Heterotrophic Sulfate-reducing Bacteria Research Articles

Molecular and isotopic signatures of oil-driven bacterial sulfate reduction at seeps in the southern Gulf of Mexico

Oil seepage is widespread in the Gulf of Mexico, which also applies to the Bay of Campeche in the southern Gulf. The ascension of crude oil and oil-derived hydrocarbons poses a challenge to most seep-dwelling organisms. On the other hand, short- and long-chain hydrocarbons have been shown to be potentially degraded by a range of heterotrophic sulfate-reducing bacteria. Here we present lipid biomarker and carbon isotope data from authigenic carbonates from the Campeche Knolls in the southern Gulf of Mexico and use methane-seep carbonates from the Makran convergent margin (southern Pakistan and Iran) for comparison. The Campeche Knolls and Makran were selected for such comparison as endmember types for oil versus methane seepage in an attempt to identify molecular signatures of oil seepage. The Campeche carbonates yielded on average higher δ13C values (−31.3‰ to −21.9‰) than the Makran methane-seep carbonates (−54.3‰ to −39.8‰) and revealed a particularly high content of ether lipids. The Campeche carbonates revealed a greater variety of alkyl chains in non-isoprenoidal dialkyl glycerol diether lipids (DAGE) and a higher relative proportion of long alkyl chains (DAGEs >C36) compared with the Makran methane-seep carbonates. Bacterial biomarkers showed an on average distinctively heavier δ13C signature than at the studied methane seeps, indicating bacterial oxidation of oil-derived hydrocarbons. Mixing calculations indicate that up to 73% of the local sulfate reduction is coupled to the oxidation of non-methane hydrocarbons at the oil seeps, contributing as much as 40% to carbonate precipitation. These data imply that oil-seep carbonates can be discriminated from methane-seep carbonates by their respective biomarker inventories in modern and, in cases of moderate to good biomarker preservation, ancient environments, setting the stage for the reconstruction of the influence of fluid composition on the compositions of chemosynthesis-based communities at seeps.

Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer

Nitrate pollution is a major threat to groundwater quality in agricultural areas. Natural attenuation of nitrate in contaminated aquifers is mediated by denitrifying microbial populations in anoxic environments. Vertical distribution of denitrifying microbial communities in aquifers is greatly influenced by groundwater redox conditions, local hydrogeological parameters, and seasonal variability in groundwater flow and recharge. In this study, we investigated groundwater geochemistry and the composition of bacterial and archaeal communities with increasing depth in a shallow nitrate-contaminated aquifer in British Columbia, Canada. High-resolution passive diffusion sampling was conducted to collect groundwater at 10-cm intervals from 4 to 20 m below ground surface (mbgs) in the aquifer. Geochemical analyses of major ions indicated a general shift in the groundwater chemistry below 16 mbgs including decreasing chloride concentrations that suggest two-end member mixing of shallow and deep groundwater with different chemistries. A redoxcline was further observed within a 2 m transition zone at 18–20 mbgs characterized by sharp declines in nitrate concentrations and increases in sulfate and total inorganic carbon. Excursions in δ15N-NO3− and δ18O-NO3− in the same depth interval are consistent with denitrification, and a concomitant decrease in δ34S-SO42− suggested that denitrification was coupled to sulfide or sulfur oxidation. Microbial communities within this depth interval were significantly dissimilar to those above and below, featuring putative lithotrophic denitrifying bacteria belonging to the genera Sulfurifustis, Sulfuritalea and Sulfuricella. These lineages were detected in greatest abundance at 19 mbgs while the abundances of putative heterotrophic sulfate-reducing bacteria belonging to the genus Desulfosporosinus were greatest at 20 mbgs. In addition to help distinguish denitrification from mixing-induced changes in groundwater chemistry, the above observed vertical stratification of the microbial key players connects nitrate removal to the locations of the aquifer sampled.

Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.

Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases."IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh.

Large sulfur bacteria of the genus Achromatium are exceptional among Bacteria and Archaea as they can accumulate high amounts of internal calcite. Although known for more than 100 years, they remain uncultured, and only freshwater populations have been studied so far. Here we investigate a marine population of calcite-accumulating bacteria that is primarily found at the sediment surface of tide pools in a salt marsh, where high sulfide concentrations meet oversaturated oxygen concentrations during the day. Dynamic sulfur cycling by phototrophic sulfide-oxidizing and heterotrophic sulfate-reducing bacteria co-occurring in these sediments creates a highly sulfidic environment that we propose induces behavioral differences in the Achromatium population compared with reported migration patterns in a low-sulfide environment. Fluctuating intracellular calcium/sulfur ratios at different depths and times of day indicate a biochemical reaction of the salt marsh Achromatium to diurnal changes in sedimentary redox conditions. We correlate this calcite dynamic with new evidence regarding its formation/mobilization and suggest general implications as well as a possible biological function of calcite accumulation in large bacteria in the sediment environment that is governed by gradients. Finally, we propose a new taxonomic classification of the salt marsh Achromatium based on their adaptation to a significantly different habitat than their freshwater relatives, as indicated by their differential behavior as well as phylogenetic distance on 16S ribosomal RNA gene level. In future studies, whole-genome characterization and additional ecophysiological factors could further support the distinctive position of salt marsh Achromatium.

Dynamic mathematical modeling of sulfate reducing gas-lift reactors

This paper presents a mathematical model able to simulate under dynamic conditions the physical, chemical and biological processes prevailing in a biological sulfate reducing gas-lift reactor. The proposed model is based on differential mass balance equations for substrates, products and bacterial groups involved in a sulfate reduction process. Heterotrophic sulfate reducing bacteria (HSRB), autotrophic sulfate reducing bacteria (ASRB), homoacetogenic bacteria (HB), methanogenic archaea (MA) and acetate degraders (AD) are the microbial groups taken into account in the model. The model is also used to validate a steady-state design model previously proposed by Esposito et al. [1].The proposed model is able to simulate the competition between the biological bacteria growing in the reactor, and predict the performance of a gas-lift reactor. The model includes two main parts: (1) a kinetic part including growth, metabolism and competition of SRB, HB, MA and AD in the system and (2) a mass-transfer part describing the thermodynamic concentration equilibria of gaseous components in the liquid and gas phase. The model has been validated using experimental data obtained by operating a laboratory-scale gas-lift reactor as described in Esposito et al. [2].The model can be applied to simulate the sulfate reduction process in a gas-lift reactor for several purposes, such as the evaluation of the optimal process conditions in terms of COD:SO42− ratio, hydraulic retention time and gas input flow. In particular, model simulations reported in this paper show the model capability to predict the prevailing bacterial species and concentrations in the reactor as a function of the hydraulic retention time.

Desulfonatronobacter acidivorans gen. nov., sp. nov. and Desulfobulbus alkaliphilus sp. nov., haloalkaliphilic heterotrophic sulfate-reducing bacteria from soda lakes

Two types of heterotrophic sulfate-reducing bacteria (SRB) were isolated from anoxic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). The isolates used propionate as an energy and carbon source. Strain APT2(T) was enriched and isolated with thiosulfate as the electron acceptor. Strains APS1(T) and ASS1 were isolated with sulfate. Strain APT2(T) was a short rod and motile with a single subpolar flagellum, while strains APS1(T) and ASS1 were lemon-shaped oval rods and motile with a single polar flagellum and thin flagella-like filaments. Strain APT2(T) grew by complete oxidation of C(3)-C(8) fatty acids with thiosulfate or sulfate as the electron acceptor, while strains APS1(T) and ASS1 were much less versatile and utilized only propionate and pyruvate as the electron donor and carbon source with sulfate or sulfite as the electron acceptor. Furthermore, strains APS1(T) and ASS1 oxidized propionate incompletely to form acetate. All of the isolates were moderately halophilic and obligately alkaliphilic. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolates in the order Desulfobacterales of the class Deltaproteobacteria. Strain APT2(T) belonged to the family Desulfobacteraceae and clustered with a halophilic SRB, Desulfosalsimonas propionicica PropA(T). Strains APS1(T) and ASS1 were closely related to each other and clustered with the genus Desulfobulbus of the family Desulfobulbaceae. On the basis of phenotypic and phylogenetic analysis, the isolates are proposed to represent two novel taxa, Desulfonatronobacter acidivorans gen. nov., sp. nov. (type strain of the type species APT2(T) = DSM 24257(T) = UNIQEM U853(T)) and Desulfobulbus alkaliphilus sp. nov. (type strain APS1(T) = DSM 24258(T) = UNIQEM U900(T)).

User-Friendly Mathematical Model for the Design of Sulfate Reducing H2∕CO2 Fed Bioreactors

This paper presents three steady-state mathematical models for the design of H2∕CO2 fed gas-lift reactors aimed at biological sulfate reduction to remove sulfate from wastewater. Models 1A and 1B are based on heterotrophic sulfate reducing bacteria (HSRB), while Model 2 is based on autotrophic sulfate reducing bacteria (ASRB) as the dominant group of sulfate reducers in the gas-lift reactor. Once the influent wastewater characteristics are known and the desired sulfate removal efficiency is fixed, all models give explicit mathematical relationships to determine the bioreactor volume and the effluent concentrations of substrates and products. The derived explicit relationships make application of the models very easy, fast, and no iterative procedures are required. Model simulations show that the size of the H2∕CO2 fed gas-lift reactors aimed at biological sulfate removal from wastewater highly depends on the number and type of trophic groups growing in the bioreactor. In particular, if the biological sulfate reduction is performed in a bioreactor where ASRB prevail, the required bioreactor volume is much smaller than that needed with HSRB. This is because ASRB can out-compete methanogenic archaea (MA) for H2 (assuming sulfate concentrations are not limiting), whereas HSRB do not necessarily out-compete MA due to their dependence on homoacetogenic bacteria (HB) for organic carbon. The reactor sizes to reach the same sulfate removal efficiency by HSRB and ASRB are only comparable when methanogenesis is inhibited. Moreover, model results indicate that acetate supply to the reactor influent does not affect the HSRB biomass required in the reactor, but favors the dominance of MA on HB as a consequence of a lower HB requirement for acetate supply.

Bioaugmented sulfate reduction using enriched anaerobic microflora in the presence of zero valent iron

Biological sulfate reduction was evaluated in batch and continuous reactors that were inoculated with enriched microflora cultivated from sulfate laden medium. Heterotrophic sulfate-reducing bacteria (SRB) principally reduced the sulphate when the chemical oxygen demand was sufficient. The heterotrophic SRB in the enriched microflora could not efficiently reduce sulphate at T < 33 °C and/or pH < 6.0. However, when 200 mg L −1 of zero valent iron (ZVI) was added to the reactor, the sulphate reduction rate was increased by 15% while the inhibition of the SRB activity occurred at T < 25 °C or pH < 4.5, broader than those noted for non-ZVI systems. In batch tests, the autotrophic SRB reduced 95% of 1500 mg L −1 sulphate in <50 h at 15 °C when the substrate was amended with 8 g L −1 ZVI. In continuous up-flow anaerobic multiple bed reactor tests conducted to evaluate the remediation of sulphate in acid mine runoff, ZVI enhanced the activity of SRB, resulting in a 61% reduction of 20.8 g L −1 sulphate when the reactor was operated at 25 °C and pH 2.6 with a hydraulic remain time of 96 h.

Occurrence of methanogenesis during start-up of a full-scale synthesis gas-fed reactor treating sulfate and metal-rich wastewater

The start-up of a full-scale synthesis gas-fed gas-lift reactor treating metal and sulfate-rich wastewater was investigated. Sludge from a pilot-scale reactor was used to seed the full-scale reactor. The main difference in design between the pilot- and full-scale reactor was that metal precipitation and sulfate reduction occurred in the same reactor. After 7 weeks the full-scale reactor achieved the sulfate conversion design rate of 15 kg/m 3 day. Zinc sulfide precipitation inside the reactor did not interfere with obtaining a high rate of sulfate reduction. 16S rRNA gene analysis demonstrated that the bacterial communities in both reactors were dominated by the sulfate-reducing genus Desulfomicrobium. Archaeal communities of both reactors were dominated by the methanogenic genus Methanobacterium. Most Probable Number (MPN) counts confirmed that heterotrophic Sulfate-Reducing Bacteria (SRB) were dominant (10 11–10 12 cells/g VSS) compared to homoacetogens (10 5–10 6 cells/g VSS) and methanogens (10 8–10 9 cells/g VSS). Methanogenesis was not suppressed during start-up of the full scale-reactor, despite the predominance of SRB, which have a lower hydrogen threshold. Due to the short sludge retention time (4–7 days) competition for hydrogen is determined by Monod kinetics, not hydrogen thresholds. As the kinetic parameters for SRB and methanogens are similar, methanogenesis may persist which results in a loss of hydrogen.

Biological Mechanisms of H2S Formation in Sewer Pipes

The purpose of this study is to gain a better understanding of the biological phenomena involved in the production of hydrogen sulfide in urban wastewater (UWW) systems. It is found that the UWW itself naturally possesses the biomass needed to consume the sulfates. These heterotrophic sulfate-reducing bacteria populations, though immediately active in strict anaerobic conditions, are present only in very low concentrations in the UWW. A concentration of them was studied within the pressure pipes, in the form of deposits, and this justifies the high concentrations of sulfides measured in certain wastewater networks. There are two reasons why the ferrous sulfate used as a treatment in any wastewater networks should not cause the production of additional sulfides. Firstly, the sulfate consumption kinetics are always too slow, relative to the residence time of the water in the pipe, for all of the sulfates to be consumed anyway. Secondly, the amount of assimilable carbon, soluble carbon, and carbon from suspended solid (SS) hydrolysis is insufficient.

Origin of a South Texas roll-type uranium deposit; I, Alteration of iron-titanium oxide minerals

The detrital Fe-Ti oxide minerals and their authigenic alteration products in samples from cores spanning 1.7 km across a roll-type uranium deposit in the mid-Tertiary Catahoula Tuff, south Texas, record important information on host-rock preparation and on development of the altered tongue of the deposit. In reduced rock, in front of and enveloping the altered tongue, iron disulfide minerals (pyrite and marcasite) have partially to completely replaced titanomagnetite and, to a lesser extent, titanohematite. Subsequent oxidation of these sulfidized Fe-Ti oxides, by processes that formed the altered tongue and uranium roll, produced ferric oxide and hydroxide phases (limonite) pseudomorphous after the sulfides. Fe-Ti oxides 1.0 km updip from the roll front were never sulfidized; titanomagnetite (partly replaced by hematite) and martite constitute nearly half of the heavy mineral fraction and limonite is absent. Oxidized rocks 210 m and closer to the nose of the roll front, however, are nearly devoid of titanomagnetite and contain abundant limonite. The redox interface that bounds the altered tongue, therefore, moved more than 210 m but less than 1.0 km. Detrital Fe-Ti oxide minerals are increasingly sulfidized in the downdip direction indicating that initial sulfidizaton was more intense in that direction. Organic carbon content is uniformly very low throughout the host sandstone, which implies that heterotrophic sulfate-reducing bacteria were not involved in the generation of sulfide. The H 2 S for the initial sulfidization may have been derived from oil and gas in formations that underlie the Catahoula Tuff. The H 2 S probably invaded the Catahoula along a fault that is 1.5 km downdip from the present roll front.