Growth with hydrogen, and further physiological characteristics of Desulfotomaculum species

Anaerobic microbial metabolism in soil columns affected by highly alkaline pH: Implication for biogeochemistry near construction and demolition waste disposal sites

Construction and demolition wastes (CDWs) have become a significant environmental concern due to urbanization. CDWs in landfill sites can generate high-pH leachate and various constituents (e.g., acetate and sulfate) following the dissolution of cement material, which may affect subsurface biogeochemical properties. However, the impact of CDW leachate on microbial reactions and community compositions in subsurface environments remains unclear. Therefore, we created columns composed of layers of concrete debris containing-soil (CDS) and underlying CDW-free soil, and fed them artificial groundwater with or without acetate and/or sulfate. In all columns, the initial pH 5.6 of the underlying soil layer rapidly increased to 10.8 (without acetate and sulfate), 10.1 (with sulfate), 10.1 (with acetate), and 8.3 (with acetate and sulfate) within 35 days. Alkaliphilic or alkaline-resistant microbes including Hydrogenophaga, Silanimonas, Algoriphagus, and/or Dethiobacter were dominant throughout the incubation in all columns, and their relative abundance was highest in the column without acetate and sulfate (50.7-86.6%). Fe(III) and sulfate reduction did not occur in the underlying soil layer without acetate. However, in the column with acetate alone, pH was decreased to 9.9 after day 85 and Fe(II) was produced with an increase in the relative abundance of Fe(III)-reducing bacteria up to 9.1%, followed by an increase in the methanogenic archaea Methanosarcina, suggestive of methanogenesis. In the column with both acetate and sulfate, Fe(III) and sulfate reduction occurred along with an increase in both Fe(III)- and sulfate-reducing bacteria (19.1 and 17.7%, respectively), while Methanosarcina appeared later. The results demonstrate that microbial Fe(III)- and sulfate-reduction and acetoclastic methanogenesis can occur even in soils with highly alkaline pH resulting from the dissolution of concrete debris.

Biostimulation of sulfate reduction for in-situ metal(loid) precipitation at an industrial site in Flanders, Belgium

A 30-month pilot study was conducted to evaluate the potential of in-situ metal(loid) removal through biostimulation of sulfate-reducing processes. The study took place at an industrial site in Flanders, Belgium, known for metal(loid) contamination in soil and groundwater. Biostimulation involved two incorporations of an organic substrate (emulsified vegetable oil) as electron donor and potassium bicarbonate to raise the pH of the groundwater by 1-1.5 units. The study focused on the most impacted permeable fine sand aquifer (8-9 m below groundwater level) confined by layers of non-permeable clay. The fine sands exhibited initially oxic conditions (50-200 mV), an acidic pH of 4.5 and sulfate concentrations ranging from 600 to 800 mg/L. At the central monitoring well, anoxic conditions (-200 to -400 mV) and a pH of 5.9 established shortly after the second substrate and reagent injection. Over the course of 12 months, there was a significant decrease in the concentration of arsenic (from 2500 to 12 μg/L), nickel (from 360 to <2 μg/L), zinc (from 78,000 to <2 μg/L), and sulfate (from 930 to 450 mg/L). Low levels of metal(loid)s were still present after 34 months (end of study). Mineralogical analysis indicated that the precipitates formed were amorphous in nature. Evidence for biologically driven metal(loid) precipitation was provided by compound specific stable isotope analysis of sulfate. In addition, changes in microbial populations were assessed using next-generation sequencing, revealing stimulation of native sulfate-reducing bacteria. These results highlight the potential of biostimulation for long-term in situ metal(loid) plume treatment/containment.

Anaerobic dissimilatory phosphite oxidation, an extremely efficient concept of microbial electron economy

Phosphite is a stable phosphorus compound that, together with phosphate, made up a substantial part of the total phosphorus content of the prebiotic Earth's crust. Oxidation of phosphite to phosphate releases electrons at an unusually low redox potential (-690 mV at pH 7.0). Numerous aerobic and anaerobic bacteria use phosphite as a phosphorus source and oxidise it to phosphate for synthesis of nucleotides and other phosphorus-containing cell constituents. Only two pure cultures of strictly anaerobic bacteria have been isolated so far that use phosphite as an electron donor in their energy metabolism, the Gram-positive Phosphitispora fastidiosa and the Gram-negative Desulfotignum phosphitoxidans. The key enzyme of this metabolism is an NAD+ -dependent phosphite dehydrogenase enzyme that phosphorylates AMP to ADP. These phosphorylating phosphite dehydrogenases were found to be related to nucleoside diphosphate sugar epimerases. The produced NADH is channelled into autotrophic CO2 fixation via the Wood-Ljungdahl (CO-DH) pathway, thus allowing for nearly complete assimilation of the substrate electrons into bacterial biomass. This extremely efficient type of electron flow connects energy and carbon metabolism directly through NADH and might have been important in the early evolution of life when phosphite was easily available on Earth.

Presence of uranium(V) during uranium(VI) reduction by Desulfosporosinus hippei DSM 8344T

Microbial U(VI) reduction influences uranium mobility in contaminated subsurface environments and can affect the disposal of high-level radioactive waste by transforming the water-soluble U(VI) to less mobile U(IV). The reduction of U(VI) by the sulfate-reducing bacterium Desulfosporosinus hippei DSM 8344^T, a close phylogenetic relative to naturally occurring microorganism present in clay rock and bentonite, was investigated. D. hippei DSM 8344^T showed a relatively fast removal of uranium from the supernatants in artificial Opalinus Clay pore water, but no removal in 30 mM bicarbonate solution. Combined speciation calculations and luminescence spectroscopic investigations showed the dependence of U(VI) reduction on the initial U(VI) species. Scanning transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy showed uranium-containing aggregates on the cell surface and some membrane vesicles. By combining different spectroscopic techniques, including UV/Vis spectroscopy, as well as uranium M₄-edge X-ray absorption near-edge structure recorded in high-energy-resolution fluorescence-detection mode and extended X-ray absorption fine structure analysis, the partial reduction of U(VI) could be verified, whereby the formed U(IV) product has an unknown structure. Furthermore, the U M₄ HERFD-XANES showed the presence of U(V) during the process. These findings offer new insights into U(VI) reduction by sulfate-reducing bacteria and contribute to a comprehensive safety concept for a repository for high-level radioactive waste.

Biological treatment of biowaste as an innovative source of CO-The role of composting process

Carbon monoxide (CO) is an essential "building block" for producing everyday chemicals on industrial scale. Carbon monoxide can also be generated though a lesser-known and sometimes forgotten biorenewable pathways that could be explored to advance biobased production from large and more sustainable sources such as bio-waste treatment. Organic matter decomposition can generate carbon monoxide both under aerobic and anaerobic conditions. While anaerobic carbon monoxide generation is relatively well understood, the aerobic is not. Yet many industrial-scale bioprocesses involve both conditions. This review summarizes the necessary basic biochemistry knowledge needed for realization of initial steps towards biobased carbon monoxide production. We analyzed for the first time, the complex information about carbon monoxide production during aerobic, anaerobic bio-waste treatment and storage, carbon monoxide-metabolizing microorganisms, pathways, and enzymes with bibliometric analysis of trends. The future directions recognizing limitations of combined composting and carbon monoxide production have been discussed in greater detail.

Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov

In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO₂, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.

Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure

High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.

Bentonite Alteration in Batch Reactor Experiments with and without Organic Supplements: Implications for the Disposal of Radioactive Waste

Bentonite is currently proposed as a potential backfill material for sealing high-level radioactive waste in underground repositories due to its low hydraulic conductivity, self-sealing ability and high adsorption capability. However, saline pore waters, high temperatures and the influence of microbes may cause mineralogical changes and affect the long-term performance of the bentonite barrier system. In this study, long-term static batch experiments were carried out at 25 °C and 90 °C for one and two years using two different industrial bentonites (SD80 from Greece, B36 from Slovakia) and two types of aqueous solutions, which simulated (a) Opalinus clay pore water with a salinity of 19 g·L−1, and (b) diluted cap rock solution with a salinity of 155 g·L−1. The bentonites were prepared with and without organic substrates to study the microbial community and their potential influence on bentonite mineralogy. Smectite alteration was dominated by metal ion substitutions, changes in layer charge and delamination during water–clay interaction. The degree of smectite alteration and changes in the microbial diversity depended largely on the respective bentonite and the experimental conditions. Thus, the low charged SD80 with 17% tetrahedral charge showed nearly no structural change in either of the aqueous solutions, whereas B36 as a medium charged smectite with 56% tetrahedral charge became more beidellitic with increasing temperature when reacted in the diluted cap rock solution. Based on these experiments, the alteration of the smectite is mainly attributed to the nature of the bentonite, pore water chemistry and temperature. A significant microbial influence on the here analyzed parameters was not observed within the two years of experimentation. However, as the detected genera are known to potentially influence geochemical processes, microbial-driven alteration occurring over longer time periods cannot be ruled out if organic nutrients are available at appropriate concentrations.

A Fixed Bed Pervious Concrete Anaerobic Bioreactor for Biological Sulphate Remediation of Acid Mine Drainage Using Simple Organic Matter

The development of low-operational-cost and low-operational-complexity active sulphate (SO4) reducing bioremediation for Acid Mine Drainage (AMD) is an ongoing pursuit towards sustainable mining. This study introduces a fixed bed pervious concrete anaerobic bioreactor as a second stage AMD remediation process. The study investigated the pH self-regulation capabilities, SO4 remediation capabilities and the rate limiting parameters of the bioreactor using glucose as an organic matter source. The AMD was pre-treated using a permeable reactive barrier. A 21-day trial comprised of an increase in the SO4 loading rate while reducing the organic loading rate was undertaken to identify performance limiting conditions. A daily average SO4 concentration reduction rate of 55.2% was achieved over the initial 13 days of the experiments. The study found that a COD to SO4 ratio and VFA to alkalinity ratio below 5:1 and 0.5:1 respectively were performance limiting. The bioreactor was capable of self-regulating pH within the neutral range of 6.5 and 7.5. The study findings indicate that the bioreactor design can reduce operational costs and operational complexity of active AMD bioremediation.

Friends or Foes-Microbial Interactions in Nature

Simple Summary

Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability.

Abstract

Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of Fe^III reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory Fe^III-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.

Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus

Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.

Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions

Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with ¹³C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.

Electrophysiology of the Facultative Autotrophic Bacterium Desulfosporosinus orientis

Electroautotrophy is a novel and fascinating microbial metabolism, with tremendous potential for CO₂ storage and valorization into chemicals and materials made thereof. Research attention has been devoted toward the characterization of acetogenic and methanogenic electroautotrophs. In contrast, here we characterize the electrophysiology of a sulfate-reducing bacterium, Desulfosporosinus orientis, harboring the Wood-Ljungdahl pathway and, thus, capable of fixing CO₂ into acetyl-CoA. For most electroautotrophs the mode of electron uptake is still not fully clarified. Our electrochemical experiments at different polarization conditions and Fe⁰ corrosion tests point to a H₂- mediated electron uptake ability of this strain. This observation is in line with the lack of outer membrane and periplasmic multi-heme c-type cytochromes in this bacterium. Maximum planktonic biomass production and a maximum sulfate reduction rate of 2 ± 0.4 mM day^–1 were obtained with an applied cathode potential of −900 mV vs. Ag/AgCl, resulting in an electron recovery in sulfate reduction of 37 ± 1.4%. Anaerobic sulfate respiration is more thermodynamically favorable than acetogenesis. Nevertheless, D. orientis strains adapted to sulfate-limiting conditions, could be tuned to electrosynthetic production of up to 8 mM of acetate, which compares well with other electroacetogens. The yield per biomass was very similar to H₂/CO₂ based acetogenesis. Acetate bioelectrosynthesis was confirmed through stable isotope labeling experiments with Na-H¹³CO₃. Our results highlight a great influence of the CO₂ feeding strategy and start-up H₂ level in the catholyte on planktonic biomass growth and acetate production. In serum bottles experiments, D. orientis also generated butyrate, which makes D. orientis even more attractive for bioelectrosynthesis application. A further optimization of these physiological pathways is needed to obtain electrosynthetic butyrate production in D. orientis biocathodes. This study expands the diversity of facultative autotrophs able to perform H₂-mediated extracellular electron uptake in Bioelectrochemical Systems (BES). We characterized a sulfate-reducing and acetogenic bacterium, D. orientis, able to naturally produce acetate and butyrate from CO₂ and H₂. For any future bioprocess, the exploitation of planktonic growing electroautotrophs with H₂-mediated electron uptake would allow for a better use of the entire liquid volume of the cathodic reactor and, thus, higher productivities and product yields from CO₂-rich waste gas streams.

The Year-Long Development of Microorganisms in Uncompacted Bavarian Bentonite Slurries at 30 and 60 °C

In the multibarrier concept for the deep geological disposal of high-level radioactive waste (HLW), bentonite is proposed as a potential barrier and buffer material for sealing the space between the steel canister containing the HLW and the surrounding host rock. In order to broaden the spectra of appropriate bentonites, we investigated the metabolic activity and diversity of naturally occurring microorganisms as well as their time-dependent evolution within the industrial B25 Bavarian bentonite under repository-relevant conditions. We conducted anaerobic microcosm experiments containing the B25 bentonite and a synthetic Opalinus Clay pore water solution, which were incubated for one year at 30 and 60 °C. Metabolic activity was only stimulated by the addition of lactate, acetate, or H₂. The majority of lactate- and H₂-containing microcosms at 30 °C were dominated by strictly anaerobic, sulfate-reducing, and spore-forming microorganisms. The subsequent generation of hydrogen sulfide led to the formation of iron-sulfur precipitations. Independent from the availability of substrates, thermophilic bacteria dominated microcosms that were incubated at 60 °C. However, in the respective microcosms, no significant metabolic activity occurred, and there was no change in the analyzed biogeochemical parameters. Our findings show that indigenous microorganisms of B25 bentonite evolve in a temperature- and substrate-dependent manner.

Effects of nanoscale zero valent iron (nZVI) concentration on the biochemical conversion of gaseous carbon dioxide (CO2) into methane (CH4)

This study presents the effects of nanoscale zero valent iron (nZVI) concentration on the biomethanation of gaseous CO₂. During anaerobic batch experiment with 9 times injection of CO₂, the CO₂ concentration in the headspace rapidly decreased by dissolution. Then, when nZVI was added at 6.25 and 12.5 g/L, the dissolved CO₂ was biochemically transformed into CH₄ at a maximum production rate of 2.38 and 3.93 μmol/hr, respectively. Biomethanation at these two nZVI concentrations continued until the end of experiment. In spite of more H₂ evolution by nZVI at 25 g/L, biomethanation did not occur, due to the significant inhibition of methanogenesis by nZVI. As the nZVI concentration increased, relative abundance of the hydrogenotrophic methanogens, especially Methanobacteriales, increased. However, at 25 g/L of nZVI concentration, acetic acid was accumulated and the relative abundance of Clostridium became predominant, indicating that homoacetogenesis was superior over methanogenesis.

Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA

We established Fe(III)-reducing co-cultures of two species of metal-reducing bacteria, the Gram-positive Desulfotomaculum reducens MI-1 and the Gram-negative Geobacter sulfurreducens PCA. Co-cultures were given pyruvate, a substrate that D. reducens can ferment and use as electron donor for Fe(III) reduction. G. sulfurreducens relied upon products of pyruvate oxidation by D. reducens (acetate, hydrogen) for use as electron donor in the co-culture. Co-cultures reduced Fe(III) to Fe(II) robustly, and Fe(II) was consistently detected earlier in co-cultures than pure cultures. Notably, faster cell growth, and correspondingly faster pyruvate oxidation, was observed by D. reducens in co-cultures. Global comparative proteomic analysis was performed to observe differential protein abundance during co-culture vs. pure culture growth. Proteins previously associated with Fe(III) reduction in G. sulfurreducens, namely c-type cytochromes and type IV pili proteins, were significantly increased in abundance in co-cultures relative to pure cultures. D. reducens ribosomal proteins were significantly increased in co-cultures, likely a reflection of faster growth rates observed for D. reducens cells while in co-culture. Furthermore, we developed multiple reaction monitoring (MRM) assays to quantitate specific biomarker peptides. The assays were validated in pure and co-cultures, and protein abundance ratios from targeted MRM and global proteomic analysis correlate significantly.

Investigation on hydrogen production from paper sludge without inoculation and its enhancement by Clostridium thermocellum

The feasibility and performance of hydrogen production from paper sludge without inoculation was investigated under thermophilic conditions. The maximum hydrogen production reached 64.32 mM with 7.4% PS. The dynamic changes in bacterial community structures during hydrogen production were investigated by analyzing 16S rDNA gene sequences using high throughput sequencing technology. The results showed that microbial community was dominated by order Clostridiales and Thermoanaerobacterales. Genus Thermoanaerobacterium and Ruminiclostridium played a leading role in the fermentation process, which was responsible for the hydrolysis of PS and hydrogen production. Effect of inoculation with Clostridium thermocellum on hydrogen production from PS was also studied. The results showed that C. thermocellum supplement significantly increased hydrogen yield and holocellulose degradation rate by 96.80% and 32.95%, respectively. In addition, inoculation of C. thermocellum enhanced VFA generation and shortened the lag phase of hydrogen production. The present study lays the foundation on the valorization of waste lignocellulose.

The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways

Methanol is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and acetogens), or through oxidation to formaldehyde using a methanol dehydrogenase by aerobes. Methanol is an important substrate in deep-subsurface environments, where thermophilic sulfate-reducing bacteria of the genus Desulfotomaculum have key roles. Here, we study the methanol metabolism of Desulfotomaculum kuznetsovii strain 17^T, isolated from a 3000-m deep geothermal water reservoir. We use proteomics to analyze cells grown with methanol and sulfate in the presence and absence of cobalt and vitamin B12. The results indicate the presence of two methanol-degrading pathways in D. kuznetsovii, a cobalt-dependent methanol methyltransferase and a cobalt-independent methanol dehydrogenase, which is further confirmed by stable isotope fractionation. This is the first report of a microorganism utilizing two distinct methanol conversion pathways. We hypothesize that this gives D. kuznetsovii a competitive advantage in its natural environment.

Microbial and mineral evolution in zero valent iron-based permeable reactive barriers during long-term operations

Impacts of subsurface biogeochemical processes over time have always been a concern for the long-term performance of zero valent iron (Fe(0))-based permeable reactive barriers (PRBs). To evaluate the biogeochemical impacts, laboratory experiments were performed using flow-through glass columns for 210 days at controlled temperature (20 °C). Two different particle sizes of Fe(0) were used in the columns, and to simulate indigenous microbial activity, extra carbon source was provided in the two columns (biotic columns) and the remaining two columns were kept abiotic using gamma radiations. Heavy metals (Zn, As) were removed efficiently in all the columns, and no exhaustion of treatment capability or clogging was observed during our experimental duration. Newly formed Fe mineral phases and precipitates were characterized using X-ray diffraction (XRD), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), and micro-XRF techniques in solid phase at the end of the experiment. In addition, 16S rRNA gene extraction was used for microbial community identification in biotic columns. During the incubation, microbial population shifted in favor of Desulfosporosinus species (sulfate-reducing bacteria) from initial dominance of Acidithiobacillus ferrooxidans in sediments. Dominant mineral phases detected in biotic columns were mackinawite (FeS) and sulfate green rust, while in abiotic columns, magnetite/maghemite phases were more prevalent.

Phylogenetic comparison of Desulfotomaculum species of subgroup 1a and description of Desulfotomaculum reducens sp. nov

A genome and physiological comparison was made of the type strains of Desulfotomaculum species belonging to subgroup 1a and of 'Desulfotomaculum reducens' strain MI-1. Phenotypically, 'Desulfotomaculum reducens' strain MI-1 can be distinguished from the other described Desulfotomaculum species of subgroup 1a by its ability to grow with propionate and butyrate. In addition, the strain is able to use a variety of metals as electron acceptors. Metal reduction has not been tested in the other species, but seems likely based on our genome analysis. Phylogenetic 16S rRNA gene sequence analysis and the average nucleotide identity between the genomes of the species of subgroup 1a show that strain MI-1 represents a novel species within the Desulfotomaculum 1a subgroup, Desulfotomaculum reducens sp. nov. The type strain is MI-1^T.

Carboxydotrophic growth of Geobacter sulfurreducens

This study shows that Geobacter sulfurreducens grows on carbon monoxide (CO) as electron donor with fumarate as electron acceptor. Geobacter sulfurreducens was tolerant to high CO levels, with up to 150 kPa in the headspace tested. During growth, hydrogen was detected in very slight amounts (∼5 Pa). In assays with cell-free extract of cells grown with CO and fumarate, production of hydrogen from CO was not observed, and hydrogenase activity with benzyl viologen as electron acceptor was very low. Taken together, this suggested that CO is not utilized via hydrogen as intermediate. In the presence of CO, reduction of NADP⁺ was observed at a rate comparable to CO oxidation coupled to fumarate reduction in vivo. The G. sulfurreducens genome contains a single putative carbon monoxide dehydrogenase-encoding gene. The gene is part of a predicted operon also comprising a putative Fe–S cluster-binding subunit (CooF) and a FAD–NAD(P) oxidoreductase and is preceded by a putative CO-sensing transcription factor. This cluster may be involved in a novel pathway for CO oxidation, but further studies are necessary to ascertain this. Similar gene clusters are present in several other species belonging to the Deltaproteobacteria and Firmicutes, for which CO utilization is currently not known.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

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.

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.

Archaea in symbioses

During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T))

Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

Desulfofrigus sp. prevails in sulfate-reducing dilution cultures from sediments of the Benguela upwelling area

Sediments of coastal upwelling areas are generally characterized by a high content of organic carbon that is mainly degraded via anaerobic microbial processes including sulfate reduction as a major terminal oxidation step. Despite the high importance of sulfate reduction in these sediments, the identity of sulfate-reducing bacteria (SRB) has remained almost unknown. Here, we applied a cultivation-based approach using selective enrichment conditions to study the diversity and distribution of active SRB in sediments along a transect perpendicular to the continental slope off the coast of Namibia (Meteor-cruise M76/1). To promote growth of the most abundant SRB, dilution series were prepared and amended with hydrogen, acetate, or a mixture of monomers representing typical substrates for SRB. Growth of SRB could be detected in the presence of all electron donors and from sediment down to 4 m depth. 16S rRNA gene-based DGGE analysis and sequencing revealed the predominance of SRB related to psychrophiles in particular to the genus Desulfofrigus, which made up 1 % of the total microbial community, accounting for an absolute abundance of up to 4.8 × 10(7)  cells mL(-1) . In general, the abundance of cultured SRB changed with depth and between the different sampling sites and correlated with the content of organic carbon as previously reported. Growth of chemolithotrophic SRB in relatively high dilution steps and the enrichment of methanogens as well as acetogens from deeper sediment point to a competition between hydrogen-utilizing microbial processes and their biogeochemical significance in deep sediment layers of the Benguela upwelling area.

Enrichment of sulfate-reducing bacteria and resulting mineral formation in media mimicking pore water metal ion concentrations and pH conditions of acidic pit lakes

Acid mine drainage sites are extreme environments with high acidity and metal ion concentrations. Under anoxic conditions, microbial sulfate reduction may trigger the formation of secondary minerals as a result of H2S production and pH increase. This process was studied in batch experiments with enrichment cultures from acidic sediments of a pit lake using growth media set at different pH values and containing elevated concentrations of Fe²⁺ and Al³⁺. At initial pH values of 5 and 6, sulfate reduction occurred shortly after inoculation. Sulfate- reducing bacteria affiliated to the genus Desulfosporosinus predominated the microbial communities as shown by 16S rRNA gene analysis performed at the end of the incubation. At initial pH values of 3 and 4, sulfate reduction and cell growth occurred only after an extended lag phase, however, at a higher rate than in the less acidic assays. At the end of the growth phase, enrichments were dominated by Thermodesulfobium spp. suggesting that these sulfate reducers were better adapted to acidic conditions. Iron sulfides in the bulk phase were common in all assays, but specific aluminum precipitates formed in close association with cell surfaces and may function as a detoxification mechanism of dissolved Al species at low pH.

Hydrogen consumption in microbial electrochemical systems (MXCs): the role of homo-acetogenic bacteria

Homo-acetogens in the anode of a microbial electrolysis cell (MEC) fed with H(2) as sole electron donor allowed current densities similar to acetate-fed biofilm anodes (∼10 A/m(2)). Evidence for homo-acetogens included accumulation of acetate at high concentrations (up to 18 mM) in the anode compartment; detection of formate, a known intermediate during reductive acetogenesis by the acetyl-CoA pathway; and detection of formyl tetrahydrofolate synthetase (FTHFS) genes by quantitative real-time PCR. Current production and acetate accumulation increased in parallel in batch and continuous mode, while both values decreased simultaneously at short hydraulic retention times (1h) in the anode compartment, which limited suspended homo-acetogens. Acetate produced by homo-acetogens accounted for about 88% of the current density of 10A/m(2), but the current density was sustained at 4A/m(2) at short hydraulic retention time because of a robust partnership of homo-acetogens and anode respiring bacteria (ARB) in the biofilm anode.

Carbon monoxide as an electron donor for the biological reduction of sulphate

Several strains of Gram-negative and Gram-positive sulphate-reducing bacteria (SRB) are able to use carbon monoxide (CO) as a carbon source and electron donor for biological sulphate reduction. These strains exhibit variable resistance to CO toxicity. The most resistant SRB can grow and use CO as an electron donor at concentrations up to 100%, whereas others are already severely inhibited at CO concentrations as low as 1-2%. Here, the utilization, inhibition characteristics, and enzymology of CO metabolism as well as the current state of genomics of CO-oxidizing SRB are reviewed. Carboxydotrophic sulphate-reducing bacteria can be applied for biological sulphate reduction with synthesis gas (a mixture of hydrogen and carbon monoxide) as an electron donor.

Structure and function of the microbial community in an in situ reactor to treat an acidic mine pit lake

Sulfate-reducing bioreactors are a promising option for the treatment of acid mine drainage. We studied the structure and function of a biofilm in a methanol-fed fixed-bed in-lake reactor for the treatment of an acidic pit lake by a combination of laboratory incubations, chemical and molecular analyses and confocal laser scanning microscopy to determine whether competition by different groups of microorganisms as well as the precipitation of minerals affect reactor performance negatively. The biofilm growing on the surface of a synthetic carrier material consisted of dense microbial colonies covered by iron-sulfide precipitates. The microorganisms continuously had to overgrow this mineral coating, resulting in a high biomass turnover. About one third of the added methanol was used by sulfate reduction, and the rest by competing reactions. Sulfate-reducing bacteria as well as methanogens and acetogens were involved in methanol consumption. Six different groups of Deltaproteobacteria, dominated by the genera Desulfomonile, Desulfobacterium and a phylotype related to Geobacter, Gram-positive sulfate reducers of the genus Desulfosporosinus, acetogenic Acetobacteria, different fermenting bacteria as well as methylotrophic methanogens were identified. The versatility of the microbial food web is probably an important factor stabilizing the biofilm function under fluctuating and partly oxidizing conditions in the reactor.

Microbial communities in subpermafrost saline fracture water at the Lupin Au mine, Nunavut, Canada

We report the first investigation of a deep subpermafrost microbial ecosystem, a terrestrial analog for the Martian subsurface. Our multidisciplinary team analyzed fracture water collected at 890 and 1,130 m depths beneath a 540-m-thick permafrost layer at the Lupin Au mine (Nunavut, Canada). 14C, 3H, and noble gas isotope analyses suggest that the Na-Ca-Cl, suboxic, fracture water represents a mixture of geologically ancient brine, approximately25-kyr-old, meteoric water and a minor modern talik-water component. Microbial planktonic concentrations were approximately10(3) cells mL(-1). Analysis of the 16S rRNA gene from extracted DNA and enrichment cultures revealed 42 unique operational taxonomic units in 11 genera with Desulfosporosinus, Halothiobacillus, and Pseudomonas representing the most prominent phylotypes and failed to detect Archaea. The abundance of terminally branched and midchain-branched saturated fatty acids (5 to 15 mol%) was consistent with the abundance of Gram-positive bacteria in the clone libraries. Geochemical data, the ubiquinone (UQ) abundance (3 to 11 mol%), and the presence of both aerobic and anaerobic bacteria indicated that the environment was suboxic, not anoxic. Stable sulfur isotope analyses of the fracture water detected the presence of microbial sulfate reduction, and analyses of the vein-filling pyrite indicated that it was in isotopic equilibrium with the dissolved sulfide. Free energy calculations revealed that sulfate reduction and sulfide oxidation via denitrification and not methanogenesis were the most thermodynamically viable consistent with the principal metabolisms inferred from the 16S rRNA community composition and with CH4 isotopic compositions. The sulfate-reducing bacteria most likely colonized the subsurface during the Pleistocene or earlier, whereas aerobic bacteria may have entered the fracture water networks either during deglaciation prior to permafrost formation 9,000 years ago or from the nearby talik through the hydrologic gradient created during mine dewatering. Although the absence of methanogens from this subsurface ecosystem is somewhat surprising, it may be attributable to an energy bottleneck that restricts their migration from surface permafrost deposits where they are frequently reported. These results have implications for the biological origin of CH4 on Mars.

Enzymatic U(VI) reduction by Desulfosporosinus species

Here we tested U(VI) reduction by a Desulfosporosinus species (sp.) isolate and type strain (DSM 765) in cell suspensions (pH 7) containing 1mM U(VI) and lactate, under an atmosphere containing N2-CO2-H2 (90:5:5). Although neither Desulfosporosinus species (spp.) reduced U(VI) in cell suspensions with 0.25 Na-bicarbonate or 0.85 NaCl, U(VI) was reduced in these solutions by a control strain, Desulfovibrio desulfuricans (ATCC 642). However, both Desulfosporosinus strains reduced U(VI) in cell suspensions depleted in bicarbonate and NaCl. No U(VI) reduction was observed without lactate and H2 electron donors or with heat-killed cells, indicating enzymatic U(VI) reduction. Uranium(VI) reduction by both strains was inhibited when 1mM CuCl2 was added to the cell suspensions. Because the Desulfosporosinus DSM 765 does not contain cytochrome c 3 used by Desulfovibrio spp. to reduce U(VI), Desulfosporosinus species reduce uranium via a different enzymatic pathway.

Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes

Both natural and anthropogenic hot environments contain appreciable levels of carbon monoxide (CO). Anaerobic microbial communities play an important role in CO conversion in such environments. CO is involved in a number of redox reactions. It is biotransformed by thermophilic methanogens, acetogens, hydrogenogens, sulfate reducers, and ferric iron reducers. Most thermophilic CO-oxidizing anaerobes have diverse metabolic capacities, but two hydrogenogenic species are obligate carboxydotrophs. Among known thermophilic carboxydotrophic anaerobes, hydrogenogens are most numerous, and based on available data they are most important in CO biotransformation in hot environments.

Hydrogenogenic CO Conversion in a Moderately Thermophilic (55 °C) Sulfate-Fed Gas Lift Reactor: Competition for CO-Derived H2

Thermophilic (55 degrees C) sulfate reduction in a gas lift reactor fed with CO gas as the sole electron donor was investigated. The reactor was inoculated with mesophilic granular sludge with a high activity of CO conversion to hydrogen and carbon dioxide at 55 degrees C. Strong competition for H(2) was observed between methanogens and sulfate reducers, while the homoacetogens present consumed only small amounts of H(2). The methanogens appeared to be more sensitive to pH and temperature shocks imposed to the reactor, but could not be completely eliminated. The fast growth rates of the methanogens (generation time of 4.5 h) enabled them to recover fast from shocks, and they rapidly consumed more than 90% of the CO-derived H(2). Nevertheless, steep increases in sulfide production in periods with low methane production suggests that once methanogenesis is eliminated, sulfate reduction with CO-rich gas as electron donor has great potential for thermophilic biodesulfurization.

Electron donors for biological sulfate reduction

Biological sulfate reduction is widely used for treating sulfate-containing wastewaters from industries such as mining, tannery, pulp and paper, and textiles. In biological reduction, sulfate is converted to hydrogen sulfide as the end product. The process is, therefore, ideally suited for treating metal-containing wastewater from which heavy metals are simultaneously removed through the formation of metal sulfides. Metal sulfide precipitates are more stable than metal hydroxides that are sensitive to pH change. Theoretically, conversion of 1 mol of sulfate requires 0.67 mol of chemical oxygen demand or electron donors. Sulfate rich wastewaters are usually deficient in electron donors and require external addition of electron donors in order to achieve complete sulfate reduction. This paper reviews various electron donors employed in biological sulfate reduction. Widely used electron donors include hydrogen, methanol, ethanol, acetate, lactate, propionate, butyrate, sugar, and molasses. The selection criteria for suitable electron donors are discussed.

H2 enrichment from synthesis gas by Desulfotomaculumcarboxydivorans for potential applications in synthesis gas purification and biodesulfurization

Desulfotomaculum carboxydivorans, recently isolated from a full-scale anaerobic wastewater treatment facility, is a sulfate reducer capable of hydrogenogenic growth on carbon monoxide (CO). In the presence of sulfate, the hydrogen formed is used for sulfate reduction. The organism grows rapidly at 200 kPa CO, pH 7.0, and 55 degrees C, with a generation time of 100 min, producing nearly equimolar amounts of H(2) and CO(2) from CO and H(2)O. The high specific CO conversion rates, exceeding 0.8 mol CO (g protein)(-1) h(-1), makes this bacterium an interesting candidate for a biological alternative of the currently employed chemical catalytic water-gas shift reaction to purify synthesis gas (contains mainly H(2), CO, and CO(2)). Furthermore, as D. carboxydivorans is capable of hydrogenotrophic sulfate reduction at partial CO pressures exceeding 100 kPa, it is also a good candidate for biodesulfurization processes using synthesis gas as electron donor at elevated temperatures, e.g., in biological flue gas desulfurization. Although high maximal specific sulfate reduction rates (32 mmol (g protein)(-1) h(-1)) can be obtained, its sulfide tolerance is rather low and pH dependent, i.e., maximally 9 and 5 mM sulfide at pH 7.2 and pH 6.5, respectively.

Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments

A novel sulfate-reducing bacterium was isolated from pristine sediments of Lake Stechlin, Germany. This strain, STP12T, was found to contain predominantlyc-type cytochromes and to reduce sulfate, sulfite and thiosulfate using lactate as an electron donor. Although STP12Tcould not utilize elemental sulfur as an electron acceptor, it could support growth by dissimilatory Fe(III) reduction. In a comparison of 16S rRNA gene sequences, STP12Twas 96.7 % similar toDesulfosporosinus auripigmentiDSM 13351T, 96.5 % similar toDesulfosporosinus meridieiDSM 13257Tand 96.4 % similar toDesulfosporosinus orientisDSM 765T. DNA–DNA hybridization experiments revealed that strain STP12Tshows only 32 % reassociation with the type strain of the type species of the genus,D. orientisDSM 765T. These data, considered in conjunction with strain-specific differences in heavy metal tolerance, cell-wall chemotaxonomy and riboprint patterns, support recognition of strain STP12T(=DSM 15449T=JCM 12239T) as the type strain of a distinct and novel species within the genusDesulfosporosinus,Desulfosporosinus lacussp. nov.

The adaptive genome of Desulfovibrio vulgaris Hildenborough

Peculiar attributes revealed by sequencing the genome of Desulfovibrio vulgaris Hildenborough are analyzed, particularly in relation to the presence of a phosphotransferase system (PTS). The PTS is a typical bacterial carbohydrate transport system functioning via group translocation. Novel avenues for investigations are proposed emphasizing the metabolic diversity of D. vulgaris Hildenborough, especially the likely utilization of mannose-type sugars. Comparative analysis with PTS from other Gram-negative and Gram-positive bacteria indicates regulatory functions for the PTS of D. vulgaris Hildenborough, including catabolite repression and inducer exclusion. Chemotaxis towards PTS substrates is considered. Evidence suggests that this organism may not be a strict anaerobic sulfate reducer typical of the ocean, but a versatile organism capable of bidirectional transmigration and adaptation to both water and terrestrial environments.

Tepidanaerobacter syntrophicus gen. nov., sp. nov., an anaerobic, moderately thermophilic, syntrophic alcohol- and lactate-degrading bacterium isolated from thermophilic digested sludges

Three anaerobic, moderately thermophilic, syntrophic primary alcohol- and lactate-degrading microbes, designated strains JLT, JE and OL, were isolated from sludges of thermophilic (55 °C) digesters that decomposed either municipal solid wastes or sewage sludge. The strains were strictly anaerobic organisms. All three strains grew at 25–60 °C and pH 5.5–8.5 and optimum growth was observed at 45–50 °C and pH 6.0–7.0. The three organisms grew chemo-organotrophically on a number of carbohydrates in the presence of yeast extract. In co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus, all strains could utilize ethanol, glycerol and lactate syntrophically for growth, although these compounds were not metabolized in pure culture without additional external electron acceptors. All strains could reduce thiosulphate. Quinones were not detected. The DNA G+C contents of strains JLT, JE and OL were 38.0, 37.3 and 37.7 mol%, respectively. Major cellular fatty acids of the strains were iso-C15 : 0, C16 : 0 and unsaturated species of C15 : 1. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belong to a deeply branched lineage of the phylum Firmicutes; the most closely related species was Thermovenabulum ferriorganovorum (16S rRNA gene sequence similarity of 88 %). The three strains were phylogenetically very closely related to each other (99–100 % 16S rRNA gene sequence similarity) and were physiologically and chemotaxonomically similar. These genetic and phenotypic properties suggest that the strains should be classified as representatives of a novel species and genus; the name Tepidanaerobacter syntrophicus gen. nov., sp. nov. is proposed. The type strain of Tepidanaerobacter syntrophicus is strain JLT (=JCM 12098T=NBRC 100060T=DSM 15584T).

Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization

Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO2-neutral) biomass. The conversion of CO with H2O to CO2 and H2 is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization ofwastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.

Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments

The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For example, the two described syntrophic propionate-oxidizing species of the genus Pelotomaculum form the novel Desulfotomaculum subcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of the Desulfotomaculum cluster I community in almost all samples examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously described Pelotomaculum species and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening for dsrAB (key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP contained dsrAB, which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members of Desulfotomaculum subcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.

Desulfotomaculum carboxydivorans sp. nov., a novel sulfate-reducing bacterium capable of growth at 100% CO

A moderately thermophilic, anaerobic, chemolithoheterotrophic, sulfate-reducing bacterium, strain CO-1-SRB(T), was isolated from sludge from an anaerobic bioreactor treating paper mill wastewater. Cells were Gram-positive, motile, spore-forming rods. The temperature range for growth was 30-68 degrees C, with an optimum at 55 degrees C. The NaCl concentration range for growth was 0-17 g l(-1); there was no change in growth rate until the NaCl concentration reached 8 g l(-1). The pH range for growth was 6.0-8.0, with an optimum of 6.8-7.2. The bacterium could grow with 100% CO in the gas phase. With sulfate, CO was converted to H(2) and CO(2) and part of the H(2) was used for sulfate reduction; without sulfate, CO was completely converted to H(2) and CO(2). With sulfate, strain CO-1-SRB(T) utilized H(2)/CO(2), pyruvate, glucose, fructose, maltose, lactate, serine, alanine, ethanol and glycerol. The strain fermented pyruvate, lactate, glucose and fructose. Yeast extract was necessary for growth. Sulfate, thiosulfate and sulfite were used as electron acceptors, whereas elemental sulfur and nitrate were not. A phylogenetic analysis of 16S rRNA gene sequences placed strain CO-1-SRB(T) in the genus Desulfotomaculum, closely resembling Desulfotomaculum nigrificans DSM 574(T) and Desulfotomaculum sp. RHT-3 (99 and 100% similarity, respectively). However, the latter strains were completely inhibited above 20 and 50% CO in the gas phase, respectively, and were unable to ferment CO, lactate or glucose in the absence of sulfate. DNA-DNA hybridization of strain CO-1-SRB(T) with D. nigrificans and Desulfotomaculum sp. RHT-3 showed 53 and 60% relatedness, respectively. On the basis of phylogenetic and physiological features, it is suggested that strain CO-1-SRB(T) represents a novel species within the genus Desulfotomaculum, for which the name Desulfotomaculum carboxydivorans is proposed. This is the first description of a sulfate-reducing micro-organism that is capable of growth under an atmosphere of pure CO with and without sulfate. The type strain is CO-1-SRB(T) (=DSM 14880(T)=VKM B-2319(T)).