Quantification of Desulfovibrio vulgaris dissimilatory sulfite reductase gene expression during electron donor- and electron acceptor-limited growth

Sulfate availability drives the reductive transformation of schwertmannite by co-cultured iron- and sulfate-reducing bacteria

Schwertmannite (Sch) is a highly bioavailable iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment rich in sulfate (SO42-). Microbial-mediated Sch transformation has been well-studied, however, the understanding of how SO42- availability affects the microbial-mediated Sch transformation and the secondary minerals influence microbes is relatively limited. This study examined the effect of SO42- availability on the iron-reducing bacteria (FeRB) and SO42--reducing bacteria (SRB) consortium-mediated Sch transformation and the resulting secondary minerals in turn on bacteria. Increased SO42- accelerated the onset of microbial SO42- reduction, which significantly accelerated Sch reduction transformation. The extent of intermediate products such as lepidocrocite (22.1 % ~ 76.3 %, all treatments) and goethite (15.3 %, 10 mM SO42-, 5 d) formed by Sch transformation depended on SO42- concentrations. Vivianite, siderite and iron‑sulfur minerals (e.g., FeS and FeS2) were the dominant secondary minerals, in which the relative content of vivianite and siderite decreased while iron‑sulfur minerals increased with increasing SO42- concentration. Correspondingly, the abundance of FeRB and SRB was negatively and positively correlated with SO42- concentration, respectively; 1 mM SO42- promoted the cymA and omcA expression of FeRB, but 10 mM SO42- lowerd the cymA and omcA expression compared to the 1 mM SO42-; the dsr expression of SRB related linearly to the SO42- concentration. These secondary minerals accumulated on the cell surface to form cell encrustations, which limited the growth and gene expression of FeRB and SRB, and even inhibited the activity of SRB in the 10 mM SO42- treatment group. The 10 mM SO42- treatment group with low-intensity ultrasound effectively restored the SRB activity for reducing SO42- by disintegrating the cell-mineral aggregation, further indicating that cell encrustations limited the microbial metabolism. The results highlight the critical role that SO42- availability can play in controlling microbial transformation of mineral, and the influence of secondary minerals on microbial metabolism.

Microbial reduction of schwertmannite by co-cultured iron- and sulfate-reducing bacteria

Schwertmannite (Sch) is an iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment. The transformation mechanism of Sch mediated by pure cultured iron-reducing bacteria (FeRB) or sulfate-reducing bacteria (SRB) has been studied. However, FeRB and SRB widely coexist in the environment, the mechanism of Sch transformation by the consortia of FeRB and SRB is still unclear. This study investigated the Sch reduction by co-cultured Shewanella oneidensis (FeRB) and Desulfosporosinus meridiei (SRB). The results showed that co-culture of FeRB and SRB could accelerate the reductive dissolution of Sch, but not synergistically, and there were two distinct phases in the reduction of Sch mediated by FeRB and SRB: an initial phase in which FeRB predominated and Fe³⁺ in Sch was reduced, accompanied with the release of SO₄^2-, and the detected secondary minerals were mainly vivianite; the second phase in which SRB predominated and mediated the reduction of SO₄^2-, producing minerals including mackinawite and siderite in addition to vivianite. Compared to pure culture, the abundance of FeRB and SRB in the consortia decreased, and more minerals aggregated inside and outside the cell; correspondingly, the transcription levels of genes (cymA, omcA, and mtrCBA) related to Fe³⁺ reduction in co-culture was down-regulated, while the transcription levels of SO₄^2--reducing genes (sat, aprAB, dsr(C)) was generally up-regulated. These phenomena suggested that secondary minerals produced in co-culture limited but did not inhibit bacterial growth, and the presence of SRB was detrimental to dissimilatory Fe³⁺ reduction, while existed FeRB was in favor of dissimilatory SO₄^2- reduction. SRB mediated SO₄^2- reduction by up-regulating the expression of SO₄^2- reduction-related genes when its abundance was limited, which may be a strategy to cope with external coercion. These findings allow for a better understanding of the process and mechanism of microbial mediated reduction of Sch in the environment.

Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors

Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L^-1 (R12) and 3901 ng L^-1 (R13) in June, and 2179 ng L^-1 (R12) and 1349 ng L^-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L^-1 in June and 0.35 mg L^-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.

Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris

A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth. Eight different variations of this model were evaluated by comparing model predictions to experimental data determined for four different growth conditions - three for sulfate respiration (with lactate, pyruvate or H₂ /CO₂ -acetate) and one for fermentation in syntrophic coculture. The final general model supports (i) a role for Hdr-Flx in the oxidation of DsrC and ferredoxin, and reduction of NAD⁺ in a flavin-based electron confurcating reaction sequence, (ii) a function of the Qmo complex in receiving electrons from the menaquinone pool and potentially from ferredoxin to reduce APS and (iii) a reduction of the soluble DsrC by LdhAB and a function of DsrC in electron transfer reactions other than sulfite reduction.

dsrAB-based analysis of sulphate-reducing bacteria in moving bed biofilm reactor (MBBR) wastewater treatment plants

Sulphate-reducing bacteria (SRB) are important members of the sulphur cycle in wastewater treatment plants (WWTPs). In this study, we investigate the diversity and activity of SRB within the developing and established biofilm of two moving bed biofilm reactor (MBBR) systems treating municipal wastewater in New Zealand. The larger of the two WWTPs (Moa Point) generates high levels of sulphide relative to the smaller Karori plant. Clone libraries of the dissimilatory (bi)sulphite reductase (dsrAB) genes and quantitative real-time PCR targeting dsrA transcripts were used to compare SRB communities between the two WWTPs. Desulfobulbus (35-53 % of total SRB sequences) and genera belonging to the family Desulfobacteraceae (27-41 %) dominated the SRB fraction of the developing biofilm on deployed plastic carriers at both sites, whereas Desulfovibrio and Desulfomicrobium were exclusively found at Moa Point. In contrast, the established biofilms from resident MBBR carriers were largely dominated by Desulfomonile tiedjei-like organisms (58-100 % of SRB sequences). The relative transcript abundance of dsrA genes (signifying active SRBs) increased with biofilm weight yet remained low overall, even in the mature biofilm stage. Our results indicate that although SRB are both present and active in the microbial community at both MBBR study sites, differences in the availability of sulphate may be contributing to the observed differences in sulphide production at these two plants.

Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments

Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.

Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK)

We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50 cm of the sediment core making up 22.4% of the total bacterial community and were 13.6% at 250 cm deep. Gene libraries for dsrA (dissimilatory sulfite reductase α-subunit) were constructed from the heavily contaminated (heavy metals) surface sediment (top 20 cm) and from the less contaminated and sulfate-depleted, deeper zone (250 cm). Certain cloned sequences were similar to dsrA found in members of the Syntrophobacteraceae, Desulfobacteraceae and Desulfovibrionaceae as well as a large fraction (60%) of novel sequences that formed a deep branching dsrA lineage. Phylogenetic analysis of metabolically active SRPs was performed by reverse transcription PCR and single strand conformational polymorphism analysis (RT-PCR-SSCP) of dsrA genes derived from extracted sediment RNA. Subsequent comparative sequence analysis of excised SSCP bands revealed a high transcriptional activity of dsrA belonging to Desulfovibrio species in the surface sediment. These results may suggest that members of the Desulfovibrionaceae are more active than other SRP groups in heavy metal-contaminated surface sediments.

Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease

In the human gastrointestinal tract, dietary components, including fiber, that reach the colon are fermented principally to short-chain fatty acids, hydrogen, and carbon dioxide. Microbial disposal of the hydrogen generated during anaerobic fermentation in the human colon is critical to optimal functioning of this ecosystem. However, our understanding of microbial hydrogenotrophy is fragmented and, at least as it occurs in the colon, is mostly theoretical in nature. Thorough investigation and integration of knowledge on the diversity of hydrogenotrophic microbes, their metabolic variation and activities as a functional group, as well as the nature of their interactions with fermentative bacteria, are necessary to understand hydrogen metabolism in the human colon. Here, we review the limited data available on the three major groups of H(2)-consuming microorganisms found in the human colon [methanogens, sulfate-reducing bacteria (SRB), and acetogens] as well as evidence that end products of their metabolism have an important impact on colonic health.

Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers

Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.

Geobacter: the microbe electric's physiology, ecology, and practical applications

Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.

Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

Background

Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors.

Results

qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited.

Conclusions

The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.