Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum , appeared to have coupled acetate oxidation to sulfate reduction. We described a novel representative of the widespread uncultured phylum Candidatus Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name Ca. “Sabulitectum silens” and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the metabolic network of fermentative and sulfate-reducing microbial populations, their niches, and adaptations to a dynamic environment.

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Butyrate Conversion by Sulfate-Reducing and Methanogenic Communities from Anoxic Sediments of Aarhus Bay, Denmark

Microorganisms ◽

10.3390/microorganisms8040606 ◽

2020 ◽

Vol 8 (4) ◽

pp. 606

Author(s):

Derya Ozuolmez ◽

Elisha K. Moore ◽

Ellen C. Hopmans ◽

Jaap S. Sinninghe Damsté ◽

Alfons J. M. Stams ◽

...

Keyword(s):

Sulfate Reduction ◽

Marine Sediments ◽

Relative Abundance ◽

Archaeal Community ◽

Community Analysis ◽

Sulfate Concentration ◽

Vertical Separation ◽

Sulfate Reducers ◽

Sulfate Reducing ◽

Initial Zone

The conventional perception that the zone of sulfate reduction and methanogenesis are separated in high- and low-sulfate-containing marine sediments has recently been changed by studies demonstrating their co-occurrence in sediments. The presence of methanogens was linked to the presence of substrates that are not used by sulfate reducers. In the current study, we hypothesized that both groups can co-exist, consuming common substrates (H2 and/or acetate) in sediments. We enriched butyrate-degrading communities in sediment slurries originating from the sulfate, sulfate–methane transition, and methane zone of Aarhus Bay, Denmark. Sulfate was added at different concentrations (0, 3, 20 mM), and the slurries were incubated at 10 °C and 25 °C. During butyrate conversion, sulfate reduction and methanogenesis occurred simultaneously. The syntrophic butyrate degrader Syntrophomonas was enriched both in sulfate-amended and in sulfate-free slurries, indicating the occurrence of syntrophic conversions at both conditions. Archaeal community analysis revealed a dominance of Methanomicrobiaceae. The acetoclastic Methanosaetaceae reached high relative abundance in the absence of sulfate, while presence of acetoclastic Methanosarcinaceae was independent of the sulfate concentration, temperature, and the initial zone of the sediment. This study shows that there is no vertical separation of sulfate reducers, syntrophs, and methanogens in the sediment and that they all participate in the conversion of butyrate.

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Pseudodesulfovibrio cashew sp. Nov., a Novel Deep-Sea Sulfate-Reducing Bacterium, Linking Heavy Metal Resistance and Sulfur Cycle

Microorganisms ◽

10.3390/microorganisms9020429 ◽

2021 ◽

Vol 9 (2) ◽

pp. 429

Author(s):

Rikuan Zheng ◽

Shimei Wu ◽

Chaomin Sun

Keyword(s):

Heavy Metal ◽

Sulfate Reduction ◽

Marine Sediments ◽

Deep Sea ◽

Sulfur Cycle ◽

Metal Sulfides ◽

Phenotypic Traits ◽

Dissimilatory Sulfate Reduction ◽

Metabolic Potential ◽

Sulfate Reducing

Sulfur cycling is primarily driven by sulfate reduction mediated by sulfate-reducing bacteria (SRB) in marine sediments. The dissimilatory sulfate reduction drives the production of enormous quantities of reduced sulfide and thereby the formation of highly insoluble metal sulfides in marine sediments. Here, a novel sulfate-reducing bacterium designated Pseudodesulfovibrio cashew SRB007 was isolated and purified from the deep-sea cold seep and proposed to represent a novel species in the genus of Pseudodesulfovibrio. A detailed description of the phenotypic traits, phylogenetic status and central metabolisms of strain SRB007 allowed the reconstruction of the metabolic potential and lifestyle of a novel member of deep-sea SRB. Notably, P. cashew SRB007 showed a strong ability to resist and remove different heavy metal ions including Co2+, Ni2+, Cd2+ and Hg2+. The dissimilatory sulfate reduction was demonstrated to contribute to the prominent removal capability of P. cashew SRB007 against different heavy metals via the formation of insoluble metal sulfides.

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Diversity of Sulfur Isotope Fractionations by Sulfate-Reducing Prokaryotes

Applied and Environmental Microbiology ◽

10.1128/aem.67.2.888-894.2001 ◽

2001 ◽

Vol 67 (2) ◽

pp. 888-894 ◽

Cited By ~ 257

Author(s):

Jan Detmers ◽

Volker Brüchert ◽

Kirsten S. Habicht ◽

Jan Kuever

Keyword(s):

Sulfate Reduction ◽

Isotope Fractionation ◽

Sulfur Isotope ◽

Reduction Rate ◽

Sulfate Reduction Rate ◽

Dissimilatory Sulfate Reduction ◽

Systematic Effect ◽

Sulfate Reducers ◽

Sulfate Reducing ◽

Sulfur Isotope Fractionation

ABSTRACT Batch culture experiments were performed with 32 different sulfate-reducing prokaryotes to explore the diversity in sulfur isotope fractionation during dissimilatory sulfate reduction by pure cultures. The selected strains reflect the phylogenetic and physiologic diversity of presently known sulfate reducers and cover a broad range of natural marine and freshwater habitats. Experimental conditions were designed to achieve optimum growth conditions with respect to electron donors, salinity, temperature, and pH. Under these optimized conditions, experimental fractionation factors ranged from 2.0 to 42.0‰. Salinity, incubation temperature, pH, and phylogeny had no systematic effect on the sulfur isotope fractionation. There was no correlation between isotope fractionation and sulfate reduction rate. The type of dissimilatory bisulfite reductase also had no effect on fractionation. Sulfate reducers that oxidized the carbon source completely to CO2 showed greater fractionations than sulfate reducers that released acetate as the final product of carbon oxidation. Different metabolic pathways and variable regulation of sulfate transport across the cell membrane all potentially affect isotope fractionation. Previous models that explained fractionation only in terms of sulfate reduction rates appear to be oversimplified. The species-specific physiology of each sulfate reducer thus needs to be taken into account to understand the regulation of sulfur isotope fractionation during dissimilatory sulfate reduction.

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Sulfur Isotope Enrichment during Maintenance Metabolism in the Thermophilic Sulfate-Reducing Bacterium Desulfotomaculum putei

Applied and Environmental Microbiology ◽

10.1128/aem.02948-08 ◽

2009 ◽

Vol 75 (17) ◽

pp. 5621-5630 ◽

Cited By ~ 22

Author(s):

Mark M. Davidson ◽

M. E. Bisher ◽

Lisa M. Pratt ◽

Jon Fong ◽

Gordon Southam ◽

...

Keyword(s):

Sulfate Reduction ◽

Batch Culture ◽

Marine Sediments ◽

Maintenance Phase ◽

Laboratory Culture ◽

Specific Rate ◽

Culture Vessel ◽

Isotope Enrichment ◽

Sulfate Reducing ◽

Sulfate Reduction Rates

ABSTRACT Values of Δ34S ( \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({=}{\delta}^{34}S_{HS}{-}{\delta}^{34}S_{SO_{4}}\) \end{document} , where δ34SHS and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\delta}^{34}S_{SO_{4}}\) \end{document} indicate the differences in the isotopic compositions of the HS− and SO4 2− in the eluent, respectively) for many modern marine sediments are in the range of −55 to −75‰, much greater than the −2 to −46‰ ε34S (kinetic isotope enrichment) values commonly observed for microbial sulfate reduction in laboratory batch culture and chemostat experiments. It has been proposed that at extremely low sulfate reduction rates under hypersulfidic conditions with a nonlimited supply of sulfate, isotopic enrichment in laboratory culture experiments should increase to the levels recorded in nature. We examined the effect of extremely low sulfate reduction rates and electron donor limitation on S isotope fractionation by culturing a thermophilic, sulfate-reducing bacterium, Desulfotomaculum putei, in a biomass-recycling culture vessel, or “retentostat.” The cell-specific rate of sulfate reduction and the specific growth rate decreased progressively from the exponential phase to the maintenance phase, yielding average maintenance coefficients of 10−16 to 10−18 mol of SO4 cell−1 h−1 toward the end of the experiments. Overall S mass and isotopic balance were conserved during the experiment. The differences in the δ34S values of the sulfate and sulfide eluting from the retentostat were significantly larger, attaining a maximum Δ34S of −20.9‰, than the −9.7‰ observed during the batch culture experiment, but differences did not attain the values observed in marine sediments.

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Competition for H2 between sulfate reducers, methanogens and homoacetogens in a gas-lift reactor

Water Science & Technology ◽

10.2166/wst.2002.0294 ◽

2002 ◽

Vol 45 (10) ◽

pp. 75-80 ◽

Cited By ~ 57

Author(s):

J. Weijma ◽

F. Gubbels ◽

L.W. Hulshoff Pol ◽

A.J.M. Stams ◽

P. Lens ◽

...

Keyword(s):

Kinetic Parameters ◽

Sulfate Reduction ◽

Growth Kinetic ◽

Settling Velocity ◽

Sulfate Reducing Bacteria ◽

Anaerobic Sludge ◽

Sulfate Reducers ◽

Sulfate Reducing ◽

Reducing Bacteria ◽

Gas Lift

Reported values for growth kinetic parameters show an order in competitivity of heterotrophic sulfate reducing bacteria>methanogens>homoacetogens for the substrate hydrogen. This order suggests that methanogens can succesfully compete with consortia of heterotrophic SRB and homoacetogens when H2/CO2 is present as sole substrate. However, we found in experiments using gas-lift reactors inoculated with anaerobic sludge and fed with H2/CO2 and sulfate, that heterotrophic sulfate reduction rapidly and completely outcompeted methanogenesis, whereas a low amount of acetate was formed. Thus, in disagreement with the above competitivity order, hydrogen is more readily consumed by homoacetogenesis than by methanogenesis, indicating that the competition is not kinetically determined. The superior settling velocity of sulfidogenic-acetogenic sludge compared to that of methanogenic sludge suggests that the former sludge is better retained, which can explain the predominance of sulfate reduction/homoacetogenesis over methanogenesis.

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Clustered Genes Related to Sulfate Respiration in Uncultured Prokaryotes Support the Theory of Their Concomitant Horizontal Transfer

Journal of Bacteriology ◽

10.1128/jb.187.20.7126-7137.2005 ◽

2005 ◽

Vol 187 (20) ◽

pp. 7126-7137 ◽

Cited By ~ 48

Author(s):

Marc Mussmann ◽

Michael Richter ◽

Thierry Lombardot ◽

Anke Meyerdierks ◽

Jan Kuever ◽

...

Keyword(s):

Sulfate Reduction ◽

Marine Sediments ◽

Horizontal Transfer ◽

Successful Implementation ◽

Dissimilatory Sulfate Reduction ◽

Prosthetic Group ◽

Sulfate Reducing ◽

Dissimilatory Sulfite Reductase ◽

Sulfur Intermediates ◽

Horizontal Transfers

ABSTRACT The dissimilatory reduction of sulfate is an ancient metabolic process central to today's biogeochemical cycling of sulfur and carbon in marine sediments. Until now its polyphyletic distribution was most parsimoniously explained by multiple horizontal transfers of single genes rather than by a not-yet-identified “metabolic island.” Here we provide evidence that the horizontal transfer of a gene cluster may indeed be responsible for the patchy distribution of sulfate-reducing prokaryotes (SRP) in the phylogenetic tree. We isolated three DNA fragments (32 to 41 kb) from uncultured, closely related SRP from DNA directly extracted from two distinct marine sediments. Fosmid ws39f7, and partially also fosmids ws7f8 and hr42c9, harbored a core set of essential genes for the dissimilatory reduction of sulfate, including enzymes for the reduction of sulfur intermediates and synthesis of the prosthetic group of the dissimilatory sulfite reductase. Genome comparisons suggest that encoded membrane proteins universally present among SRP are critical for electron transfer to cytoplasmic enzymes. In addition, novel, conserved hypothetical proteins that are likely involved in dissimilatory sulfate reduction were identified. Based on comparative genomics and previously published experimental evidence, a more comprehensive model of dissimilatory sulfate reduction is presented. The observed clustering of genes involved in dissimilatory sulfate reduction has not been previously found. These findings strongly support the hypothesis that genes responsible for dissimilatory sulfate reduction were concomitantly transferred in a single event among prokaryotes. The acquisition of an optimized gene set would enormously facilitate a successful implementation of a novel pathway.

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Genomic variation of microbial populations on a continuous 10,000-year sediment sequence from Lake Cadagno (Piora Valley, Switzerland)

10.5194/egusphere-egu21-8230 ◽

2021 ◽

Author(s):

Paula Catalina Rodriguez Ramirez ◽

Jasmine Berg ◽

Longhui Deng ◽

Hendrik Vogel ◽

Mark A. Lever ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sulfate Reduction ◽

Microbial Populations ◽

Gene Copy ◽

Sulfur Cycling ◽

Rrna Gene ◽

Sediment Layer ◽

Metagenomic Sequencing ◽

Sulfate Reducing

Lake Cadagno is a meromictic Alpine lake located in the Piora Valley, Switzerland. In 2019, a 10,000-year (10 m)sediment sequence was collected and found to contain three main lithological units: glacial sediment deposited under oxic conditions; a Mn-rich and organic-matter-rich sediment layer deposited during the transition from an oxic late-glacial lake to the onset of anoxia, and dark, sulfidic sediments deposited during the period of euxinia to the present. This study investigates the relationships between the physical-chemical properties and microorganisms of the sediment sequenceusing genome-resolved and targeted metagenomics.&#160; &#160;Results show that 16S rRNA gene abundance peaks in upper 1-32 cm of the sediment core (108 copies per gram of sediment) and decreases with depth. The abundance of a marker gene for sulfate reduction, dsrB, is positively correlated to 16S rRNA gene copy numbers, decreasing with depth from approximately 108 copies per gram of sediment in the top 30 cm to 104 gene copies per gram of sediment at 900 cm below the sediment depth.&#160; These results suggest that sulfate-reducing microbial communities in surface sediments harvest the bioavailable oxidized sulfur inorganic species. In contrast, the presence of sulfate-reducing genes in sediments with sulfate concentrations below detection may indicate the engagement of microbial populations in sulfur cycling using alternative metabolic strategies (e.g. secondary fermentation).&#160;Moreover, a clear differentiation between surface and deep sediment communities is observed. Sequencing of dsrB amplicons show a decrease in dsrB sequence richness with depth and sediment age. A clear transition from a surface section dominated (>80% relative abundance) by Deltaproteobacteria-related dsrB sequences from well-studied groups, to a deeper section below 40 cm dominated by a group of unclassified dsrB sequences most likely related to Firmicutes or Chloroflexi is also observed. The identity of these unclassified dsrB sequences will be determined by genome-resolved metagenomic sequencing (currently in progress). Furthermore, these analyses will give information on the presence of complete sulfate-reduction pathways and/or genes related to sulfur cycling in these microbial groups. By reconstructing the genomes of sulfate reducers and other microbial populations throughout the core, we will investigate whether there are genomic changes associated with the main geochemical trends. This work will enable us to assess the influence of a changing lake with the evolution of sediment-dwelling prokaryotic populations over thousands of years.&#160;&#160;&#160;

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Effects of two diamine biocides on the microbial community from an oil field

Canadian Journal of Microbiology ◽

10.1139/w98-105 ◽

1998 ◽

Vol 44 (11) ◽

pp. 1060-1065 ◽

Cited By ~ 18

Author(s):

Anita J Telang ◽

Sara Ebert ◽

Julia M Foght ◽

Donald WS Westlake ◽

Gerrit Voordouw

Keyword(s):

Sulfate Reduction ◽

Microbial Population ◽

Oil Field ◽

Microbial Populations ◽

Microbial Corrosion ◽

Broad Distribution ◽

Sulfate Reducing ◽

Production Water ◽

Field Samples ◽

Reducing Bacteria

The effects of diamine (R1-NH-R2-NH2) biocides A and B on the microbial population from an oil field were investigated with reverse sample genome probing (RSGP), a technique designed to track multiple oil field bacteria in a single assay. RSGP studies of sessile microbial populations scraped from corrosion coupons obtained from biocide-treated oil field installations indicated dominance of Desulfovibrio spp. Lac6 and Eth3, or of selected heterotrophs. RSGP of planktonic production water samples indicated a broad distribution of microorganisms that changed with the addition of medium for the growth of sulfate-reducing bacteria, containing different organic acids as electron donors for sulfate reduction. Use of lactate, propionate, or acetate enriched Desulfovibrio spp., Desulfobulbus sp. Pro4, or Desulfobacter spp., respectively. Treatment of lactate- or mixed organic acid-fed planktonic populations with biocides indicated resistance of Lac6 and Eth3 to 400 ppm of biocide B and 40 ppm of biocide A. The dominance of these two Desulfovibrio spp. in many sessile field samples is, therefore, likely caused by biocide selection.Key words: Desulfovibrio, sulfate reduction, microbial corrosion, souring, biocide.

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Sulfate-Reducing Bacteria Methylate Mercury at Variable Rates in Pure Culture and in Marine Sediments

Applied and Environmental Microbiology ◽

10.1128/aem.66.6.2430-2437.2000 ◽

2000 ◽

Vol 66 (6) ◽

pp. 2430-2437 ◽

Cited By ~ 220

Author(s):

Jeffrey K. King ◽

Joel E. Kostka ◽

Marc E. Frischer ◽

F. Michael Saunders

Keyword(s):

Sulfate Reduction ◽

Marine Sediments ◽

Marine Sediment ◽

Pure Culture ◽

Sulfate Reducing Bacteria ◽

Mercury Methylation ◽

Sulfate Reducing ◽

The Family ◽

Pure Cultures ◽

Reducing Bacteria

ABSTRACT Differences in methylmercury (CH3Hg) production normalized to the sulfate reduction rate (SRR) in various species of sulfate-reducing bacteria (SRB) were quantified in pure cultures and in marine sediment slurries in order to determine if SRB strains which differ phylogenetically methylate mercury (Hg) at similar rates. Cultures representing five genera of the SRB (Desulfovibrio desulfuricans, Desulfobulbus propionicus,Desulfococcus multivorans, Desulfobacter sp. strain BG-8, and Desulfobacterium sp. strain BG-33) were grown in a strictly anoxic, minimal medium that received a dose of inorganic Hg 120 h after inoculation. The mercury methylation rates (MMR) normalized per cell were up to 3 orders of magnitude higher in pure cultures of members of SRB groups capable of acetate utilization (e.g., the family Desulfobacteriaceae) than in pure cultures of members of groups that are not able to use acetate (e.g., the family Desulfovibrionaceae). Little or no Hg methylation was observed in cultures of Desulfobacterium orDesulfovibrio strains in the absence of sulfate, indicating that Hg methylation was coupled to respiration in these strains. Mercury methylation, sulfate reduction, and the identities of sulfate-reducing bacteria in marine sediment slurries were also studied. Sulfate-reducing consortia were identified by using group-specific oligonucleotide probes that targeted the 16S rRNA molecule. Acetate-amended slurries, which were dominated by members of the Desulfobacterium and Desulfobacter groups, exhibited a pronounced ability to methylate Hg when the MMR were normalized to the SRR, while lactate-amended and control slurries had normalized MMR that were not statistically different. Collectively, the results of pure-culture and amended-sediment experiments suggest that members of the family Desulfobacteriaceae have a greater potential to methylate Hg than members of the familyDesulfovibrionaceae have when the MMR are normalized to the SRR. Hg methylation potential may be related to genetic composition and/or carbon metabolism in the SRB. Furthermore, we found that in marine sediments that are rich in organic matter and dissolved sulfide rapid CH3Hg accumulation is coupled to rapid sulfate reduction. The observations described above have broad implications for understanding the control of CH3Hg formation and for developing remediation strategies for Hg-contaminated sediments.

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Desulfovibrio marinus sp. nov., a moderately halophilic sulfate-reducing bacterium isolated from marine sediments in Tunisia

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64790-0 ◽

2007 ◽

Vol 57 (9) ◽

pp. 2167-2170 ◽

Cited By ~ 19

Author(s):

O. Ben Dhia Thabet ◽

M.-L. Fardeau ◽

C. Suarez-Nuñez ◽

M. Hamdi ◽

P. Thomas ◽

...

Keyword(s):

Marine Sediments ◽

Rrna Gene ◽

Strictly Anaerobic ◽

The Novel ◽

Bacterial Strains ◽

Terminal Electron Acceptor ◽

Moderately Halophilic ◽

Sulfate Reducing ◽

Gene Sequence Analysis ◽

Genomic Relatedness

Two novel sulfate-reducing bacterial strains, designated E-2T and IMP-2, were isolated from geographically distinct locations. Strain E-2T was recovered from marine sediments near Sfax (Tunisia), whereas strain IMP-2 originated from oilfield production fluids in the Gulf of Mexico. Cells were Gram-negative, non-sporulated, motile, vibrio-shaped or sigmoid. They were strictly anaerobic, mesophilic and moderately halophilic. Sulfate, sulfite, thiosulfate and elemental sulfur served as electron acceptors, but not nitrate or nitrite. H2 (with acetate as carbon source), formate, fumarate, lactate, malate, pyruvate, succinate and fructose were used as electron donors in the presence of sulfate as terminal electron acceptor. Lactate was oxidized incompletely to acetate. Fumarate and pyruvate were fermented. Desulfoviridin and c-type cytochromes were present. 16S rRNA gene sequence analysis of the two strains showed that they were phylogenetically similar (99.0 % similarity) and belonged to the genus Desulfovibrio, with Desulfovibrio indonesiensis and Desulfovibrio gabonensis as their closest phylogenetic relatives. The G+C content of the DNA was respectively 60.4 and 62.7 mol% for strains E-2T and IMP-2. DNA–DNA hybridization experiments revealed that the novel strains had a high genomic relatedness, suggesting that they belong to the same species. We therefore propose that the two isolates be affiliated to a novel species of the genus Desulfovibrio, Desulfovibrio marinus sp. nov. The type strain is strain E-2T (=DSM 18311T =JCM 14040T).

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