Oil reservoirs, an exceptional habitat for microorganisms

The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities

Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.

Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

Synergistic inhibitory effects of free nitrous acid and imidazoline derivative on metal corrosion in a simulated water injection system

To maintain the integrity of the internal surfaces of the pipelines in oil and gas industry, chemicals, including corrosion inhibitors and biocides, are commonly dosed to prevent corrosion. Imidazoline and its derivatives are widely used corrosion inhibitors for the protection of oil pipelines, which have been shown effective in reducing general corrosion. As an effective biocide, free nitrous acid (FNA) is suitable to inhibit microbially influenced corrosion, induced by for example sulfate-reducing bacteria. In this paper, we hypothesize that the continuous addition of imidazoline and intermittent dosing of FNA, when used in combination, would yield effective control of both general and pitting corrosions. As a typical imidazoline derivative, N-b-hydroxyethyl oleyl imidazoline (HEI-17) was applied in conjunction with intermittent dosing of FNA in the experimental system, with the results compared with two control systems, one receiving HEI-17 only, and one receiving no chemical dosing. The corrosion properties were monitored with open circuit potential, electrochemical impedance spectroscopy, linear polarization resistance, 3D optical profiling, and weight-loss measurement. Following a single dose of FNA, the general corrosion rates in the experimental reactor dropped up to 50% of that in the reactor receiving continuous HEI-17 dosing (0.27 ± 0.04 vs. 0.54 ± 0.08 mm/y), but gradually recovered to 93.4% of that in 2.5 months. After the FNA treatment, the pitting corrosion was decreased by 64.6% compared with continuous HEI-17 dosing reactor for a month from measuring the cumulative distribution of the pitting depth. HEI-17 treatment alone showed moderate pitting corrosion inhibition effect (approx. 27%), and the FNA treatment inhibited the formation of deep pits effectively. The combined application of HEI-17 and FNA has shown synergistic effects and high efficiency in mitigating MIC in the simulated water injection system. This treatment strategy has strong potential to be applied in the practical oilfield operations.

Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt

Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interactions among them. In this study, we investigated how SRMs compete with the established methanogenic communities in sediment from a long-term, electron acceptor-depleted, asphalt-exposed ecosystem and how they affect the composition of the organic material. We hypothesized that, upon addition of sulfate, SRMs (i) outcompete the methanogenic communities and (ii) markedly contribute to transformations of the organic material. We sampled sediments from the test and proximate control sites under anoxic conditions and incubated them in seawater medium with or without sulfate. Abundance and activity pattern of SRMs and methanogens, as well as the total prokaryotic community, were followed for 6 weeks by using qPCR targeting selected marker genes. Some of these genes were also subjected to amplicon sequencing to assess potential shifts in diversity patterns. Alterations of the organic material in the microcosms were determined by mass spectrometry. Our results indicate that the competition of SRMs with methanogens upon sulfate addition strongly depends on the environment studied and the starting microbiome composition. In the asphalt-free sediments (control), the availability of easily degradable organic material (mainly plant-derived) allows SRMs to use a larger variety of substrates, reducing interspecies competition with methanogens. In contrast, the abundant presence of recalcitrant compounds in the asphalt-exposed sediment was associated with a strong competition between SRMs and methanogens, ultimately detrimental for the latter. Our data underpin the importance of the quality of bioavailable organic materials in anoxic environments as a driver for microbial community structure and function.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico

Oil reservoirs contain microbial populations that are both autochthonously and allochthonously introduced by industrial development. These microbial populations are greatly influenced by external factors including, but not limited to, salinity and temperature. In this study, we used metagenomics to examine the microbial populations within five wells of the same hydrocarbon reservoir system in the Gulf of Mexico. These elevated salinity (149–181 ppt salinity, 4–5× salinity of seawater) reservoirs have limited taxonomic and functional microbial diversity dominated by methanogens, Halanaerobium and other Firmicutes lineages, and contained less abundant lineages such as Deltaproteobacteria. Metagenome assembled genomes (MAGs) were generated and analyzed from the various wells. Methanogen MAGs were closely related to Methanohalophilus euhalobius, a known methylotrophic methanogen from a high salinity oil environment. Based on metabolic reconstruction of genomes, the Halanaerobium perform glycine betaine fermentation, potentially produced by the methanogens. Industrial introduction of methanol to prevent methane hydrate formation to this environment is likely to be consumed by these methanogens. As such, this subsurface oil population may represent influences from industrial processes.

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.

Densely Populated Water Droplets in Heavy-Oil Seeps

Most of the microbial degradation in oil reservoirs is believed to take place at the oil-water transition zone (OWTZ). However, a recent study indicates that there is microbial life enclosed in microliter-sized water droplets dispersed in heavy oil of Pitch Lake in Trinidad and Tobago. This life in oil suggests that microbial degradation of oil also takes place in water pockets in the oil-bearing rock of an oil leg independent of the OWTZ. However, it is unknown whether microbial life in water droplets dispersed in oil is a generic property of oil reservoirs rather than an exotic exception. Hence, we took samples from three heavy-oil seeps, Pitch Lake (Trinidad and Tobago), the La Brea Tar Pits (California, USA), and an oil seep on the McKittrick oil field (California, USA). All three tested oil seeps contained dispersed water droplets. Larger droplets between 1 and 10 μl revealed high cell densities of up to 10⁹ cells ml^-1 Testing for ATP content and LIVE/DEAD staining showed that these populations consist of active and viable microbial cells with an average of 60% membrane-intact cells and ATP concentrations comparable to those of other subsurface ecosystems. Microbial community analyses based on 16S rRNA gene amplicon sequencing revealed the presence of known anaerobic oil-degrading microorganisms. Surprisingly, the community analyses showed similarities between all three oil seeps, revealing common OTUs, although the sampling sites were thousands of kilometers apart. Our results indicate that small water inclusions are densely populated microhabitats in heavy oil and possibly a generic trait of degraded-oil reservoirs.IMPORTANCE Our results confirmed that small water droplets in oil are densely populated microhabitats containing active microbial communities. Since these microhabitats occurred in three tested oil seeps which are located thousands of kilometers away from each other, such populated water droplets might be a generic trait of biodegraded oil reservoirs and might be involved in the overall oil degradation process. Microbial degradation might thus also take place in water pockets in the oil-bearing oil legs of the reservoir rock rather than only at the oil-water transition zone.

Novel clostridial lineages recovered from metagenomes of a hot oil reservoir

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name ^UPetromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that ^UPetromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.

Decreasing microbially influenced metal corrosion using free nitrous acid in a simulated water injection system

Microbially influenced corrosion (MIC) is the main cause of metal corrosion in anoxic environments. Biocides are often dosed to the corrosive media to inhibit and kill the microbes which cause MIC. In this study, intermittent dosages of free nitrous acid (FNA), which was previously found to be a biocide, were applied to a simulated water injection system containing carbon steel coupons with mature biofilm, to study the effect of FNA on mitigation of metal corrosion. In each treatment, 0.49 mg-N/L FNA was dosed using 200 mg-N/L nitrite at pH 6 for 24 h. The corrosion properties were monitored by open circuit potential (OCP), electrochemical impedance spectroscopy (EIS), linear polarization resistance (LPR), 3D optical profiling, and direct weight measurement. The biofilm viability was monitored by measuring cellular ATP level. The general corrosion rate (calculated by weight-loss measurement) was decreased by up to 31%, which was supported by LPR tests and reduced ATP levels of the corrosion-inducing biofilm. The 3D optical profiling results showed that FNA decreased the average pitting corrosion rate by 59%, with 2 intermittent treatments and 82-day interval over 304 days. Intermittent dosing of FNA has strong potential to be an effective and efficient strategy for controlling MIC in oil recovery infrastructure.

Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA

We report on the characterization of a novel genomic assembly (ARYD3) recovered from formation water (17.6% salinity) and crude oil enrichment amended by isolated soy proteins (0.2%), and incubated for 100 days under anaerobic conditions at 50°C. Phylogenetic and phylogenomic analysis demonstrated that the ARYD3 is unaffiliated with all currently described bacterial phyla and candidate phyla, as evident by the low AAI (34.7%), shared gene content (19.4%), and 78.9% 16S rRNA gene sequence similarity to Halothiobacillus neapolitanus, its closest cultured relative. Genomic characterization predicts a slow-growing, non-spore forming, and non-motile Gram-negative rod. Adaptation to high salinity is potentially mediated by the production of the compatible solutes cyclic 2,3-diphosphoglycerate (cDPG), α-glucosylglycerate, as well as the uptake of glycine betaine. Metabolically, the genome encodes primarily aminolytic capabilities for a wide range of amino acids and peptides. Interestingly, evidence of propionate degradation to succinate via methyl-malonyl CoA was identified, suggesting possible capability for syntrophic propionate degradation. Analysis of ARYD3 global distribution patterns identified its occurrence in a very small fraction of Earth Microbiome Project datasets examined (318/27,068), where it consistently represented an extremely rare fraction (maximum 0.28%, average 0.004%) of the overall community. We propose the Candidatus name Mcinerneyibacterium aminivorans gen. nov, sp. nov. for ARYD3^T, with the genome serving as the type material for the novel family Mcinerneyibacteriaceae fam. nov., order Mcinerneyibacteriales ord. nov., class Mcinerneyibacteria class nov., and phylum Mcinerneyibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number VSIX00000000.

Complementary DNA/RNA-Based Profiling: Characterization of Corrosive Microbial Communities and Their Functional Profiles in an Oil Production Facility

DNA and RNA-based sequencing of the 16S rRNA gene and transcripts were used to assess the phylogenetic diversity of microbial communities at assets experiencing corrosion in an oil production facility. The complementary methodological approach, coupled with extensive bioinformatics analysis, allowed to visualize differences between the total and potentially active communities present in several locations of the production facility. According to the results, taxa indicative for thermophiles and oil-degrading microorganisms decreased their relative abundances in the active communities, whereas sulfate reducing bacteria and methanogens had the opposite pattern. The differences in the diversity profile between total and active communities had an effect on the microbial functional capability predicted from the 16S rRNA sequences. Primarily, genes involved in methane metabolism were enriched in the RNA-based sequencing approach. Comparative analysis of microbial communities in the produced water, injection water and deposits in the pipelines showed that deposits host more individual species than other sample sources in the facility. Similarities in the number of cells and microbial profiles of active communities in biocide treated and untreated sampling locations suggested that the treatment was ineffective at controlling the growth of microbial populations with a known corrosive metabolism. Differences in the results between DNA and RNA-based profiling demonstrated that DNA results alone can lead to the underestimation of active members in the community, highlighting the importance of using a complementary approach to obtain a broad general overview not only of total and active members but also in the predicted functionality.

Low-Abundance Dietzia Inhabiting a Water-Flooding Oil Reservoir and the Application Potential for Oil Recovery

With the development of molecular ecology, increasing low-abundance microbial populations were detected in oil reservoirs. However, our knowledge about the oil recovery potential of these populations is lacking. In this study, the oil recovery potential of low-abundance Dietzia that accounts for less than 0.5% in microbial communities of a water-flooding oil reservoir was investigated. On the one hand, Dietzia sp. strain ZQ-4 was isolated from the water-flooding reservoir, and the oil recovery potential was evaluated from the perspective of metabolisms and oil-displacing test. On the other hand, the strain has alkane hydroxylase genes alkB and P450 CYP153 and can degrade hydrocarbons and produce surfactants. The core-flooding test indicated that displacing fluid with 2% ZQ-4 fermentation broth increased 18.82% oil displacement efficiency, and in situ fermentation of ZQ-4 increased 1.97% oil displacement efficiency. Furthermore, the responses of Dietzia in the reservoir accompanied by the nutrient stimulation process was investigated and showed that Dietzia in some oil production wells significantly increased in the initial phase of nutrient injection and sharply decreased along with the continuous nutrient injection. Overall, this study indicates that Dietzia sp. strain has application potential for enhancing oil recovery through an ex situ way, yet the ability of oil recovery in situ based on nutrient injection is limited.

Stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery

Low permeability oil reservoirs are a widespread petroleum reservoir type all over the world. Therefore, methods to recover these reservoirs efficiently are of importance to guarantee energy supply. Here we report our novel stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery. We aimed to investigate the characteristics of indigenous bacterial communities with changes in water cut in reservoirs by high-throughput sequencing technology, and reveal the mechanism and characteristics of the crude oil biotreatment under different crude oil-water ratio conditions and the optimum activation time of indigenous functional microbial groups in reservoirs. The indigenous microbial metabolism products were characterized by gas chromatography mass spectrometry. Results showed that Acinetobacter (47.1%) and Pseudomones (19.8%) were the main functional genus of crude oil degradation at the optimal activation time, and can reduce the viscosity of crude oil from 8.33 to 5.75 mPa·s. The dominant bacteria genus for oil recovery after activation of the production fluids was similar to those in the reservoirs with water cut of 60-80%. Furthermore seven mechanism pathways of enhancing oil recovery by the synergistic of functional microbial groups and their metabolites under different water cut conditions in low permeability reservoirs have been established.

Composition of Bacterial and Archaeal Communities in an Alkali-Surfactant-Polyacrylamide-Flooded Oil Reservoir and the Responses of Microcosms to Nutrients

The microbial communities in alkali-surfactant-polyacrylamide-flooded (ASP-flooded) oil reservoirs have rarely been investigated compared to those in water-flooded oil reservoirs. Here, the bacterial and archaeal communities in an ASP-flooded reservoir and the adjacent water-flooded block, and responses of the microbial communities in microcosms to nutrients were investigated by 16S rRNA gene sequencing and cultivation. Compared with the water-flooded block, both the bacterial and archaeal communities inhabiting the ASP-flooded block had lower Sobs indices (91:232 and 34:55, respectively), lower Shannon indices (1.296:2.256 and 0.845:1.627, respectively) and higher Simpson indices (0.391:0.248 and 0.678:0.315, respectively). Halomonas (58.4-82.1%) and Anoxynatronum (14.5-18.2%) predominated in the ASP-flooded production wells, and were less than 0.05% in the bacterial communities of the adjacent water-flooded production wells, which were dominated by Pseudomonas and Thauera. Methanobacterium accounted for 65.0-94.5% of the archaeal communities inhabiting the ASP-flooded production wells, and Methanosaeta (36.7-94.5%) dominated the adjacent water-flooded production wells. After nutrients stimulation, the quantity of cultivable microorganisms increased from 103/mL to 107/mL. Community analysis indicated that the relative abundances of some species that belonged to Halomonas and Pseudomonas obviously increased, yet there were no oil emulsification or dispersion and changes of surface tension of the water-oil mixture. In addition, 6 alkali-tolerating strains showing 98% similarity of 16S rRNA genes with those of Halomonas alkalicola and Halomonas desiderata and 2 strains with 99% similarity with Pseudomonas stutzeri gene were isolated from the nutrients stimulated brines. In summary, this study indicated that Halomonas, Anoxynatronum, and Methanobacterium were dominant populations in the ASP-flooded reservoir, the extreme environment decreased microbial diversity, and restricted microbial growth and metabolisms.