14 Search Results

Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a muchmore » wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond—an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.« less

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 monitoredmore » 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.« less

Iron reduction and sulfate reduction often occur simultaneously in anoxic systems, and where that is the case, the molar ratio between the reactions (i.e., Fe/SO₄^2- reduced) influences their impact on water quality and carbon storage. Previous research has shown that pH and the supply of electron donors and acceptors affect that ratio, but it is unclear how their influences compare and affect one another. This study examines impacts of pH and the supply of acetate, sulfate, and goethite on the ratio of iron to sulfate reduction in semi-continuous sediment bioreactors. We examined which parameter had the greatest impact on thatmore » ratio and whether the parameter influences depended on the state of each other. Results show that pH had a greater influence than acetate supply on the ratio of iron to sulfate reduction, and that the impact of acetate supply on the ratio depended on pH. In acidic reactors (pH 6.0 media), the ratio of iron to sulfate reduction decreased from 3:1 to 2:1 as acetate supply increased (0-1 mM). In alkaline reactors (pH 7.5 media), iron and sulfate were reduced in equal proportions, regardless of acetate supply. Secondly, a comparison of experiments with and without sulfate shows that the extent of iron reduction was greater if sulfate reduction was occurring and that the effect was larger in alkaline reactors than acidic reactors. Thus, the influence of sulfate supply on iron reduction extent also depended on pH and suggests that iron reduction grows more dependent on sulfate reduction as pH increases. Our results compare well to trends in groundwater geochemistry and provide further evidence that pH is a major control on iron and sulfate reduction in systems with crystalline (oxyhydr)oxides. pH not only affects the ratio between the reactions but also the influences of other parameters on that ratio.« less

DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. Furthermore, we exemplify inconsistencies that have arisen from this practice andmore » endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.« less

Methanogenesis and iron reduction play major roles in determining global fluxes of greenhouse gases. Despite their importance, environmental factors that influence their interactions are poorly known. Here, we present evidence that pH significantly influences the balance between each reaction in anoxic environments that contain ferric (oxyhydr)oxide minerals. In sediment bioreactors that contained goethite as a source of ferric iron, both iron reduction and methanogenesis occurred but the balance between them varied significantly with pH. Compared to bioreactors receiving acidic media (pH 6), electron donor oxidation was 85% lower for iron reduction and 61% higher for methanogenesis in bioreactors receiving alkalinemore » media (pH 7.5). Thus, methanogenesis displaced iron reduction considerably at alkaline pH. Geochemistry data collected from U.S. aquifers demonstrate that a similar pattern also exists on a broad spatial scale in natural settings. In contrast, in bioreactors that were not augmented with goethite, clay minerals served as the source of ferric iron and the balance between each reaction did not vary significantly with pH. We therefore conclude that pH can regulate the relative contributions of microbial iron reduction and methanogenesis to carbon fluxes from terrestrial environments. We further propose that the availability of ferric (oxyhydr)oxide minerals influences the extent to which the balance between each reaction is sensitive to pH. Here, the results of this study advance our understanding of environmental controls on microbial methane generation and provide a basis for using pH and the occurrence of ferric minerals to refine predictions of greenhouse gas fluxes.« less

Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differencesmore » in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10-12 to 5.9 × 10-10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R2 = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain.« less

Insight into the mechanisms for arsenic detoxification byGeobacterspecies is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 differentGeobactergenomes showed that all of these species have genes coding for an arsenic detoxification system (arsoperon), and several have genes required for arsenic respiration (arroperon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome ofG. sulfurreducens; however, only one (ArsR1) regulated transcription of thearsoperon. Elimination ofarsR1from theG. sulfurreducenschromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the genemore » coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, whilearsCdeletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on howGeobacterinfluences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. This study examines arsenic transformation mechanisms utilized byGeobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments.Geobacterspecies play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies ofGeobactershould shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 differentGeobactergenomes and found that all of these species possess genes coding for an arsenic detoxification system (arsoperon), and some also have genes required for arsenic respiration (arroperon) and arsenic methylation (arsM).« less