogenetic groups. This means that, in addition to protein expression and activity regulation, the adaptation of the population to low OSRs is due to changes in the community composition.

Behavior of sulfate reducing bacteria under oligotrophic conditions and oxygen stress in particle-free systems related to drinking water

The response of sulfate reducing bacteria (SRB) to oxygen stress under oligotrophic conditions in particle-free systems was studied in (i) sterile Berlin drinking water; (ii) mineral medium; and (iii) in coculture experiments with aerobic bacteria. Using a polyphasic approach including anaerobic cultivation, fluorescent in situ hybridization (FISH) and digital image analysis, the behavior of the strains zt3l and zt10e, isolated from Berlin groundwater and affiliated to the family Desulfovibrionaceae, was compared to the type strains Desulfomicrobium baculatum and Desulfovibrio desulfuricans. Anaerobic deep agar dilution series were performed for the determination of cell culturability. FISH and subsequent digital image analysis of probe-conferred fluorescence intensities were used for the assessment of metabolic activity. For the in situ identification of both isolates in coculture tests, two strain-specific oligonucleotides were developed and evaluated. The total cell counts of stressed SRB in drinking water decreased during the course of the assay dependent on the strain. Both environmental isolates could be cultured for a longer period than cells of D. baculatum and D. desulfuricans, respectively. The FISH intensities showed a strain-specific behavior. When exposed to simultaneous oxygen stress and carbon limitation in mineral medium, total cell counts of all four strains remained constant throughout a period of 72 days. The rate of culturability differed between the investigated strains. The decrease of metabolic activity as assessed by FISH was a strain-specific property. Exposure of SRB to oxygen stress and carbon starvation in coculture experiments with Aquabacterium commune resulted in strain dependent prolonged culturability and a delayed decrease of the metabolic activity compared to pure culture tests for all strains tested. Total cell counts of SRB were constant throughout the whole experiment.

Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores

Molecular ecology techniques were applied to assess changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Microsensor measurements showed that oxygen was depleted from 140 microM at the floodwater/soil interface to nondetectable amounts at a depth of approximately 2.0 mm and below. Bacterial 16S rRNA gene (rDNA)-based community fingerprint patterns were obtained from 200-microm-thick soil slices of both the oxic and anoxic zones by using the T-RFLP (terminal restriction fragment length polymorphism) technique. The fingerprints revealed a tremendous shift in the community patterns in correlation to the oxygen depletion measured with depth. 16S rDNA clone sequences recovered from the oxic or anoxic zone directly corresponded to those terminal restriction fragments which were highly characteristic of the respective zone. Comparative sequence analysis of these clones identified members of the alpha and beta subclasses of Proteobacteria as the abundant populations in the oxic zone. In contrast, members of clostridial cluster I were determined to be the predominant bacterial group in the oxygen-depleted soil. The extraction of total RNA followed by reverse transcription-PCR of the bacterial 16S rRNA and T-RFLP analysis resulted for both oxic and anoxic zones of flooded soil cores in community fingerprint patterns similar to those obtained by the rDNA-based analysis. This finding suggests that the microbial groups detected on the rDNA level are the metabolically active populations within the oxic and anoxic soil slices examined.

Unexpected population distribution in a microbial mat community: sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia

The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with group-specific hybridization probes to quantify 16S rRNA extracted from 100-microm depth intervals. This revealed a preferential localization of SRB within the region defined by the oxygen chemocline. Among the different groups of SRB quantified, including members of the provisional families "Desulfovibrionaceae" and "Desulfobacteriaceae," Desulfonema-like populations dominated and accounted for up to 30% of total rRNA extracted from certain depth intervals of the chemocline. These data suggest that recognized genera of SRB are not necessarily restricted by high levels of oxygen in this mat community and the possibility of significant sulfur cycling within the chemocline. In marked contrast, eukaryotic populations in this community demonstrated a preference for regions of anoxia.

Sulfate-reducing bacteria in rice field soil and on rice roots

Rice plants that were grown in flooded rice soil microcosms were examined for their ability to exhibit sulfate reducing activity. Washed excised rice roots showed sulfate reduction potential when incubated in anaerobic medium indicating the presence of sulfate-reducing bacteria. Rice plants, that were incubated in a double-chamber (phylloshpere and rhizosphere separated), showed potential sulfate reduction rates in the anoxic rhizosphere compartment. These rates decreased when oxygen was allowed to penetrate through the aerenchyma system of the plants into the anoxic root compartment, indicating that sulfate reducers on the roots were partially inhibited by oxygen or that sulfate was regenerated by oxidation of reduced S-compounds. The potential activity of sulfate reducers on rice roots was consistent with MPN enumerations showing that H2-utilizing sulfate-reducing bacteria were present in high numbers on the rhizoplane (4.1 x 10(7) g-1 root fresh weight) and in the adjacent rhizosperic soil (2.5 x 10(7) g-1 soil dry weight). Acetate-oxidizing sulfate reducers, on the other hand, showed highest numbers in the unplanted bulk soil (1.9 x 10(6) g-1 soil dry weight). Two sulfate reducing bacteria were isolated from the highest dilutions of the MPN series and were characterized physiologically and phylogenetically. Strain F1-7b which was isolated from the rhizoplane with H2 as electron donor was related to subgroup II of the family Desulfovibrionaceae. Strain EZ-2C2, isolated from the rhizoplane on acetate, grouped together with Desulforhabdus sp. and Syntrophobacter wolinii. Other strains of sulfate-reducing bacteria originated from bulk soil of rice soil microcosms and were isolated using different electron donors. From these isolates, strains R-AcA1, R-IbutA1, R-PimA1 and R-AcetonA170 were Gram-positive bacteria which were affiliated with the genus Desulfotomaculum. The other isolates were members of subgroup II of the Desulfovibrionaceae (R-SucA1 and R-LacA1), were related to Desulforhabdus sp. (strain BKA11), Desulfobulbus (R-PropA1), or culstered between Desulfobotulus sapovorans and Desulfosarcina variabilis (R-ButA1 and R-CaprA1).

Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of spartina alterniflora

The population composition and biogeochemistry of sulfate-reducing bacteria (SRB) in the rhizosphere of the marsh grass Spartina alterniflora was investigated over two growing seasons by molecular probing, enumerations of culturable SRB, and measurements of SO42- reduction rates and geochemical parameters. SO42- reduction was rapid in marsh sediments with rates up to 3.5 &mgr;mol ml-1 day-1. Rates increased greatly when plant growth began in April and decreased again when plants flowered in late July. Results with nucleic acid probes revealed that SRB rRNA accounted for up to 43% of the rRNA from members of the domain Bacteria in marsh sediments, with the highest percentages occurring in bacteria physically associated with root surfaces. The relative abundance (RA) of SRB rRNA in whole-sediment samples compared to that of Bacteria rRNA did not vary greatly throughout the year, despite large temporal changes in SO42- reduction activity. However, the RA of root-associated SRB did increase from <10 to >30% when plants were actively growing. rRNA from members of the family Desulfobacteriaceae comprised the majority of the SRB rRNA at 3 to 34% of Bacteria rRNA, with Desulfobulbus spp. accounting for 1 to 16%. The RA of Desulfovibrio rRNA generally comprised from <1 to 3% of the Bacteria rRNA. The highest Desulfobacteriaceae RA in whole sediments was 26% and was found in the deepest sediment samples (6 to 8 cm). Culturable SRB abundance, determined by most-probable-number analyses, was high at >10(7) ml-1. Ethanol utilizers were most abundant, followed by acetate utilizers. The high numbers of culturable SRB and the high RA of SRB rRNA compared to that of Bacteria rRNA may be due to the release of SRB substrates in plant root exudates, creating a microbial food web that circumvents fermentation.

Sulfate-reducing bacteria and their activities in cyanobacterial mats of solar lake (Sinai, Egypt)

The sulfate-reducing bacteria within the surface layer of the hypersaline cyanobacterial mat of Solar Lake (Sinai, Egypt) were investigated with combined microbiological, molecular, and biogeochemical approaches. The diurnally oxic surface layer contained between 10(6) and 10(7) cultivable sulfate-reducing bacteria ml-1 and showed sulfate reduction rates between 1,000 and 2, 200 nmol ml-1 day-1, both in the same range as and sometimes higher than those in anaerobic deeper mat layers. In the oxic surface layer and in the mat layers below, filamentous sulfate-reducing Desulfonema bacteria were found in variable densities of 10(4) to 10(6) cells ml-1. A Desulfonema-related, diurnally migrating bacterium was detected with PCR and denaturing gradient gel electrophoresis within and below the oxic surface layer. Facultative aerobic respiration, filamentous morphology, motility, diurnal migration, and aggregate formation were the most conspicuous adaptations of Solar Lake sulfate-reducing bacteria to the mat matrix and to diurnal oxygen stress. A comparison of sulfate reduction rates within the mat and previously published photosynthesis rates showed that CO2 from sulfate reduction in the upper 5 mm accounted for 7 to 8% of the total photosynthetic CO2 demand of the mat.

Microbial Community Composition of Wadden Sea Sediments as Revealed by Fluorescence In Situ Hybridization

The microbial community composition of Wadden Sea sediments of the German North Sea coast was investigated by in situ hybridization with group-specific fluorescently labeled, rRNA-targeted oligonucleotides. A large fraction (up to 73%) of the DAPI (4',6-diamidino-2-phenylindole)-stained cells hybridized with the bacterial probes. Nearly 45% of the total cells could be further identified as belonging to known phyla. Members of the Cytophaga-Flavobacterium cluster were most abundant in all layers, followed by the sulfate-reducing bacteria.

Psychrotolerant sulfate-reducing bacteria from an oxic freshwater sediment, description of Desulfovibrio cuneatus sp. nov. and Desulfovibrio litoralis sp. nov

The most abundant culturable sulfate-reducing bacteria were isolated from the littoral sediment of the oligotrophic Lake Stechlin. The strains STL1 and STL4 were obtained from the oxic uppermost layer, while strain STL6 was isolated from the anoxic zone in 20 to 30 mm depth. The isolates showed a striking morphological feature in tapering off at one end of the cell. Physiological characteristics related them to the genus Desulfovibrio. They contained desulfoviridin. H2, formate, pyruvate, lactate, and fumarate were utilized with sulfate, sulfite, thiosulfate, or elemental sulfur as electron acceptors. All isolates were able to reduce oxygen and survived 120 h of aeration. However, aerobic growth was not observed. The isolates were psychrotolerant, and grew with rates of up to 0.29 d-1 at 4 degrees C. Analysis of the 16S rDNA confirmed that the strains belong to the genus Desulfovibrio. However, they were not closely related to any known member of this genus and formed a new cluster with at least two new species. Strain STL1 and STL4, exhibiting 99.7% sequence similarity in 16S rRNA, are proposed as the new species Desulfovibrio cuneatus sp. nov., while strain STL6 is assigned to the new species Desulfovibrio litoralis sp. nov.