Background:
Fossil fuels are likely to remain a significant energy source for at least the next 30 years as economies transition globally towards more renewable energy sources.1–3 Extracting trapped oil from aging wells can not only increase the overall production of existing wells but also minimize the need to drill new wells and, ultimately, decrease the cost of extracting oil from existing reservoirs. Expensive polymer and/or surfactant/polymer formulations that require large amounts of funding and research effort are used to extract oil not recovered by primary extraction techniques.4–6 Additionally, native and exogenous microbes have been harnessed as a more cost-effective alternative for secondary and tertiary oil recovery – an approach coined microbial enhanced oil recovery (MEOR).7,8 Microbial activity in oil wells, however, can either be harnessed to benefit the oil recovery process or be disruptive and hinder the process. Microbial metabolic products can liberate trapped oil: produced gases displace immobile oil, organic acids dissolve carbonaceous deposits and increase well permeability, solvents dissolve and mobilize large hydrocarbons from the pores, and biosurfactants act as emulsifiers.7,9 On the other hand, microbes can also degrade and sour oil, and produce metabolites that corrode the well casing, flowlines, and pipelines. Globally, pipeline corrosion alone can result in nearly $2 billion dollars (USD) of damage and loss each year.7,10 This corrosion is due primarily to oxidation of microbially-produced hydrogen sulfide (H2S) to sulfuric acid.10,11Engineering the composition and metabolism of oil well microbial communities promises to enhance the productivity and economic viability of oil extraction operations.
Engineering microbiomes has emerged as a sustainable approach to develop processes for a number of industries from health and nutrition to agriculture and fuels.12–14 To engineer microbial communities, there are two common general approaches: bottom-up and top-down microbiome engineering.15 Generally, bottom-up microbiome engineering pertains to constructing communities of microbial species and strains with desired attributes and synergies to carry out a task or set of tasks. In MEOR, bottom-up approaches often focus on biofilm or surfactant production via communities centered around natural and/or engineered strains of Pseudomonas ,Bacillus , and Enterobacter which are able to extract up to 26% of the additional trapped oil. 7,16–19However, the ecology of engineering bottom-up communities is very complex and developing stable communities that colonize a natural, fluid ecosystem, like that of the oil well microbiome, is exceedingly difficult.20 Strains may fail to colonize because they do not fill a particular ecological niche in the community and can change the native microbiome composition in unpredicted and uncontrollable ways.21 Emerging bottom-up strategies to overcome this challenge such as artificial syntrophy where microbes exchange metabolites for mutual survival are difficult to develop and can fail catastrophically if a single species is lost due to unanticipated competition with native microbes.22,23Lastly, strains used in bottom-up approaches are often genetically engineered, which raises both ecological concerns and creates regulatory burden related to the introduction of genetically modified organisms in the environment.14,24
In contrast, top-down microbiome engineering manipulates environmental factors such as nutrients, pH, temperature, and ionic strength to tailor a native community for a desired outcome or task.15This strategy does not require any bacterial species to be introduced into the community or colonize a new environment, but instead leverages the present microbes.20,25 Tuning environmental factors, or synthetic ecology, is typically more cost-effective and is easily testable in controlled parallel experiments.26Similarly, top-down MEOR is often much more economical than the synthetic polymers used for standard secondary and tertiary oil recovery.27,28 However, not all microbiomes will respond to changes in these environmental factors and they are likely to have different responses depending on the composition of microbes and environmental factors surrounding them.29 Up to 89% of MEOR trials have successfully produced additional oil but to varying degrees.29,30 Therefore, top-down microbiome engineering conditions must be rapidly screened in vitro in a high-throughput, cost-effective manner to identify both candidate oil well communities and optimal MEOR intervention conditions. Taken together, the facts that top-down engineering approaches are cost-effective, can be rapidly screened, and do not require scientific ecological barriers suggest that it is an attractive strategy for developing MEOR formulations for field trials.
In this study, we use top-down engineering strategies to screen wells and optimize oil extraction operations for the Illinois basin via MEOR. Through in vitro cultivation, we identified candidate wells that would be responsive to MEOR intervention and characterized the response of their microbial community as a function of specific nutrient supplementation. We established that simple molasses injection coupled with inorganic salt solutions could be used to stimulate microbial activity that reduced H2S production and stimulated desired gas and organic acid production. Simulation of field recovery operations via a miniature coreflood experiment confirmed the ability of these interventions to reduce oil souring and modify the specific hydrocarbon composition of produced oil. Ultimately, this work demonstrates that top-down microbiome engineering strategies can significantly benefit oil recovery operations while improving economic and environmental sustainability.
Results and Discussion :