Oil reservoirs, an exceptional habitat for microorganisms

Pannekens, Mark; Kroll, Lisa; Müller, Hubert; Mbow, Fatou Tall; Meckenstock, Rainer U.

doi:10.1016/j.nbt.2018.11.006

Cited by 135 publications

(99 citation statements)

References 109 publications

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“…Since methanogens can only use a restricted range of substrates and thrive closer to the thermodynamic limit ( Thauer et al, 1977 ; Liu and Whitman, 2008 ), this suggests that SRMs prefer more easily degradable substrates in the presence of recalcitrant asphalt compounds. Considering that hydrocarbon-degrading microorganisms thrive in the oil-water interphase ( Pannekens et al, 2019 ), life is spatially restricted to specific niches in hydrocarbon-saturated environments, as has been shown for water droplets in the oil body itself ( Meckenstock et al, 2014 ). Thus, the competing microbes are restricted to a limited space which probably intensifies the negative interactions among them.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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“…Both traditional microbiological methods and omics approaches have been widely used to assess microbial community degraders and hydrocarbon biodegradation potential in petroleum and gas industry-associated environments. These scientific efforts have started long time ago aiming at a deeper understanding of the role of microorganisms in petroleum deterioration, as well as at bioprospecting specific properties of indigenous microorganisms for improving/optimizing biotechnological processes, such as Microbial Enhanced Oil Recovery (MEOR) (Röling et al, 2003;Youssef et al, 2009;Wentzel et al, 2013;Pannekens et al, 2019).…”

Section: Pah Biodegradation In Upstream Operations: Petroleum Reservoirsmentioning

confidence: 99%

“…In this reservoir, the anthropogenic perturbation with seawater injection was assumed to alter the indigenous microbial community toward fast-growing opportunists that had little effect on the hydrocarbon degradation due to the likely use of other easily available carbon sources or due to the combination of high salinity and temperature limiting in situ conditions (Sierra-Garcia et al, 2020). Generally, water injection practices lower temperatures, increase salinity (in seawater injections), and promote the enrichment with exogenous chemicals/nutrients and/or microorganisms, stimulating changes in indigenous microbial communities (Pannekens et al, 2019). Therefore, besides the well-known factors that limit life (nutrient availability, metabolic products, temperature and salinity), indigenous microbial communities in oil reservoirs are affected by the anthropogenic factor, that for a long time has exploited the deep geological resources leading to changes in microbial ecology and activity, ultimately resulting in the modulation of beneficial and/or detrimental microbial processes (Pannekens et al, 2019).…”

Section: Pah Biodegradation In Upstream Operations: Petroleum Reservoirsmentioning

confidence: 99%

“…Generally, water injection practices lower temperatures, increase salinity (in seawater injections), and promote the enrichment with exogenous chemicals/nutrients and/or microorganisms, stimulating changes in indigenous microbial communities (Pannekens et al, 2019). Therefore, besides the well-known factors that limit life (nutrient availability, metabolic products, temperature and salinity), indigenous microbial communities in oil reservoirs are affected by the anthropogenic factor, that for a long time has exploited the deep geological resources leading to changes in microbial ecology and activity, ultimately resulting in the modulation of beneficial and/or detrimental microbial processes (Pannekens et al, 2019).…”

Section: Pah Biodegradation In Upstream Operations: Petroleum Reservoirsmentioning

confidence: 99%

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

et al. 2020

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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.

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“…Hence, it is commonly assumed that no degradation takes place within the oil leg itself (1,4). However, indicators for microbial life are found in almost all oil and water samples from reservoirs and even in heavy oil or asphalt seeps with temperatures up to 82 °C (5)(6)(7)(8)(9)(10)(11)(12)(13)(14). This includes the largest natural asphalt lake, the "Pitch Lake" located on the island of Trinidad, Trinidad and Tobago.…”

Section: Introductionmentioning

confidence: 99%

Densely Populated Water Droplets in Heavy-Oil Seeps

Pannekens

Voskuhl

Meier

et al. 2020

Appl Environ Microbiol

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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.

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Oil reservoirs, an exceptional habitat for microorganisms

Cited by 135 publications

References 109 publications

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

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

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

Densely Populated Water Droplets in Heavy-Oil Seeps

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