Diversity of culturable sulfidogenic bacteria in two oil–water separation tanks in the north-eastern oil fields of India

Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem

Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.

Snorkels enhance alkanes respiration at ambient and increased hydrostatic pressure (10 MPa) by either supporting the TCA cycle or limiting alternative routes for acetyl-CoA metabolism

The impact of piezosensitive microorganisms is generally underestimated in the ecology of underwater environments exposed to increasing hydrostatic pressure (HP), including the biodegradation of crude oil components. Yet, no isolated pressure-loving (piezophile) microorganism grows optimally on hydrocarbons, and no isolated piezophile at all has a HP optimum <10 MPa (e.g. 1000 m below sea water level). Piezosensitive heterotrophs are thus largely accountable for oil clean up < 10 MPa, however, they are affected by such a mild HP increase in ways which are not completely clear. In a first study, the application of a bioelectrochemical system (called "oil-spill snorkel") enhanced the alkane oxidation capacity in sediments collected at surface water but tested up to 10 MPa. Here, the fingerprint left on transcript abundance was studied to explore which metabolic routes are 1) supported by snorkels application and 2) negatively impacted by HP increase. Transcript abundance was comparable for beta-oxidation across all treatments (also at a taxonomical level), while the metabolism of acetyl-CoA was highly impacted: at either 0.1 or 10 MPa, snorkels supported acetyl-CoA oxidation within the TCA cycle, while in negative controls using non-conductive rods several alternative routes for acetyl-CoA were stimulated (including those leading to internal carbon reserves e.g. 2,3 butanediol and dihydroxyacetone). In general, increased HP had opposite effects as compared to snorkels, thus indicating that snorkels could enhance hydrocarbons oxidation by alleviating in part the stressing effects imposed by increased HP on the anaerobic, respiratory electron transport chain. 16S rRNA gene analysis of sediments and biofilms on snorkels suggest a crosstalk between oil-degrading, sulfate-reducing microorganisms and sulfur oxidizers. In fact, no sulfur was deposited on snorkels, however, iron, aluminum and phosphorous were found to preferentially deposit on snorkels at 10 MPa. This data indicates that a passive BES such as the oil-spill snorkel can mitigate the stress imposed by increased HP on piezosensitive microorganisms (up to 10 MPa) without being subjected to passivation. An improved setup applying these principles can further support this deep-sea bioremediation strategy.

Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting

Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.

Partition of nanoswimmers between two immiscible phases: a soft and penetrable boundary

The behavior of run-and-tumble nanoswimmers which can self-propel in two immiscible liquids such as water-oil systems and are able to cross the interface is investigated by dissipative particle dynamics. At the steady-state, the partition ratio (φ) of nanoswimmers between the two immiscible liquids is obtained, and it depends on the active force (F_a), run time (τ), and swimmer-solvent interactions. The partition ratio φ is found to grow generally with increasing F_a²τ. At sufficiently large F_a, it is surprising to find that hydrophilic nanoswimmers prefer to stay in the oil phase rather than in the water phase. The partition ratio is also influenced by the hydrophobicity of swimmers in the oil phase. Two simple models are proposed to describe the partition ratio, including a near-equilibrium model and a kinetic model. Surface accumulation appearing at an impenetrable interface is also observed at the fluid-fluid interface for small F_a but it vanishes for sufficiently large F_a.

Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale

Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013; Daly et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with ¹³C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and ¹⁵N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of ¹³C and ¹⁵N incorporation in individual cells, while isotope ratio monitoring–gas chromatography–mass spectrometry (IRM–GC–MS) was used to measure ¹³CO₂, and ¹³CH₄ as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. ¹³CO₂ production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia. The primary genera detected in the incubations, Halanaerobium and Fusibacter, are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.

Effect of inorganic nutrients on bacterial community composition in oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery

Microbial Enhanced Oil Recovery (MEOR) is a promising strategy to improve recovery of residual oil in reservoirs, which can be performed by promoting specific indigenous microorganisms. In this study, we performed preliminary evaluation of the possibility of conducting MEOR at Mae Soon reservoir, an onshore reservoir in Northern Thailand. The reservoir’s physicochemical characteristics, including the characteristics of the wells, the oil-bearing sandstone cores, and the reservoir’s produced water, were determined. The microbiological characteristics of the oil wells in the reservoir were also investigated by submerging the reservoir’s sandstone core samples, obtained from 6 oil wells, in the reservoir’s produced water and in the produced water added with inorganic nutrients (KNO₃ and NaH₂PO₄). The uncultured bacteria in both treatments were determined, using tagged 16S rRNA gene amplicon with Ion Torrent Sequencing Analysis. The effects of inorganic nutrients and the reservoir’s parameters on the bacterial communities were analysed. A total number of 16,828 OTUs were taxonomically classified into 89 classes and 584 genera. In the controls (sandstone cores submerged in the produced water), the dominant bacterial populations were related to Deinococcus-Thermus, and Betaproteobacteria; while in the nutrient treated samples, there was a marked increase in the relative abundance of Gammaproteobacteria in three samples. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera, and these are potential microorganisms for MEOR. Analysis of correlations between physiochemical properties of the reservoir and bacterial genera, using spearman’s correlation analysis, suggested that some of the reservoir’s properties, especially of the well and the rock, could influence some bacterial genera. To our knowledge, this is the first demonstration of the effect of inorganic nutrients on alteration of bacterial communities attached to reservoir’s rock, and how the bacterial, physical, and chemical properties of a reservoir were co-analysed to serve as a basis for designing a MEOR process.

Schwertmannite transformation via direct or indirect electron transfer by a sulfate reducing enrichment culture

Understanding the mechanism of the microbial transformation of Fe(III)-oxyhydroxysulfate minerals is of considerable interest, because this transformation plays an important role in controlling the behaviour of toxic metals from acid mine drainage (AMD). In this study, we examined a sulfate reducing enrichment culture from AMD-contaminated sediments and predicted the possible pathway of electron transfer when incubated with schwertmannite, a common Fe(III)-oxyhydroxysulfate occurring in the AMD environment. Experiments were designed to distinguish the mechanisms by which bacteria facilitate direct (i.e., bacteria allowed to adhere to the mineral) or indirect (i.e., bacteria separated from the mineral by dialysis bag) electron transfer to reduce the mineral. The effects of adding anthraquinone-2,6-disulfonate (AQDS) as an exogenous electron shuttle were also investigated. Vivianite was detected as the main product of schwertmannite transformation. Reduction of sulfate and iron were more pronounced in direct treatments, while more non-reductive dissolution were observed in indirect treatments. The addition of AQDS lead to the production of more dissolved Fe²⁺ over 20 d than in the absence of AQDS. Microbial community composition differed in direct and indirect treatments, while the addition of AQDS did not significantly affect the community structure in each treatment. After incubation for 20 d, the growth of Desulfovibrio exceeded that of the originally dominant Citrobacter in direct treatments, while an unknown genus most closely related to Citrobacter within Enterobacteriaceae was predominant in indirect treatments. This monodominant community in indirect treatments was assumed not to transfer electron directly to schwertmannite but to rely on shuttling mechanism. PICRUSt results implied that bacteria in indirect treatment have potential to produce shuttling compounds or complexing agents. The absence of dsr genes and the putative fermentative process suggested that the Enterobacteriaceae might indirectly facilitate the dissolution and transformation of schwertmannite.

Identification of the traditional and non-traditional sulfate-reducing bacteria associated with corroded ship hull

Pitting corrosion due to microbial activity is the most severe type of corrosion that occurs in ship hull. Since biogenic sulfide produced by sulfate-reducing bacteria (SRB) is involved in the acceleration of pitting corrosion of marine vessels, so it is important to collect information about SRB community involved in maritime vessel failure. We investigated the SRB community on corroded hull portion of the ship. With the use of common cultural method and 16S rDNA sequencing, ten bacteria with sulfate reduction ability were isolated and identified. They belonged to both traditional (Desulfovibrio, Desulfotomaculum) and non-traditional (Citrobacter) sulfate-reducing bacteria. All the isolates were able to produce a high amount of sulfide. However, only traditional isolates were showing the amplification for the SRB-specific gene, dsrAB. Further studies on corrosion potential of these two groups of bacteria showed that in spite of high sulfide and biofilm production by non-traditional SRB, they are less aggressive towards the mild steel compare to the traditional group.

Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management

Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80-90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures.

Enrichment and optimization of anaerobic bacterial mixed culture for conversion of syngas to ethanol

The main aim of the present study was to enrich anaerobic mixed bacterial culture capable of producing ethanol from synthesis gas fermentation. Screening of thirteen anaerobic strains together with enrichment protocol helped to develop an efficient mixed culture capable of utilizing syngas for ethanol production. Physiological and operational parameters were optimized for enhanced ethanol production. The optimized value of operational parameters i.e. initial media pH, incubation temperature, initial syngas pressure, and agitation speed were 6.0±0.1, 37°C, 2kgcm(-2) and 100rpm respectively. Under these conditions ethanol and acetic acid production by the selected mixed culture were 1.54gL(-1) and 0.8gL(-1) respectively. Furthermore, up-scaling studies in semi-continuous fermentation mode further enhanced ethanol and acetic acid production up to 2.2gL(-1) and 0.9gL(-1) respectively. Mixed culture TERI SA1 was efficient for ethanol production by syngas fermentation.

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines

Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.

Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments

Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review.

Corrosion of carbon steel by bacteria from North Sea offshore seawater injection systems: laboratory investigation

Influence of sulfidogenic bacteria, from a North Sea seawater injection system, on the corrosion of S235JR carbon steel was studied in a flow bioreactor; operating anaerobically for 100days with either inoculated or filtrated seawater. Deposits formed on steel placed in reactors contained magnesium and calcium minerals plus iron sulfide. The dominant biofilm-forming organism was an anaerobic bacterium, genus Caminicella, known to produce hydrogen sulfide and carbon dioxide. Open Circuit Potentials (OCP) of steel in the reactors was, for nearly the entire test duration, in the range -800<E(OCP)/mV (vs. SCE)<-700. Generally, the overall corrosion rate, expressed as 1/(Rp/Ω), was lower in the inoculated seawater though they varied significantly on both reactors. Initial and final corrosion rates were virtually identical, namely initial 1/(Rp/Ω)=2×10(-6)±5×10(-7) and final 1/(Rp/Ω)=1.1×10(-5)±2.5×10(-6). Measured data, including electrochemical noise transients and statistical parameters (0.05<Localized Index<1; -5<Skewness<-5; Kurtosis>45), suggested pitting on steel samples within the inoculated environment. However, the actual degree of corrosion could neither be directly correlated with the electrochemical data and nor with the steel corrosion in the filtrated seawater environment. Further laboratory tests are thought to clarify the noticed apparent discrepancies.

Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments

BACKGROUND

The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30' N, 64°40' W), B (10°40' N, 64°45' W) and D (10°43'N, 64°32'W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands.

RESULTS

DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability.

CONCLUSIONS

In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.

Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale

The Barnett Shale in north central Texas contains natural gas generated by high temperatures (120 to 150°C) during the Mississippian Period (300 to 350 million years ago). In spite of the thermogenic origin of this gas, biogenic sulfide production and microbiologically induced corrosion have been observed at several natural gas wells in this formation. It was hypothesized that microorganisms in drilling muds were responsible for these deleterious effects. Here we collected drilling water and drilling mud samples from seven wells in the Barnett Shale during the drilling process. Using quantitative real-time PCR and microbial enumerations, we show that the addition of mud components to drilling water increased total bacterial numbers, as well as the numbers of culturable aerobic heterotrophs, acid producers, and sulfate reducers. The addition of sterile drilling muds to microcosms that contained drilling water stimulated sulfide production. Pyrosequencing-based phylogenetic surveys of the microbial communities in drilling waters and drilling muds showed a marked transition from typical freshwater communities to less diverse communities dominated by Firmicutes and Gammaproteobacteria. The community shifts observed reflected changes in temperature, pH, oxygen availability, and concentrations of sulfate, sulfonate, and carbon additives associated with the mud formulation process. Finally, several of the phylotypes observed in drilling muds belonged to lineages that were thought to be indigenous to marine and terrestrial fossil fuel formations. Our results suggest a possible alternative exogenous origin of such phylotypes via enrichment and introduction to oil and natural gas reservoirs during the drilling process.

Efficacy of natural biocide on control of microbial induced corrosion in oil pipelines mediated by Desulfovibrio vulgaris and Desulfovibrio gigas

We compared the efficacy of a natural biocide with four chemical tetrakishydroxymethyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, and formaldehyde, glutaraldehyde, to control microbial induced corrosion in oil pipelines. The efficacy of biocides were monitored against Desulfovibrio vulgaris and Desulfovibrio gigas in experimental pipes by measuring cell counts, H2S production, Fe(II) production, production of extracellular polymeric substances and structure of biofilm. The treatment with cow urine had minimum planktonic cell counts of 3 x 10(2) CFU/mL as well as biofilm cell counts of 9 x 10(1) CFU/mL as compared with tetrakishydroxyl methyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, formaldehyde and glutaraldehyde. Sulfide production was the lowest with cow urine (0.08 mmol/L), followed by tetrakishydroxymethyl phosphonium sulfonate 0.72 mmol/L. On day 90 of treatment, Fe(II) production was also found to be the lowest with cow urine. The scanning electron microscopic studies indicated that the biofilm bacteria were killed by cow urine. These results demonstrate the cow urine mediated control of microbially induced corrosion, and this is indicative of its potential as a viable substitute of toxic biocides. To the best of our knowledge, this seems to be the first report which screens possible biocidal activity by cow urine as compared to the most common biocides which oil industry is currently using.