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 :