Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria

Diversity and ecology of NrfA-dependent ammonifying microorganisms

Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.

Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs

Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.

A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.

Chemical solutions for restoring scaling-induced injectivity impairment in offshore produced water re-injection

Produced water re-injection (PWRI) is a promising and sustainable strategy to manage substantial quantities of produced water for subsurface energy production systems. This approach offers an alternative to the environmentally harmful practice of marine disposal. Nonetheless, produced water re-injection may lead to considerable reductions in the injectivity. The injectivity loss can be attributed to several factors, including inorganic scaling, which can obstruct the flow pathway through porous media near the wellbore as well as subsurface facilities (e.g., tubing). Scaling can also contribute to the formation of mixed organic-inorganic schmoo-like complexes. Iron-containing (FexSy, FexOy-FexOyHz), carbonate-, and sulfate-based scales (e.g., BaSO4, SrSO4, and CaCO3) are the primary precipitates that have disruptive effects during PWRI scheme, especially in reservoirs suffering from microbial souring activities. In this work, we first screened the mineral scales that may form under the relevant re-injection conditions using the composition of produced water and seawater samples from the Danish North Sea. Subsequently, we assessed the efficiency of a commercial scale inhibitor against the scaling of targeted mineral phases through a series of batch experiments, followed by the development of a model to simulate its inhibitory performance. To reduce the precipitation or deposition of different minerals in water injection applications, we evaluated the combined effect of adding other chemicals (i.e., an acid, an oxidizer, and a chelating agent) to the injection water along with the scale inhibitor. To do this, we described the relevant mineral-aqueous interactions (dissolution, precipitation, and solution complexation) in PHREEQC. This predictive model represents an alternative to time- and resource-intensive experiments and may aid in achieving optimized chemical recipes required to mitigate mineral scaling in water injection systems under various physiochemical conditions. This work can contribute to the development of more sustainable and efficient strategies for managing produced water, ultimately helping to reduce the environmental impacts of hydrocarbon production.

Watershed characteristics and chemical properties govern methyl mercury concentrations within headwater streams of boreal forests in Ontario, Canada

Methyl mercury (MeHg) concentrations in boreal headwater streams are influenced by complex natural processes and disturbances such as forestry management. Understanding drivers of MeHg within boreal streams in Ontario, Canada, is of particular interest as there are legacy MeHg concerns. However, models accounting for the complexity of underlying processes have not yet been developed. We assessed how catchment characteristics and stream water chemistry influence MeHg concentrations within 19 watersheds of the Dryden - Wabigoon Forest in Ontario, Canada, using a structural equation modelling (SEM) approach. Despite the study area encompassing a large variation of boreal forest watersheds in the Canadian Shield, our SEM had substantial explanatory power across the region (χ251 = 45.37, p-value = 0.70, R2 = 0.75). Nitrate concentrations (p-value <0.001), water temperature (p-value = 0.002), and the latent watershed characteristic (p-value <0.001) had a positive influence on MeHg concentrations once variable interactions were accounted. Due to the inherent strengths of applying an SEM approach, we describe two plausible pathways driving MeHg concentrations: 1) indirect effect of forest-derived nutrients increases in-situ MeHg production in Dryden - Wabigoon Forest streams, and 2) direct supply of MeHg from inundated soils following consistent precipitation and inundation events (i.e., fill, sit, and spill).

Simultaneous nitrate and sulfate biotransformation driven by different substrates: comparison of carbon sources and metabolic pathways at different C/N ratios

Nitrate (NO₃^-) and sulfate (SO₄^2-) often coexist in organic wastewater. The effects of different substrates on NO₃^- and SO₄^2- biotransformation pathways at various C/N ratios were investigated in this study. This study used an activated sludge process for simultaneous desulfurization and denitrification in an integrated sequencing batch bioreactor. The results revealed that the most complete removals of NO₃^- and SO₄^2- were achieved at a C/N ratio of 5 in integrated simultaneous desulfurization and denitrification (ISDD). Reactor Rb (sodium succinate) displayed a higher SO₄^2- removal efficiency (93.79%) with lower chemical oxygen demand (COD) consumption (85.72%) than reactor Ra (sodium acetate) on account of almost 100% removal of NO₃^- in both Ra and Rb. Ra produced more S^2- (5.96 mg L^-1) and H₂S (25 mg L^-1) than Rb, which regulated the biotransformation of NO₃^- from denitrification to dissimilatory nitrate reduction to ammonium (DNRA), whereas almost no H₂S accumulated in Rb which can avoid secondary pollution. Sodium acetate-supported systems were found to favor the growth of DNRA bacteria (Desulfovibrio); although denitrifying bacteria (DNB) and sulfate-reducing bacteria (SRB) were found to co-exist in both systems, Rb has a greater keystone taxa diversity. Furthermore, the potential carbon metabolic pathways of the two carbon sources have been predicted. Both succinate and acetate could be generated in reactor Rb through the citrate cycle and the acetyl-CoA pathway. The high prevalence of four-carbon metabolism in Ra suggests that the carbon metabolism of sodium acetate is significantly improved at a C/N ratio of 5. This study has clarified the biotransformation mechanisms of NO₃^- and SO₄^2- in the presence of different substrates and the potential carbon metabolism pathway, which is expected to provide new ideas for the simultaneous removal of NO₃^- and SO₄^2- from different media.

Global change effects on biogeochemical mercury cycling

Past and present anthropogenic mercury (Hg) release to ecosystems causes neurotoxicity and cardiovascular disease in humans with an estimated economic cost of $117 billion USD annually. Humans are primarily exposed to Hg via the consumption of contaminated freshwater and marine fish. The UNEP Minamata Convention on Hg aims to curb Hg release to the environment and is accompanied by global Hg monitoring efforts to track its success. The biogeochemical Hg cycle is a complex cascade of release, dispersal, transformation and bio-uptake processes that link Hg sources to Hg exposure. Global change interacts with the Hg cycle by impacting the physical, biogeochemical and ecological factors that control these processes. In this review we examine how global change such as biome shifts, deforestation, permafrost thaw or ocean stratification will alter Hg cycling and exposure. Based on past declines in Hg release and environmental levels, we expect that future policy impacts should be distinguishable from global change effects at the regional and global scales.

Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in oil reservoir and biological control of SRB: a review

Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.

Simultaneous sulfate and nitrate reduction in coastal sediments

The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.

Response to substrate limitation by a marine sulfate-reducing bacterium

Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (K_m) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the K_m for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol^-1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.

Denitrification Biokinetics: Towards Optimization for Industrial Applications

Denitrification is a microbial process that converts nitrate (NO₃^–) to N₂ and can play an important role in industrial applications such as souring control and microbially enhanced oil recovery (MEOR). The effectiveness of using NO₃^– in souring control depends on the partial reduction of NO₃^– to nitrite (NO₂^–) and/or N₂O while in MEOR complete reduction of NO₃^– to N₂ is desired. Thauera has been reported as a dominant taxon in such applications, but the impact of NO₃^– and NO₂^– concentrations, and pH on the kinetics of denitrification by this bacterium is not known. With the goal of better understanding the effects of such parameters on applications such as souring and MEOR, three strains of Thauera (K172, NS1 and TK001) were used to study denitrification kinetics when using acetate as an electron donor. At low initial NO₃^– concentrations (∼1 mmol L^–1) and at pH 7.5, complete NO₃^– reduction by all strains was indicated by non-detectable NO₃^– concentrations and near-complete recovery (> 97%) of the initial NO₃-N as N₂ after 14 days of incubation. The relative rate of denitrification by NS1 was low, 0.071 mmol L^–1 d^–1, compared to that of K172 (0.431 mmol L^–1 d^–1) and TK001 (0.429 mmol L^–1 d^–1). Transient accumulation of up to 0.74 mmol L^–1 NO₂^– was observed in cultures of NS1 only. Increased initial NO₃^– concentrations resulted in the accumulation of elevated concentrations of NO₂^– and N₂O, particularly in incubations with K172 and NS1. Strain TK001 had the most extensive NO₃^– reduction under high initial NO₃^– concentrations, but still had only ∼78% of the initial NO₃-N recovered as N₂ after 90 days of incubation. As denitrification proceeded, increased pH substantially reduced denitrification rates when values exceeded ∼ 9. The rate and extent of NO₃^– reduction were also affected by NO₂^– accumulation, particularly in incubations with K172, where up to more than a 2-fold rate decrease was observed. The decrease in rate was associated with decreased transcript abundances of denitrification genes (nirS and nosZ) required to produce enzymes for reduction of NO₂^– and N₂O. Conversely, high pH also contributed to the delayed expression of these gene transcripts rather than their abundances in strains NS1 and TK001. Increased NO₂^– concentrations, N₂O levels and high pH appeared to cause higher stress on NS1 than on K172 and TK001 for N₂ production. Collectively, these results indicate that increased pH can alter the kinetics of denitrification by Thauera strains used in this study, suggesting that liming could be a way to achieve partial denitrification to promote NO₂^– and N₂O production (e.g., for souring control) while pH buffering would be desirable for achieving complete denitrification to N₂ (e.g., for gas-mediated MEOR).

Sulfate reducing microorganisms in high temperature oil reservoirs

High temperature reservoirs offer a window into the microbial life of the deep biosphere. Sulfate reducing microorganisms have been recovered from high temperature oil reservoirs around the globe and characterized using culture-dependent and culture-independent approaches. The activities of sulfate reducers contribute to reservoir souring and hydrocarbon degradation among other attracting considerable interest from the oil industry for the last 100 years. The extremes of temperature and pressure shape the activities and distribution of sulfate reducing bacteria and archaea in high temperature reservoirs. This chapter will attempt to summarize the key findings on the diversity and activities of sulfate reducing microorganisms in high temperature reservoirs.

Exploration and verification of the feasibility of sulfide-driven partial denitrification coupled with anammox for wastewater treatment

Anaerobic ammonia oxidation (anammox) is a well-developed biotechnology for treating high-strength ammonium wastewaters. Recently, partial denitrification has been considered as an alternative to supply anammox with the required nitrite. In this study, a process of sulfide-driven partial denitrification and anammox (SPDA) was developed and operated continuously in an upflow anaerobic sludge blanket (UASB) reactor for 392 days. This reactor was fed with synthetic wastewater containing 100 mgN/L nitrate, 80 mgN/L ammonium and 20-80 mgS/L sulfide. After 160 days of operation, the reactor reached stable performance, and the nitrogen removal efficiency and rate were maintained at 80% and 0.29 kgN/(m³•d), respectively. The estimated nitrogen removal via anammox and sulfide-driven denitrification were 87.2% and 12.8%. Additional batch experiments were conducted to investigate the effects of sulfide on anammox and the mechanisms of nitrogen removal in the SPDA system. The following results were obtained: (1) sulfide had an inhibitory effect on the specific anammox activity with IC₅₀ of 9.7 mgS-H₂S/L. (2) The rapid oxidation of sulfide by sulfur-oxidizing bacteria (SOB) could relieve the toxic effects of sulfide on the anammox in the SPDA system. (3) Sulfide bio-oxidation was a two-step reaction with biologically produced elemental sulfur (BPS⁰) as the intermediate, and the second step using BPS⁰ as the electron donor, can efficiently produce nitrite via partial denitrification (NO₃^- → NO₂^-) as a supply for anammox. Finally, a high-throughput sequencing analysis identified Thiobacillus and Sulfurimonas as the dominant genera of SOB in the SPDA system, and Candidatus Kuenenia as the dominant anammox bacteria. Overall, this research gives the foundation for the practical application of sulfide-driven partial denitrification and anammox process in the future.

Research on enhancement of zero-valent iron on dissimilatory nitrate/nitrite reduction to ammonium of Desulfovibrio sp. CMX

The process of nitrate dissimilation to ammonium (DNRA) is an important way for storing nitrogen in nature and DNRA is a key step in efficient recovery of nitrogen in wastewater. However, in view of the low conversion efficiency of DNRA, zero-valent iron (ZVI) was used to enhance the DNRA process of Desulfovibrio sp. CMX. ZVI can obviously promote the nitrate/nitrite reduction. The experiment indicated that 5 g/L 300 mesh ZVI could convert 5 mmol/L nitrate or nitrite to ammonium in 48 h or 36 h respectively, and the conversion ratio of NO₂^- to NH₄⁺ could reach more than 90%. The ZVI provided a suitable growth environment for the Desulfovibrio sp. CMX through chemical reduction of nitrite, production of divalent iron (Fe²⁺), reduction of oxidation-reduction potential (ORP) and adjustment of pH, which strengthened the DNRA performance. This experiment is advantageous for increasing efficiency of DNRA and provides a new idea for efficient recovery of nitrogen resources.

Active sulfur cycling in the terrestrial deep subsurface

The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.

Oil reservoir simulating bioreactors: tools for understanding petroleum microbiology

Various aspects of the oil fields in terms of microbial activity (souring, biocorrosion, etc.) and oil production (polymer flooding, etc.) have been evaluated through a variety of experiments. The primary step to study these properties in the laboratory requires the construction and operation of up-flow oil reservoir simulating bioreactors (ORSBs) in real time. Souring by reduction of sulfate to sulfide is a major contributor in enhancing corrosion of metal infrastructure used for oil production and processing. Whether the injection of biocides prevents or remediates reservoir souring can be addressed by flooding up-flow ORSBs. The potential of biopolymers/biosurfactants produced by different microbial strains have also been investigated for the role in maintaining additional oil recovery using ORSB. Additionally, key issues of polymer behavior during flooding of reservoirs could be understood during laboratory studies by monitoring the in situ porous medium rheology. Besides, the change in various ORSB parameters helps in adjudging the effect of different biosurfactants/biopolymers in enhancing oil recovery. Parameters such as permeability reduction, adsorption, interaction with porous matrix, and formation damage can be evaluated using ORSB. The analysis of earlier studies indicated that running bioreactors for longer duration of time can help in drawing conclusion with sharpness and less ambiguity. The current review discusses the construction and application of various types of ORSBs including the experimental studies employing ORSBs.

Advances in sulfur conversion-associated enhanced biological phosphorus removal in sulfate-rich wastewater treatment: A review

Recently an innovative sulfur conversion-associated enhanced biological phosphorus removal (S-EBPR) process has been developed for treating sulfate-rich wastewater. This process has successfully integrated sulfur (S), carbon (C), nitrogen (N) and P cycles for simultaneous metabolism or removal of C, N and P; moreover this new process relies on the synergy among the slow-growing sulfate-reducing bacteria and sulfur-oxidizing bacteria, hence generating little excess sludge. To elucidate this new process, researchers have investigated the microorganisms proliferated in the system, identified the biochemical pathways and assessed the impact of operational and environmental factors on process performance as well as trials on process optimization. This paper for the first time reviews the recent advances that have been achieved, particularly relating to the areas of S-EBPR microbiology and biochemistry, as well as the effects of environmental factors (e.g., electron donors/acceptors, pH, temperature, etc.). Moreover, future directions for researches and applications are proposed.

Resistance and Resilience of Sulfidogenic Communities in the Face of the Specific Inhibitor Perchlorate

Hydrogen sulfide is a toxic and corrosive gas, produced by the activity of sulfate-reducing microorganisms (SRM). Owing to the environmental, economic and human-health consequences of sulfide, there is interest in developing specific inhibitors of SRM. Recent studies have identified perchlorate as a promising emerging inhibitor. The aim of this work is to quantitatively dissect the inhibitory dynamics of perchlorate. Sulfidogenic mixed continuous-flow systems were treated with perchlorate. SRM number, sulfide production and community structure were monitored pre-, during and post-treatment. The data generated was compared to a simple mathematical model, where SRM growth slows as a result of inhibition. The experimental data supports the interpretation that perchlorate largely acts to suppress SRM growth rates, rendering planktonic SRM increasingly susceptible to wash-out. Surface-attachment was identified as an important parameter preventing SRM wash-out and thus governing inhibitory dynamics. Our study confirmed the lesser depletion of surface-attached SRM as compared to planktonic SRM during perchlorate treatment. Indirect effects of perchlorate (bio-competitive exclusion of SRM by dissimilatory perchlorate-reducing bacteria, DPRB) were also assayed by amending reactors with DPRB. Indeed, low concentrations of perchlorate coupled with DRPB amendment can drive sulfide concentrations to zero. Further, inhibition in a complex community was compared to that in a pure culture, highlighting similarities and differences between the two scenarios. Finally, we quantified susceptibility to perchlorate across SRM in various culture conditions, showing that prediction of complex behavior in continuous systems from batch results is possible. This study thus provides an overview of the sensitivity of sulfidogenic communities to perchlorate, as well as mechanisms underlying these patterns.

Change in the microbial community of saline geothermal fluids amended with a scaling inhibitor: effects of heat extraction and nitrate dosage

Geothermal plants are often affected by corrosion caused by microbial metabolites such as H₂S. In the Bad Blumau (Austria) geothermal system, an increase in microbially produced H₂S was observed in the hot (107 °C) and scaling inhibitor-amended saline fluids and in fluids that had cooled down (45 °C). Genetic fingerprinting and quantification revealed the dominance, increasing abundance and diversity of sulfate reducers such as Desulfotomaculum spp. that accompanied the cooling and processing of the geothermal fluids. In addition, a δ³⁴S isotopic signature showed the microbial origin of the H₂S that has been produced either chemolithotrophically or chemoorganotrophically. A nitrate addition test in a test pipe as a countermeasure against the microbial H₂S formation caused a shift from a biocenosis dominated by bacteria of the phylum Firmicutes to a community of Firmicutes and Proteobacteria. Nitrate supported the growth of nitrate-reducing sulfur-oxidizing Thiobacillus thioparus, which incompletely reduced nitrate to nitrite. The addition of nitrate led to a change in the composition of the sulfate-reducing community. As a result, representatives of nitrate- and nitrite-reducing SRB, such as Desulfovibrio and Desulfonatronum, emerged as additional community members. The interaction of sulfate-reducing bacteria and nitrate-reducing sulfur-oxidizing bacteria (NR-SOB) led to the removal of H₂S, but increased the corrosion rate in the test pipe.

Metabolites of an Oil Field Sulfide-Oxidizing, Nitrate-Reducing Sulfurimonas sp. Cause Severe Corrosion

Ambiguous reports of corrosion problems associated with the injection of nitrate for souring control necessitate a deeper understanding of this frequently applied bioengineering strategy. Sulfide-oxidizing, nitrate-reducing bacteria have been proposed as key culprits, despite the underlying microbial corrosion mechanisms remaining insufficiently understood. This study provides a comprehensive characterization of how individual metabolic intermediates of the microbial nitrogen and sulfur cycles can impact the integrity of carbon steel infrastructure. The results help explain the dramatic increases seen at times in corrosion rates observed during nitrate injection in field and laboratory trials and point to strategies for reducing adverse integrity-related side effects of nitrate-based souring mitigation.

Oil reservoir souring and associated material integrity challenges are of great concern to the petroleum industry. The bioengineering strategy of nitrate injection has proven successful for controlling souring in some cases, but recent reports indicate increased corrosion in nitrate-treated produced water reinjection facilities. Sulfide-oxidizing, nitrate-reducing bacteria (soNRB) have been suggested to be the cause of such corrosion. Using the model soNRB Sulfurimonas sp. strain CVO obtained from an oil field, we conducted a detailed analysis of soNRB-induced corrosion at initial nitrate-to-sulfide (N/S) ratios relevant to oil field operations. The activity of strain CVO caused severe corrosion rates of up to 0.27 millimeters per year (mm y⁻¹) and up to 60-μm-deep pitting within only 9 days. The highest corrosion during the growth of strain CVO was associated with the production of zero-valent sulfur during sulfide oxidation and the accumulation of nitrite, when initial N/S ratios were high. Abiotic corrosion tests with individual metabolites confirmed biogenic zero-valent sulfur and nitrite as the main causes of corrosion under the experimental conditions. Mackinawite (FeS) deposited on carbon steel surfaces accelerated abiotic reduction of both sulfur and nitrite, exacerbating corrosion. Based on these results, a conceptual model for nitrate-mediated corrosion by soNRB is proposed.

IMPORTANCE Ambiguous reports of corrosion problems associated with the injection of nitrate for souring control necessitate a deeper understanding of this frequently applied bioengineering strategy. Sulfide-oxidizing, nitrate-reducing bacteria have been proposed as key culprits, despite the underlying microbial corrosion mechanisms remaining insufficiently understood. This study provides a comprehensive characterization of how individual metabolic intermediates of the microbial nitrogen and sulfur cycles can impact the integrity of carbon steel infrastructure. The results help explain the dramatic increases seen at times in corrosion rates observed during nitrate injection in field and laboratory trials and point to strategies for reducing adverse integrity-related side effects of nitrate-based souring mitigation.

Combined use of coagulation (M. oleifera) and electrochemical techniques in the treatment of industrial paint wastewater for reuse and/or disposal

In this work, water-based paint (WBP) wastewater was treated using a natural coagulant, Moringa oleifera aqueous extract (MOAE), fortified with Ca²⁺ (from nitrate and chloride salts). In order to improve the quality of the treated wastewater and render it suitable for disposal, an electrolytic flow process was associated with the wastewater treatment using a filter-press reactor with a boron doped diamond (BDD) electrode. The feasibility of the treatment was evidenced by the reuse of the treated wastewater in the production of a new paint (manufactured by the company supplying the raw wastewater), whose quality was compatible with the water used by the manufacturer. The best conditions for the coagulation-flocculation process involved the use of 80 mL of MOAE (50 g/L of MO and 0.125 mol/L of Ca²⁺) for every 1.0 L of wastewater at pH 6.5. The limiting current density (35 mA/cm²) and an electrolysis time of 90 min (charge passed of 3.68 A h/L) were used in the electrochemical treatment. Biotoxicity assays using the brine shrimp Artemia salina revealed that the mortality (in %) of microcrustaceans was reduced from 100% (raw wastewater) to only 11% at the end of the electrolysis process, in addition to eliminating the strong odor and 85% of the organic load. Moreover, microbiological tests showed that the number of mesophiles decreased by more than six orders of magnitude and there was no growth of thermotolerant coliforms (TC).

Attenuating Sulfidogenesis in a Soured Continuous Flow Column System With Perchlorate Treatment

Hydrogen sulfide production by sulfate reducing bacteria (SRB) is the primary cause of oil reservoir souring. Amending environments with chlorate or perchlorate [collectively denoted (per)chlorate] represents an emerging technology to prevent the onset of souring. Recent studies with perchlorate reducing bacteria (PRB) monocultures demonstrated that they have the innate capability to enzymatically oxidize sulfide, thus PRB may offer an effective means of reversing souring. (Per)chlorate may be effective by (i) direct toxicity to SRB; (ii) competitive exclusion of SRB by PRB; or (iii) reversal of souring through re-oxidation of sulfide by PRB. To determine if (per)chlorate could sweeten a soured column system and assign a quantitative value to each of the mechanisms we treated columns flooded with San Francisco bay water with temporally decreasing amounts (50, 25, and 12.5 mM) of (per)chlorate. Geochemistry and the microbial community structure were monitored and a reactive transport model was developed, Results were compared to columns treated with nitrate or untreated. Souring was reversed by all treatments at 50 mM but nitrate-treated columns began to re-sour when treatment concentrations decreased (25 mM). Re-souring was only observed in (per)chlorate-treated columns when concentrations were decreased to 12.5 mM and the extent of re-souring was less than the control columns. Microbial community analyses indicated treatment-specific community shifts. Nitrate treatment resulted in a distinct community enriched in genera known to perform sulfur cycling metabolisms and genera capable of nitrate reduction. (Per)chlorate treatment enriched for (per)chlorate reducing bacteria. (Per)chlorate treatments only enriched for sulfate reducing organisms when treatment levels were decreased. A reactive transport model of perchlorate treatment was developed and a baseline case simulation demonstrated that the model provided a good fit to the effluent geochemical data. Subsequent simulations teased out the relative role that each of the three perchlorate inhibition mechanisms played during different phases of the experiment. These results indicate that perchlorate addition is an effective strategy for both souring prevention and souring reversal. It provides insight into which organisms are involved, and illuminates the interactive effects of the inhibition mechanisms, further highlighting the versatility of perchlorate as a sweetening agent.

Comprehensive Analysis of Changes in Crude Oil Chemical Composition during Biosouring and Treatments

Biosouring in crude oil reservoirs by sulfate-reducing microbial communities (SRCs) results in hydrogen sulfide production, precipitation of metal sulfide complexes, increased industrial costs of petroleum production, and exposure issues for personnel. Potential treatment strategies include nitrate or perchlorate injections into reservoirs. Gas chromatography with vacuum ultraviolet ionization and high-resolution time-of-flight mass spectrometry (GC-VUV-HTOF) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with electrospray ionization were applied in this study to identify hydrocarbon degradation patterns and product formations in crude oil samples from biosoured, nitrate-treated, and perchlorate-treated bioreactor column experiments. Crude oil hydrocarbons were selectively transformed based on molecular weight and compound class in the biosouring control environment. Both the nitrate and the perchlorate treatments significantly reduced sulfide production; however, the nitrate treatment enhanced crude oil biotransformation, while the perchlorate treatment inhibited crude oil biotransformation. Nitrogen- and oxygen-containing biodegradation products, particularly with chemical formulas consistent with monocarboxylic and dicarboxylic acids containing 10-60 carbon atoms, were observed in the oil samples from both the souring control and the nitrate-treated columns but were not observed in the oil samples from the perchlorate-treated column. These results demonstrate that hydrocarbon degradation and product formation of crude oil can span hydrocarbon isomers and molecular weights up to C₆₀ and double-bond equivalent classes ranging from straight-chain alkanes to polycyclic aromatic hydrocarbons. Our results also strongly suggest that perchlorate injections may provide a preferred strategy to treat biosouring through inhibition of biotransformation.

Isolation of nitrate-reducing bacteria from an offshore reservoir and the associated biosurfactant production

Biosurfactant producing nitrate-reducing bacteria (NRB) in anaerobic reservoir environments are closely associated with souring (H₂S) control in the offshore oil and gas industry. Five NRB strains were screened from offshore produced water samples and all were identified as Pseudomonas stutzeri. Their biosurfactant producing abilities when fed on either glucose or glycerol media were investigated. P. stutzeri CX3 reduced the medium surface tension to 33.5 and 29.6 mN m⁻¹, respectively, while growing on glucose or glycerol media. The CX3 strain was further inoculated to examine its growth performance, resulting in 32.4% and 94.5% of nitrate consumption over 228 hours of monitoring in two media, respectively. The composition analysis of the biosurfactant product generated by P. stutzeri CX3 was conducted through thin-layer chromatography, gas chromatography with a flame ionization detector (FID) and Fourier transform infrared spectroscopy (FT-IR). The biosurfactant product was identified as a mixture of a small part of lipopeptides and a large part of glycolipids while its critical micellar concentration (CMC) was as low as 35 mg L⁻¹. The biosurfactant product demonstrated high stability over a wide range of temperature (4–121 °C), pH (2–10), and salinity (0–20% w/v) concentration. The results provided valuable technical and methodological support for effective offshore reservoir souring control and associated enhanced oil recovery activities.

Biosurfactant producing nitrate-reducing bacteria (NRB) in anaerobic reservoir environments are closely associated with souring (H₂S) control in the offshore oil and gas industry.

Control of corrosive bacterial community by bronopol in industrial water system

ABSTRACT

Ten aerobic corrosive bacterial strains were isolated from a cooling tower water system (CWS) which were identified based on the biochemical characterization and 16S rRNA gene sequencing. Out of them, dominant corrosion-causing bacteria, namely, Bacillus thuringiensis EN2, Terribacillus aidingensis EN3, and Bacillus oleronius EN9, were selected for biocorrosion studies on mild steel 1010 (MS) in a CWS. The biocorrosion behaviour of EN2, EN3, and EN9 strains was studied using immersion test (weight loss method), electrochemical analysis, and surface analysis. To address the corrosion problems, an anti-corrosive study using a biocide, bronopol was also demonstrated. Scanning electron microscopy and Fourier-transform infrared spectroscopy analyses of the MS coupons with biofilm developed after exposure to CWS confirmed the accumulation of extracellular polymeric substances and revealed that biofilms was formed as microcolonies, which subsequently cause pitting corrosion. In contrast, the biocide system, no pitting type of corrosion, was observed and weight loss was reduced about 32 ± 2 mg over biotic system (286 ± 2 mg). FTIR results confirmed the adsorption of bronopol on the MS metal surface as protective layer (co-ordination of NH2-Fe3+) to prevent the biofilm formation and inhibit the corrosive chemical compounds and thus led to reduction of corrosion rate (10 ± 1 mm/year). Overall, the results from WL, EIS, SEM, XRD, and FTIR concluded that bronopol was identified as effective biocide and corrosion inhibitor which controls the both chemical and biocorrosion of MS in CWS.

GRAPHICAL ABSTRACT

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.

Microbial Community Structure and Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine Water

Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L⁻¹ sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance.

Effect of Thermophilic Nitrate Reduction on Sulfide Production in High Temperature Oil Reservoir Samples

Oil fields can experience souring, the reduction of sulfate to sulfide by sulfate-reducing microorganisms. At the Terra Nova oil field near Canada's east coast, with a reservoir temperature of 95°C, souring was indicated by increased hydrogen sulfide in produced waters (PW). Microbial community analysis by 16S rRNA gene sequencing showed the hyperthermophilic sulfate-reducing archaeon Archaeoglobus in Terra Nova PWs. Growth enrichments in sulfate-containing media at 55-70°C with lactate or volatile fatty acids yielded the thermophilic sulfate-reducing bacterium (SRB) Desulfotomaculum. Enrichments at 30-45°C in nitrate-containing media indicated the presence of mesophilic nitrate-reducing bacteria (NRB), which reduce nitrate without accumulation of nitrite, likely to N2. Thermophilic NRB (tNRB) of the genera Marinobacter and Geobacillus were detected and isolated at 30-50°C and 40-65°C, respectively, and only reduced nitrate to nitrite. Added nitrite strongly inhibited the isolated thermophilic SRB (tSRB) and tNRB and SRB could not be maintained in co-culture. Inhibition of tSRB by nitrate in batch and continuous cultures required inoculation with tNRB. The results suggest that nitrate injected into Terra Nova is reduced to N2 at temperatures up to 45°C but to nitrite only in zones from 45 to 65°C. Since the hotter zones of the reservoir (65-80°C) are inhabited by thermophilic and hyperthermophilic sulfate reducers, souring at these temperatures might be prevented by nitrite production if nitrate-reducing zones of the system could be maintained at 45-65°C.

The Effectiveness of Nitrate-Mediated Control of the Oil Field Sulfur Cycle Depends on the Toluene Content of the Oil

The injection of nitrate is one of the most commonly used technologies to impact the sulfur cycle in subsurface oil fields. Nitrate injection enhances the activity of nitrate-reducing bacteria, which produce nitrite inhibiting sulfate-reducing bacteria (SRB). Subsequent reduction of nitrate to di-nitrogen (N₂) alleviates the inhibition of SRB by nitrite. It has been shown for the Medicine Hat Glauconitic C (MHGC) field, that alkylbenzenes especially toluene are important electron donors for the reduction of nitrate to nitrite and N₂. However, the rate and extent of reduction of nitrate to nitrite and of nitrite to nitrogen have not been studied for multiple oil fields. Samples of light oil (PNG, CPM, and Tundra), light/heavy oil (Gryphon and Obigbo), and of heavy oil (MHGC) were collected from locations around the world. The maximum concentration of nitrate in the aqueous phase, which could be reduced in microcosms inoculated with MHGC produced water, increased with the toluene concentration in the oil phase. PNG, Gryphon, CPM, Obigbo, MHGC, and Tundra oils had 77, 17, 5.9, 4.0, 2.6, and 0.8 mM toluene, respectively. In incubations with 49 ml of aqueous phase and 1 ml of oil these were able to reduce 22.2, 12.3, 7.9, 4.6, 4.0, and 1.4 mM of nitrate, respectively. Nitrate reduced increased to 35 ± 4 mM upon amendment of all these oils with 570 mM toluene prior to incubation. Souring control by nitrate injection requires that the nitrate is directed toward oxidation of sulfide, not toluene. Hence, the success of nitrate injections will be inversely proportional to the toluene content of the oil. Oil composition is therefore an important determinant of the success of nitrate injection to control souring in a particular field.

Effects of electron acceptors on sulphate reduction activity in activated sludge processes

The concentration of sulphate present in wastewater can vary from 10 to 500 mg SO₄²⁻/L. During anaerobic conditions, sulphate is reduced to sulphide by sulphate-reducing bacteria (SRB). Sulphide generation is undesired in wastewater treatment plants (WWTPs). Previous research indicated that SRB are inhibited by the presence of electron acceptors (such as O₂, NO₃ and NO₂). However, the contact times and concentrations used in those studies are by far higher than occur in WWTPs. Since sulphide can influence the biological nitrogen and phosphorus removal processes, this research aimed to understand how the different electron acceptors commonly present in biological nutrient removal (BNR) systems can affect the proliferation of SRB. For this purpose, a culture of SRB was enriched in a sequencing batch reactor (approx. 88% of the total bacteria population). Once enriched, the SRB were exposed for 2 h to typical concentrations of electron acceptors like those observed in BNR systems. Their activity was assessed using three different types of electron donors (acetate, propionate and lactate). Oxygen was the most inhibiting electron acceptor regardless the carbon source used. After exposure to oxygen and when feeding acetate, an inactivation time in the sulphate reduction activity was observed for 1.75 h. Once the sulphate reduction activity resumed, only 60% of the original activity was recovered. It is suggested that the proliferation of SRB is most likely to occur in BNR plants with an anaerobic fraction higher than 15% and operating at sludge retention times higher than 20 days (at a temperature of 20 °C). These results can be used to implement strategies to control the growth of sulphate reducers that might compete for organic carbon with phosphate-accumulating organisms.

Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment

The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N₂, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.

Use of Acetate, Propionate, and Butyrate for Reduction of Nitrate and Sulfate and Methanogenesis in Microcosms and Bioreactors Simulating an Oil Reservoir

Acetate, propionate, and butyrate (volatile fatty acids [VFA]) occur in oil field waters and are frequently used for microbial growth of oil field consortia. We determined the kinetics of use of these VFA components (3 mM each) by an anaerobic oil field consortium in microcosms containing 2 mM sulfate and 0, 4, 6, 8, or 13 mM nitrate. Nitrate was reduced first, with a preference for acetate and propionate. Sulfate reduction then proceeded with propionate (but not butyrate) as the electron donor, whereas the fermentation of butyrate (but not propionate) was associated with methanogenesis. Microbial community analyses indicated that Paracoccus and Thauera (Paracoccus-Thauera), Desulfobulbus, and Syntrophomonas-Methanobacterium were the dominant taxa whose members catalyzed these three processes. Most-probable-number assays showed the presence of up to 10⁷/ml of propionate-oxidizing sulfate-reducing bacteria (SRB) in waters from the Medicine Hat Glauconitic C field. Bioreactors with the same concentrations of sulfate and VFA responded similarly to increasing concentrations of injected nitrate as observed in the microcosms: sulfide formation was prevented by adding approximately 80% of the nitrate dose needed to completely oxidize VFA to CO₂ in both. Thus, this work has demonstrated that simple time-dependent observations of the use of acetate, propionate, and butyrate for nitrate reduction, sulfate reduction, and methanogenesis in microcosms are a good proxy for these processes in bioreactors, monitoring of which is more complex.IMPORTANCE Oil field volatile fatty acids acetate, propionate, and butyrate were specifically used for nitrate reduction, sulfate reduction, and methanogenic fermentation. Time-dependent analyses of microcosms served as a good proxy for these processes in a bioreactor, mimicking a sulfide-producing (souring) oil reservoir: 80% of the nitrate dose required to oxidize volatile fatty acids to CO₂ was needed to prevent souring in both. Our data also suggest that propionate is a good substrate to enumerate oil field SRB.

Potential of wheat bran to promote indigenous microbial enhanced oil recovery

Microbial enhanced oil recovery (MEOR) is an emerging oil extraction technology that utilizes microorganisms to facilitate recovery of crude oil in depleted petroleum reservoirs. In the present study, effects of wheat bran utilization were investigated on stimulation of indigenous MEOR. Biostimulation conditions were optimized with the response surface methodology. The co-application of wheat bran with KNO₃ and NH₄H₂PO₄ significantly promoted indigenous MEOR (IMEOR) and exhibited sequential aerobic (O-), facultative (A_n-) and anaerobic (A₀-) metabolic stages. The surface tension of fermented broth decreased by approximately 35%, and the crude oil was highly emulsified. Microbial community structure varied largely among and in different IMEOR metabolic stages. Pseudomonas sp., Citrobacter sp., and uncultured Burkholderia sp. dominated the O-, A_n- and early A₀-stages. Bacillus sp., Achromobacter sp., Rhizobiales sp., Alcaligenes sp. and Clostridium sp. dominated the later A₀-stage. This study illustrated occurrences of microbial community succession driven by wheat bran stimulation and its industrial potential.

Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface

Members of the genus Thermodesulfovibrio belong to the Nitrospirae phylum and all isolates characterized to date are neutrophiles. They have been isolated from terrestrial hot springs and thermophilic methanogenic anaerobic sludges. Their molecular signatures have, however, also been detected in deep subsurface. The purpose of this study was to characterize and analyze the genome of a newly isolated, facultatively alkaliphilic Thermodesulfovibrio from a 2 km deep aquifer system in Western Siberia, Russia. The new isolate, designated N1, grows optimally at pH 8.5 and at 65°C. It is able to reduce sulfate, thiosulfate or sulfite with a limited range of electron donors, such as formate, pyruvate, and lactate. Analysis of the 1.93 Mb draft genome of strain N1 revealed that it contains a set of genes for dissimilatory sulfate reduction, including sulfate adenyltransferase, adenosine-5′-phosphosulfate reductase AprAB, membrane-bound electron transfer complex QmoABC, dissimilatory sulfite reductase DsrABC, and sulfite reductase-associated electron transfer complex DsrMKJOP. Hydrogen turnover is enabled by soluble cytoplasmic, membrane-linked, and soluble periplasmic hydrogenases. The use of thiosulfate as an electron acceptor is enabled by a membrane-linked molybdopterin oxidoreductase. The N1 requirement for organic carbon sources corresponds to the lack of the autotrophic C1-fixation pathways. Comparative analysis of the genomes of Thermodesulfovibrio (T. yellowstonii, T. islandicus, T. àggregans, T. thiophilus, and strain N1) revealed a low overall genetic diversity and several adaptive traits. Consistent with an alkaliphilic lifestyle, a multisubunit Na⁺/H⁺ antiporter of the Mnh family is encoded in the Thermodesulfovibrio strain N1 genome. Nitrogenase genes were found in T. yellowstonii, T. aggregans, and T. islandicus, nitrate reductase in T. islandicus, and cellulose synthetase in T. aggregans and strain N1. Overall, our results provide genomic insights into metabolism of the Thermodesulfovibrio lineage in microbial communities of the deep subsurface biosphere.

Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut

The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, ‘Candidatus Endomicrobium trichonymphae' and ‘Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of ‘Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of ‘Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of ‘Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, ‘Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, ‘Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and ‘Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut.

Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms

Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm^-3 h^-1) and oxygen consumption rates (0.01 μmol cm^-3 h^-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm^-3 h^-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm^-3 h^-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic relationship.

Characterization of a newly isolated strain Pseudomonas sp. C27 for sulfide oxidation: Reaction kinetics and stoichiometry

Sulfide biooxidation by the novel sulfide-oxidizing bacteria Pseudomonas sp. C27, which could perform autotrophic and heterotrophic denitrification in mixotrophic medium, was studied in batch and continuous systems. Pseudomonas sp. C27 was able to oxidize sulfide at concentrations as high as 17.66 mM. Sulfide biooxidation occurred in two distinct stages, one resulting in the formation of sulfur with nitrate reduction to nitrite, followed by thiosulfate formation with nitrite reduction to N₂. The composition of end-products was greatly impacted by the ratio of sulfide to nitrate initial concentrations. At a ratio of 0.23, thiosulfate represented 100% of the reaction products, while only 30% with a ratio of 1.17. In the continuous bioreactor, complete removal of sulfide was observed at sulfide concentration as high as 9.38 mM. Overall sulfide removal efficiency decreased continuously upon further increases in influent sulfide concentrations. Based on the experimental data kinetic parameter values were determined. The value of maximum specific growth rate, half saturation constant, decay coefficient, maintenance coefficient and yield were to be 0.11 h⁻¹, 0.68 mM sulfide, 0.11 h⁻¹, 0.21 mg sulfide/mg biomass h and 0.43 mg biomass/mg sulfide, respectively, which were close to or comparable with those reported in literature by other researches.

Control of Microbial Sulfide Production with Biocides and Nitrate in Oil Reservoir Simulating Bioreactors

Oil reservoir souring by the microbial reduction of sulfate to sulfide is unwanted, because it enhances corrosion of metal infrastructure used for oil production and processing. Reservoir souring can be prevented or remediated by the injection of nitrate or biocides, although injection of biocides into reservoirs is not commonly done. Whether combined application of these agents may give synergistic reservoir souring control is unknown. In order to address this we have used up-flow sand-packed bioreactors injected with 2 mM sulfate and volatile fatty acids (VFA, 3 mM each of acetate, propionate and butyrate) at a flow rate of 3 or 6 pore volumes (PV) per day. Pulsed injection of the biocides glutaraldehyde (Glut), benzalkonium chloride (BAC) and cocodiamine was used to control souring. Souring control was determined as the recovery time (RT) needed to re-establish an aqueous sulfide concentration of 0.8–1 mM (of the 1.7–2 mM before the pulse). Pulses were either for a long time (120 h) at low concentration (long-low) or for a short time (1 h) at high concentration (short-high). The short-high strategy gave better souring control with Glut, whereas the long-low strategy was better with cocodiamine. Continuous injection of 2 mM nitrate alone was not effective, because 3 mM VFA can fully reduce both 2 mM nitrate to nitrite and N₂ and, subsequently, 2 mM sulfate to sulfide. No synergy was observed for short-high pulsed biocides and continuously injected nitrate. However, use of continuous nitrate and long-low pulsed biocide gave synergistic souring control with BAC and Glut, as indicated by increased RTs in the presence, as compared to the absence of nitrate. Increased production of nitrite, which increases the effectiveness of souring control by biocides, is the most likely cause for this synergy.

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp.

IMPORTANCE

The NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB.