An Aminoimidazole Radical Intermediate in the Anaerobic Biosynthesis of the 5,6-Dimethylbenzimidazole Ligand to Vitamin B12.

Organisms that perform the de novo biosynthesis of cobalamin (vitamin B12) do so via unique pathways depending on the presence of oxygen in the environment. The anaerobic biosynthesis pathway of 5,6-dimethylbenzimidazole, the so-called "lower ligand" to the cobalt center, has been recently identified. This process begins with the conversion of 5-aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (HBI) by the radical S-adenosyl-l-methionine (SAM) enzyme BzaF, also known as HBI synthase. In this work we report the characterization of a radical intermediate in the reaction of BzaF using electron paramagnetic resonance spectroscopy. Using various isotopologues of AIR, we extracted hyperfine parameters for a number of nuclei, allowing us to propose plausible chemical compositions and structures for this intermediate. Specifically, we find that an aminoimidazole radical is formed in close proximity to a fragment of the ribose ring. These findings induce the revision of past proposed mechanisms and illustrate the ability of radical SAM enzymes to tightly control the radical chemistry that they engender.

Isotopic effects of PCE induced by organohalide-respiring bacteria.

Reductive dechlorination performed by organohalide-respiring bacteria (OHRB) enables the complete detoxification of certain emerging groundwater pollutants such as perchloroethene (PCE). Environmental samples from a contaminated site incubated in a lab-scale microcosm (MC) study enable documentation of such reductive dechlorination processes. As compound-specific isotope analysis is used to monitor PCE degradation processes, nucleic acid analysis-like 16S-rDNA analysis-can be used to determine the key OHRB that are present. This study applied both methods to laboratory MCs prepared from environmental samples to investigate OHRB-specific isotope enrichment at PCE dechlorination. This method linkage can enhance the understanding of isotope enrichment patterns of distinct OHRB, which further contribute to more accurate evaluation, characterisation and prospection of natural attenuation processes. Results identified three known OHRB genera (Dehalogenimonas, Desulfuromonas, Geobacter) in diverse abundance within MCs. One species of Dehalogenimonas was potentially involved in complete reductive dechlorination of PCE to ethene. Furthermore, the isotopic effects of PCE degradation were clustered and two isotope enrichment factors (ε) (- 11.6‰, - 1.7‰) were obtained. Notably, ε values were independent of degradation rates and kinetics, but did reflect the genera of the dechlorinating OHRB.

Specific and efficient electrochemical selection of Geoalkalibacter subterraneus and Desulfuromonas acetoxidans in high current-producing biofilms.

Two different saline sediments were used to inoculate potentiostatically controlled reactors (a type of microbial bioelectrochemical system, BES) operated in saline conditions (35 gNaCl l(-1)). Reactors were fed with acetate or a mixture of acetate and butyrate at two pH values: 7.0 or 5.5. Electroactive biofilm formation lag-phase, maximum current density production and coulombic efficiency were used to evaluate the overall performance of reactors. High current densities up to 8.5 A m(-2) were obtained using well-defined planar graphite electrodes. Additionally, biofilm microbial communities were characterized by CE-SSCP and 454 pyrosequencing. As a result of this procedure, two anode-respiring bacteria (ARB) always dominated the anodic biofilms: Geoalkalibacter subterraneus and/or Desulfuromonas acetoxidans. This suggests that a strong electrochemically driven selection process imposed by the applied potential occurs in the BES system. Moreover, the emergence of Glk. subterraneus in anodic biofilms significantly contributes to broaden the spectrum of high current producing microorganisms electrochemically isolated from environmental samples.

[Mechanisms of electron transfer to insoluble terminal acceptors in chemoorganotrophic bacteria].

The mechanisms of electron transfer of association of chemoorganotrophic bacteria to the anode in microbial fuel cells are summarized in the survey. These mechanisms are not mutually exclusive and are divided into the mechanisms of mediator electron transfer, mechanisms of electron transfer with intermediate products of bacterial metabolism and mechanism of direct transfer of electrons from the cell surface. Thus, electron transfer mediators are artificial or synthesized by bacteria riboflavins and phenazine derivatives, which also determine the ability of bacteria to antagonism. The microorganisms with hydrolytic and exoelectrogenic activity are involved in electron transfer mechanisms that are mediated by intermediate metabolic products, which are low molecular carboxylic acids, alcohols, hydrogen etc. The direct transfer of electrons to insoluble anode is possible due to membrane structures (cytochromes, pili, etc.). Association of microorganisms, and thus the biochemical mechanisms of electron transfer depend on the origin of the inoculum, substrate composition, mass transfer, conditions of aeration, potentials and location of electrodes and others, that are defined by technological and design parameters.

Impact of initial conditions on extant microbial kinetic parameter estimates: application to chlorinated ethene dehalorespiration.

Monod kinetics are the foundation of mathematical models of many environmentally important biological processes, including the dehalorespiration of chlorinated ethene groundwater contaminants. The Monod parameters--qmax, the maximum specific substrate utilization rate, and KS, the half-saturation constant--are typically estimated in batch assays, which are superficially simple to prepare and maintain. However, if initial conditions in batch assays are not chosen carefully, it is unlikely that the estimated parameter values will be meaningful because they do not reflect microbial activity in the environmental system of interest, and/or they are not mathematically identifiable. The estimation of qmax and KS values that are highly correlated undoubtedly contributes significantly to the wide range in reported parameter values and may undermine efforts to use mathematical models to demonstrate the occurrence of natural attenuation or predict the performance of engineered bioremediation approaches. In this study, a series of experimental and theoretical batch kinetic assays were conducted using the tetrachloroethene-respirer Desulfuromonas michiganensis to systematically evaluate the effects of initial batch assay conditions, expressed as the initial substrate (S0)-to-initial biomass concentration (X0) ratio (S0/X0) and the S0/KS ratio on parameter correlation. An iterative approach to obtain meaningful Monod parameter estimates was developed and validated using three different strains and can be broadly applied to a range of other substrates and populations. While the S0/X0 ratio is critical to obtaining kinetic parameter estimates that reflect in situ microbial activity, this study shows that optimization of the S0/KS ratio is key to minimizing Monod parameter correlation.

Sulfur oxidation to sulfate coupled with electron transfer to electrodes by Desulfuromonas strain TZ1.

Microbial oxidation of elemental sulfur with an electrode serving as the electron acceptor is of interest because this may play an important role in the recovery of electrons from sulfidic wastes and for current production in marine benthic microbial fuel cells. Enrichments initiated with a marine sediment inoculum, with elemental sulfur as the electron donor and a positively poised (+300 mV versus Ag/AgCl) anode as the electron acceptor, yielded an anode biofilm with a diversity of micro-organisms, including Thiobacillus, Sulfurimonas, Pseudomonas, Clostridium and Desulfuromonas species. Further enrichment of the anode biofilm inoculum in medium with elemental sulfur as the electron donor and Fe(III) oxide as the electron acceptor, followed by isolation in solidified sulfur/Fe(III) medium yielded a strain of Desulfuromonas, designated strain TZ1. Strain TZ1 effectively oxidized elemental sulfur to sulfate with an anode serving as the sole electron acceptor, at rates faster than Desulfobulbus propionicus, the only other organism in pure culture previously shown to oxidize S° with current production. The abundance of Desulfuromonas species enriched on the anodes of marine benthic fuel cells has previously been interpreted as acetate oxidation driving current production, but the results presented here suggest that sulfur-driven current production is a likely alternative.

Dehalorespiration model that incorporates the self-inhibition and biomass inactivation effects of high tetrachloroethene concentrations.

In the vicinity of dense nonaqueous phase liquid (DNAPL) contaminant source zones, aqueous concentrations of tetrachloroethene (PCE) in groundwater may approach saturation levels. In this study, the ability of two PCE-respiring strains (Desulfuromonas michiganensis and Desulfitobacterium strain PCE1) to dechlorinate high concentrations of PCE was experimentally evaluated and depended on the initial biomass concentration. This suggests high PCE concentrations permanently inactivated a fraction of biomass, which, if sufficiently large, prevented dechlorination from proceeding. The toxic effects of PCE were incorporated into a model of dehalorespirer growth by adapting the transformation capacity concept previously applied to describe biomass inactivation by products of cometabolic TCE oxidation. The inactivation growth model was coupled to the Andrews substrate utilization model, which accounts for the self-inhibitory effects of PCE on dechlorination rates, and fit to the experimental data. The importance of incorporating biomass inactivation and self-inhibition effects when modeling reductive dechlorination of high PCE concentrations was demonstrated by comparing the goodness-of-fit of the Andrews biomass inactivation and three alternate models that do capture these factors. The new dehalorespiration model should improve our ability to predict contaminant removal in DNAPL source zones and determine the inoculum size needed to successfully implement bioaugmentation of DNAPL source zones.

Characterization of microbial community structure and population dynamics of tetrachloroethene-dechlorinating tidal mudflat communities.

Tetrachloroethene (PCE) and trichloroethene (TCE) are common groundwater contaminants that also impact tidal flats, especially near urban and industrial areas. However, very little is known about dechlorinating microbial communities in tidal flats. Titanium pyrosequencing, 16S rRNA gene clone libraries, and dechlorinator-targeted quantitative real-time PCR (qPCR) characterized reductive dechlorinating activities and populations in tidal flat sediments collected from South Korea's central west coast near Kangwha. In microcosms established with surface sediments, PCE dechlorination to TCE began within 10 days and 100% of the initial amount of PCE was converted to TCE after 37 days. cis-1,2-Dichloroethene (cis-DCE) was observed as dechlorination end product in microcosms containing sediments collected from deeper zones (i.e., 35-40 cm below ground surface). Pyrosequencing of bacterial 16S rRNA genes and 16S rRNA gene-targeted qPCR results revealed Desulfuromonas michiganensis-like populations predominanted in both TCE and cis-DCE producing microcosms. Other abundant groups included Desulfuromonas thiophila and Pelobacter acidigallici-like populations in the surface sediment microcosms, and Desulfovibrio dechloracetivorans and Fusibacter paucivorans-like populations in the deeper sediment microcosms. Dehalococcoides spp. populations were not detected in these sediments before and after incubation with PCE. The results suggest that tidal flats harbor novel, salt-tolerant dechlorinating populations and that titanium pyrosequencing provides more detailed insight into community structure dynamics of the dechlorinating microcosms than conventional 16S rRNA gene sequencing or fingerprinting methods.

Constraint-based modeling analysis of the metabolism of two Pelobacter species.

BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. RESULTS: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. CONCLUSIONS: We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community.

Determination of intrinsic monod kinetic parameters for two heterotrophic tetrachloroethene (PCE)-respiring strains and insight into their application.

A complete set of mathematically identifiable and meaningful kinetic parameters estimates is needed to accurately describe the activity of individual populations that dehalorespire tetrachloroethene (PCE) and other chlorinated ethenes. These data may be difficult to extract from the literature because kinetic parameter estimates obtained using mixed cultures may reflect the activity of multiple dehalorespiring populations, while those obtained at low initial substrate-to-biomass ratios (S(0)/X(0)) are influenced by culture history and are generally not relevant to other systems. This study focused on estimation of electron donor and acceptor utilization kinetic parameters for the heterotrophic dehalorespirers Desulfuromonas michiganensis strain BB1 and Desulfitobacterium sp. strain PCE1. Electron acceptor utilization kinetic parameters that are identifiable and independent of culture history, i.e., intrinsic, could be estimated at S(0)/X(0) >or= 10, with both concentrations expressed as chemical oxygen demand (COD). However, the parameter estimates did not accurately describe dechlorination kinetics at lower S(0)/X(0) ratios. The maximum specific substrate utilization rates (q(max)) and half-saturation constants (K(S)) for PCE and trichloroethene (TCE) estimated for the two heterotrophic strains are higher than the values reported for Dehalococcoides cultures. These results suggest that the natural niche of Dehalococcoides strains that can metabolize a range of chlorinated ethenes may be to respire dichloroethene and vinyl chloride produced by Desulfuromonas and Desulfitobacterium strains or other populations that dechlorinate PCE and TCE at faster rates. Few data exist on the electron donor utilization kinetics of heterotrophic dehalorespirers. The results of this study suggest that Desulfuromonas and Desulfitobacterium strains should be able to compete for organic electron donors with other heterotrophic populations in the subsurface.

Assessment of chromium biostabilization in contaminated soils using standard leaching and sequential extraction techniques.

The iron reducing microorganism Desulfuromonas palmitatis was evaluated as potential biostabilization agent for the remediation of chromate contaminated soils. D. palmitatis were used for the treatment of soil samples artificially contaminated with Cr(VI) at two levels, i.e. 200 and 500 mg kg(-1). The efficiency of the treatment was evaluated by applying several standard extraction techniques on the soil samples before and after treatment, such as the EN12457 standard leaching test, the US EPA 3060A alkaline digestion method and the BCR sequential extraction procedure. The water soluble chromium as evaluated with the EN leaching test, was found to decrease after the biostabilization treatment from 13 to less than 0.5 mg kg(-1) and from 120 to 5.6 mg kg(-1) for the soil samples contaminated with 200 and 500 mg Cr(VI) per kg soil respectively. The BCR sequential extraction scheme, although not providing accurate estimates about the initial chromium speciation in contaminated soils, proved to be a useful tool for monitoring the relative changes in element partitioning, as a consequence of the stabilization treatment. After bioreduction, the percentage of chromium retained in the two least soluble BCR fractions, i.e. the "oxidizable" and "residual" fractions, increased from 54 and 73% to more than 96% in both soils.

Removal of heavy metals and arsenic from contaminated soils using bioremediation and chelant extraction techniques.

A combined chemical and biological treatment scheme was evaluated in this study aiming at obtaining the simultaneous removal of metalloid arsenic and cationic heavy metals from contaminated soils. The treatment involved the use of the iron reducing microorganism Desulfuromonas palmitatis, whose activity was combined with the chelating strength of EDTA. Taking into consideration that soil iron oxides are the main scavengers of As, treatment with iron reducing microorganisms aimed at inducing the reductive dissolution of soil oxides and thus obtaining the release of the retained As. The main objective of using EDTA was the removal of metal contaminants, such as Pb and Zn, through the formation of soluble metal chelates. Experimental results however indicated that EDTA was also indispensable for the biological reduction of Fe(III) oxides. The bacterial activity was found to have a pronounced positive effect on the removal of arsenic, which increased from the value of 35% obtained during the pure chemical treatment up to 90% in the presence of D. palmitatis. In the case of Pb, the major part, i.e. approximately 85%, was removed from soil with purely chemical mechanisms, whereas the biological activity slightly improved the extraction, increasing the final removal up to 90%. Co-treatment had negative effect only for Zn, whose removal was reduced from 80% under abiotic condition to approximately 50% in the presence of bacteria.

Mercury methylation by dissimilatory iron-reducing bacteria.

The Hg-methylating ability of dissimilatory iron-reducing bacteria in the genera Geobacter, Desulfuromonas, and Shewanella was examined. All of the Geobacter and Desulfuromonas strains tested methylated mercury while reducing Fe(III), nitrate, or fumarate. In contrast, none of the Shewanella strains produced methylmercury at higher levels than abiotic controls under similar culture conditions. Geobacter and Desulfuromonas are closely related to known Hg-methylating sulfate-reducing bacteria within the Deltaproteobacteria.

Analysis of trace hydrogen metabolism.

H2 maintains an important role in bacterial metabolism in anaerobic environments. The ability to measure and analyze H2 concentrations in biological systems is often useful for determining the physiological state of the microbiota. Methods for precisely analyzing H2 in bacterial cultures and environmental samples are now available. This chapter discusses H2 measurements from both the theoretical and practical methodology perspective of the analysis and the interpretation of data.