Efficient production of heavy oil from the reservoirs with strong bottom aquifer has proven to be a challenge. While providing enough energy to produce the field under the primary depletion, the strong bottom aquifer in combination with unfavorable oil/water mobility contrast leads to rapid development of water coning thereby limiting oil recovery. Drilling of long horizontal producing wells in the upper part of the oil column maximizes the distance from the aquifer and allows relatively high production rates. This slows down the water cone development and increases primary recovery. Even with further optimization of the primary production, the recovery factor remains relatively low and consequently application of Enhanced Oil Recovery (EOR) techniques is required to increase the recovery. Сrude oil from Nimr-E field is medium-heavy with the viscosity of 250-700cP under reservoir conditions. The field has been developed with mostly horizontal producing wells with relatively short inter-well distance. Due to strong bottom aquifer the reservoir pressure is maintained at the initial level despite the production under primary depletion. To increase the recovery factor polymer flooding was selected with expectation to increase the recovery by 5-10%. A field trial was conducted to understand the influence of polymer injection on oil recovery and address major uncertainties identified as key enablers for the full-field project. The pilot surveillance program, the surface facilities and the subsurface configurations were specifically designed to meet these objectives. The paper presents field data of polymer injection trial in Nimr field and focuses on the performance results and principal operational challenges. The injection of polymer resulted in the incremental oil production that was assessed using field data and simulations. A significant increase of initial oil production and clear watercut reversal due to polymer injection was observed and incremental recovery reached approximately 7% of the initial oil in place. Injectivity issues encountered in the pilot wells were mitigated by the techniques and chemicals developed to solve the issues. The results prove the subsurface and operational success of polymer field trial that leads the way to a commercial development.

The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others. Moreover, MetaHCR implements the Minimum Information about any Sequence-hydrocarbon resource specification from the Genomic Standards Consortium; it integrates a user-friendly web interface and relational database model, and it enables the generation of complex custom search. MetaHCR has been tested with 36 publicly available metagenomic studies, and its modular architecture can be easily customized for other types of environmental and metagenomics studies.

Three hydrocarbon reservoir cores were obtained from a high temperature non-waterflooded offshore reservoir. All three cores were taken from a 56-m section of the same well. Under sterile conditions, DNA was recovered from the inner section of each core and the microbial community profiles were deduced by sequencing the 16S rRNA marker gene. Taxonomic analysis of the Operational Taxonomic Units (OTUs) recovered, identified a high proportion of members from the Oxalobacteraceae family (38.5%) followed by members from the Pseudomonadaceae and Comamonadaceae families (29.1% and 12.8% respectively). Representatives of all these families are known to degrade hydrocarbons as well as to use nitrate as a terminal electron acceptor under anaerobic conditions. Assuming these predominant microorganisms are indigenous to the reservoir and have not been introduced with the drilling fluids they might exhibit a relatively rapid response to nitrate injection for souring control. On the contrary, very few sulfate reducing bacteria (SRBs) were detected in these cores (<0.01%) suggesting unfavorable conditions to SRB growth. This however may well rapidly change upon seawater injections in the absence of nitrate addition.This study sets the microbial profiling “baseline” for the prediction of souring through modelling as well as for any upcoming biomonitoring surveys.

Abstract MY01 is an offshore field located in Malaysia. Although souring mitigation by nitrate injection was applied from the start of the seawater flood, hydrogen sulphide (H2S) has been detected in several producers after injected seawater breakthrough. The objectives of this work are to understand the causes of reservoir souring in MY01 and to provide key considerations for improving souring prediction in low temperature reservoirs, as generalised from the learnings from this field. Reservoir souring potential was assessed using a Joint Industrial Project (JIP) developed program (SourSimRL). SourSimRL is a reservoir model post-processor which simulates the microbial generation, scavenging, adsorption and transport processes of H2S in fields subjected to waterflood, based on fluid dynamics, reservoir conditions and water chemistries as dictated by the reservoir model. The MY01 reservoir model was split into two parts: (i) a history matched model that allows calibration on reservoir souring simulator input parameters; and (ii) a forecast model on which souring development is predicted. Extensive sensitivity studies were conducted to define key factors promoting or inhibiting H2S production to match the actual H2S levels seen in the producers. Furthermore, the application of microbiological analysis to understand the reservoir souring behaviour, including screening of bacteria present using DNA-based techniques is also discussed. The simulations demonstrated that carbon is the souring limiting factor in MY01. To match the H2S field data, other metabolisable carbon sources should be available in addition to the volatile fatty acids (VFA's) in the formation water. The souring development in such field could be driven by the mechanism of the carbon supply. Therefore, it is critical to identify the type and quantify the level of dissolved organic carbon, including oil-derived BTEX or microbial degradation products. Since MY01 reservoir conditions are favourable for souring activities, microbial development is likely to take place both in the biofilm that forms at the injector face as well as at flood fronts deeper into the reservoir.

Microbiology of a hypersaline oil reservoir located in Central Africa was investigated with molecular and culture methods applied to preserved core samples. Here we show that the community structure was partially acquired during sedimentation, as many prokaryotic 16S rRNA gene sequences retrieved from the extracted DNA are phylogenetically related to actual Archaea inhabiting surface evaporitic environments, similar to the Cretaceous sediment paleoenvironment. Results are discussed in term of microorganisms and/or DNA preservation in such hypersaline and Mg-rich solutions. High salt concentrations together with anaerobic conditions could have preserved microbial/molecular diversity originating from the ancient sediment basin wherein organic matter was deposited.

Microbially influenced corrosion (MIC) in oil field pipeline systems can be attributed to many different types of hydrogenotrophic microorganisms including sulfate reducers, methanogens and acetogens. Samples from a low temperature oil reservoir in Nigeria were analyzed using DNA pyrotag sequencing. The microbial community compositions of these samples revealed an abundance of anaerobic methanogenic archaea. Activity of methanogens was demonstrated by incubating samples anaerobically in a basal salts medium, in the presence of carbon steel and carbon dioxide. Methane formation was measured in all enrichments and correlated with metal weight loss. Methanogens were prominently represented in pipeline solids samples, scraped from the inside of a pipeline, comprising over 85% of all pyrosequencing reads. Methane production was only witnessed when carbon steel beads were added to these pipeline solids samples, indicating that no methane was formed as a result of degradation of the oil organics present in these samples. These results were compared to those obtained for samples taken from a low temperature oil field in Canada, which had been incubated with oil, either in the presence or in the absence of carbon steel. Again, methanogens present in these samples catalyzed methane production only when carbon steel was present. Moreover, acetate production was also found in these enrichments only in the presence of carbon steel. From these studies it appears that carbon steel, not oil organics, was the predominant electron donor for acetate production and methane formation in these low temperature oil fields, indicating that the methanogens and acetogens found may contribute significantly to MIC.

Here we introduce a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources. The proposed MIxS-HCR package incorporates the core features of the MIxS standard for marker gene (MIMARKS) and metagenomic (MIMS) sequences along with a hydrocarbon resources customized environmental package. Adoption of the MIxS-HCR standard will enable the comparison and better contextualization of investigations related to hydrocarbon rich environments. The insights from such standardized way of reporting could be highly beneficial for the successful development and optimization of hydrocarbon recovery processes and management of microbiological issues in petroleum production systems.

Abstract Microbiologically Influenced Corrosion (MIC) is considered as one of the more notorious corrosion mechanisms as it results in the characteristic pitted-type of corrosion and is therefore often very difficult to predict. Among several environmental parameters, risk for MIC is therefore most often identified based on enumeration of MIC-related microbes (Sulfate Reducing Prokaryotes (SRP), Methanogenic Archaea (MA), etc.). Historically, the enumeration of microbes was performed through use of dilution or Most Probable Number (MPN) series. More recently, however, DNA-based methods like Fluorescent In-Situ Hybridization (FISH), quantitative PCR (qPCR) and metagenomics have been applied. Although these new DNA-based methods are promising, there are also cases where inconsistencies have been experienced. Several case studies showed that qPCR for specific microbial groups such as; SRP, MA, and Nitrate Reducing Prokaryotes (NRP), is unreliable due to the lack of adequate coverage of the target microbial community. As such the claims of DNA-based methods, to be more accurate and indicative, are not always properly met. The current study proposes an improved biomonitoring standard (data analysis and reporting) that is based on the combination of qPCR (for Total Bacteria and Total Archaea) and single gene (16S rRNA) metagenomic data analysis for the purpose of MIC risk assessment. It also aims to generate ‘calculated numbers’ for oil field relevant microbial groups by combining qPCR counts for Total Prokaryotes and relative abundance (%) of the respectively individual bacterial and archaeal microbial families and genera from single gene (16S rRNA) metagenomic analysis. The ‘conventional’ qPCR approach (on functional genes) and proposed method are compared through a field case study. In contrast to the ‘conventional’ qPCR approach, the proposed method resulted in reliable, internally consistent and better interpretable results, indicating MIC to be the root cause of a pipeline failure. The proposed biomonitoring standard has been communicated with several biomonitoring service providers that are used by the different oil majors. The proposed biomonitoring standard is aimed to be used as the improved cross-business standard for biomonitoring for the purpose of MIC risk assessment and as such to be implemented in existing NACE standards.

This study reports the ability of one hyperthermophilic and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. Aeropyrum pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in Ae. pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with the observations made on Ar. fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions.

The genus Moorella contains, up to now, only one sequenced genome, that of M. thermoacetica. Sequencing more strains is essential in understanding their common and specific physiology. Moreover, Moorella species typically grow with one-carbon substrates, but there are differences in their ability to grow with for example carbon monoxide. By comparing the already sequenced genomes of the type strains M. thermoacetica with close related strains we can assess which genes are responsible for the physiological differences.

Samples were obtained from the Obigbo field, located onshore in the Niger delta, Nigeria, from which oil is produced by injection of low-sulfate groundwater, as well as from the offshore Bonga field from which oil is produced by injection of high-sulfate (2,200 ppm) seawater, amended with 45 ppm of calcium nitrate to limit reservoir souring. Despite low concentrations of sulfate (0–7 ppm) and nitrate (0 ppm), sulfate-reducing bacteria (SRB) and heterotrophic nitrate-reducing bacteria (NRB) were present in samples from the Obigbo field. Biologically active deposits (BADs), scraped from corrosion-failed sections of a water- and of an oil-transporting pipeline (both Obigbo), had high counts of SRB and high sulfate and ferrous iron concentrations. Analysis of microbial community composition by pyrosequencing indicated anaerobic, methanogenic hydrocarbon degradation to be a dominant process in all samples from the Obigbo field, including the BADs. Samples from the Bonga field also had significant activity of SRB, as well as of heterotrophic and of sulfide-oxidizing NRB. Microbial community analysis indicated high proportions of potentially thermophilic NRB and near-absence of microbes active in methanogenic hydrocarbon degradation. Anaerobic incubation of Bonga samples with steel coupons gave moderate general corrosion rates of 0.045–0.049 mm/year, whereas near-zero general corrosion rates (0.001–0.002 mm/year) were observed with Obigbo water samples. Hence, methanogens may contribute to corrosion at Obigbo, but the low general corrosion rates cannot explain the reasons for pipeline failures in the Niger delta. A focus of future work should be on understanding the role of BADs in enhancing under-deposit pitting corrosion.

Perchlorate and chlorate anions [(per) chlorate] exist in the environment from natural and anthropogenic sources, where they can serve as electron acceptors for bacteria. We performed growth experiments combined with genomic and proteomic analyses of the hyperthermophile Archaeoglobus fulgidus that show (per) chlorate reduction also extends into the archaeal domain of life. The (per) chlorate reduction pathway in A. fulgidus relies on molybdo-enzymes that have similarity with bacterial enzymes; however, chlorite is not enzymatically split into chloride and oxygen. Evidence suggests that it is eliminated by an interplay of abiotic and biotic redox reactions involving sulfur compounds. Biological (per) chlorate reduction by ancient archaea at high temperature may have prevented accumulation of perchlorate in early terrestrial environments and consequently given rise to oxidizing conditions on Earth before the rise of oxygenic photosynthesis.

Today there is a renewed interest towards biological aspects in oil reservoir systems. This interest not only comes from academia, but also from the petroleum industry. Fields of common interest are ‘Microbial Enhanced Oil Recovery’ (MEOR), efforts to lower H2S production and subsequently microbial corrosion (caused by sulfate reducing microorganisms) and the analysis of microorganisms found in oil wells as additional information source for reservoir conditions.

Abstract Gas production from subsurface shales requires fracture technologies in which fracturing fluid, consisting of guar gum-suspended sand, is forced into the fractures to "prop" them open. The guar gum is easily degraded by bacteria both downhole and at the surface, compromising water reuse or disposal. Samples from the Pinedale shale gas field had high activity of mesophilic acid-producing bacteria (APB), converting guar gum to sugars and then to acetic and propionic acids and of heterotrophic nitrate-reducing bacteria (hNRB), using sugars or acids from guar gum as electron donor for nitrate reduction. Activity of sulfate-reducing bacteria (SRB) was considerably lower with guar gum, reflecting a low initial population size of SRB using the organic acids produced by APB for reduction of sulfate to sulfide. The low concentrations of sulfate in the samples (0–0.4 mM; 0–40 ppm) may be the root cause for this low SRB activity. Indeed, most probable numbers (MPNs) of SRB, determined on standard lactate-sulfate medium were 10- to 100-fold lower than those for APB, determined on standard phenol red-glucose medium. Interestingly, lactate-utilizing SRB appeared to be able to grow in APB medium, indicating that some SRB can also maintain themselves by fermentative metabolism, when sulfate is absent. Culture independent surveys of community composition confirmed that the microbial community at Pinedale samples was dominated by classes of fermentative bacteria (APB). Overall, we conclude that monitoring of the MPN of glucose-fermenting APB most accurately reflects microbial activity and associated biofouling at Pinedale. The success of biocide treatment to reduce microbial activity and associated biofouling is, therefore, also more accurately determined with the APB assay than with that for lactate-utilizing SRB.

ABSTRACT Community analysis of a mesothermic oil field, subjected to continuous field-wide injection of nitrate to remove sulfide, with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes indicated the presence of heterotrophic and sulfide-oxidizing, nitrate-reducing bacteria (hNRB and soNRB). These reduce nitrate by dissimilatory nitrate reduction to ammonium (e.g., Sulfurospirillum and Denitrovibrio ) or by denitrification (e.g., Sulfurimonas , Arcobacter , and Thauera ). Monitoring of ammonium concentrations in producing wells (PWs) indicated that denitrification was the main pathway for nitrate reduction in the field: breakthrough of nitrate and nitrite in two PWs was not associated with an increase in the ammonium concentration, and no increase in the ammonium concentration was seen in any of 11 producing wells during periods of increased nitrate injection. Instead, ammonium concentrations in produced waters decreased on average from 0.3 to 0.2 mM during 2 years of nitrate injection. Physiological studies with produced water-derived hNRB microcosms indicated increased biomass formation associated with denitrification as a possible cause for decreasing ammonium concentrations. Use of anammox-specific primers and cloning of the resulting PCR product gave clones affiliated with the known anammox genera “ Candidatus Brocadia” and “ Candidatus Kuenenia,” indicating that the anammox reaction may also contribute to declining ammonium concentrations. Overall, the results indicate the following: (i) that nitrate injected into an oil field to oxidize sulfide is primarily reduced by denitrifying bacteria, of which many genera have been identified by DGGE, and (ii) that perhaps counterintuitively, nitrate injection leads to decreasing ammonium concentrations in produced waters.

Abstract Flow cells (or ‘transparent micromodels’) are widely used to observe complex processes in two dimensional (2D) porous media. The objective of this study is to design, develop, and apply a wet-etched glass micromodel suitable for the observation of biofilm formation, transport of microorganisms and flow measurements using Particle Image Velocimetry (PIV). PIV in this case can be used for the visualisation and quantification of flow diversion. The wet-etching technique applied here is relatively straightforward. The paper addresses all aspects involved necessary to perform these experiments. The chosen etching depth of around 25 μm proved to be well suited for transport experiments with microorganisms. We show that the micromodel containing a wet-etched cell (wafer) provides a high quality image of transport and growth of microorganisms in porous media. The microorganism Pseudomonas chlororaphis was used as a model strain to perform the experiments on biofilm formation and transport. In the transparent cell, we could clearly observe biofilm formation. Moreover, we showed that PIV techniques can indeed visualize the change in flow pattern caused by biofilm presence.

The phylogenetic diversity of Bacteria and Archaea in water retrieved from a Dutch oil field and units of the associated oil-water separation site were determined using two culture-independent methods. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments was used to scan the microbial diversity in (1) the oil-water emulsion produced, (2) two different oil-water separator tanks, (3) a wash tank and (4) a water injector. Longer 16S rRNA gene fragments were amplified, cloned and sequenced to determine the diversity in more detail. One of the questions addressed was whether the detected microorganisms could serve as indicators for the environments from which they were retrieved. It was observed that the community found in the production water resembled those reported previously in oil reservoirs, indicating that these ecosystems harbor specific microbial communities. It was shown that changes, like a decrease in temperature, cause a distinctive shift in these communities. The addition of SO(3)(2-) to the wash tank as ammonium bisulphite, used in the oil industry to scavenge oxygen, resulted in a complete community change, giving rise to an unwanted sulphate-reducing community. The fact that these changes in the community can be linked to changes in their environment might indicate that these tools can be used for the monitoring of changing conditions in oil reservoirs upon, for example, water flooding.

The degradation of methanethiol (MT) at 30 °C under saline–alkaline (pH 8–10, 0.5 M Na+) conditions was studied in a lab-scale Upflow Anaerobic Sludge Blanket (UASB) reactor inoculated with estuarine sediment from the Wadden Sea (The Netherlands). At a sodium concentration of 0.5 M and a pH between 8 and 9 complete MT degradation to sulfide, methane and carbon dioxide was possible at a maximum loading rate of 22 mmol MT L−1 day−1 and a hydraulic retention time of 6 h. The presence of yeast extract (100 mg/L) in the medium was essential for complete MT degradation. 16S rRNA based DGGE and sequence analysis revealed that species related to the genera Methanolobus and Methanosarcina dominated the archaeal community in the reactor sludge. Their relative abundance fluctuated in time, possibly as a result of the changing operational conditions in the reactor. The most dominant MT-degrading archaeon was enriched from the reactor and obtained in pure culture. This strain WR1, which was most closely related to Methanolobus taylorii, degraded MT, dimethyl sulfide (DMS), methanol and trimethylamine. Its optimal growth conditions were 0.2 M NaCl, 30 °C and pH 8.4. In batch and reactor experiments operated at pH 10, MT was not degraded.