Energy: The Next Biotechnology Challenge

Editor’s note: This is the second-to-last installment in this yearlong series examining R&D needs and potential. This article explores the challenges of applying biotechnology to the oil and gas sector and hints at the possibility of genetically modified organisms to achieve superior results. The current scientific uncertainty on just how future organisms will be included in the global energy picture suggests full speed ahead on the science, with the understanding that the issue of industry acceptance will need to be properly evaluated and managed.

Today the impact of biotechnology is most noticeable in the health and pharmaceutical sectors, chemical industry, and in environmental technologies. The time is coming when it also will play a role in the energy sector. This is the result of progress in two major areas that are likely to have important consequences. The first one is the growing awareness of the major chemical fluxes fueled in the depths of the Earth’s crust by the deep biosphere: microorganisms that live without oxygen and form the basis of previously unrecognized element cycles completely different from those that take place at the surface, driven by solar energy and oxygen. The simultaneous presence of minerals, gases, hydrocarbons, and bacteria in the anoxic deep biosphere is the basis of new speculation on carbon cycling in anoxic regions. Microbiologists now have new tools to detect and monitor biological activity in the environment, among which are the powerful techniques of specific DNA amplification and detection, which are best known to nonexperts for their applications in crime forensics. In just about the same way, specific types of bacteria can be detected in minimal amounts from any type of environment and recognized and functionally identified—for example, sulfate recycling bacteria (associated with the souring of reservoirs and oil-extraction systems) living at extraordinary depths and temperatures.

The second major field of influence will be biological fuel synthesis and carbon capture from renewables. Interest in these possibilities blossomed and waned in the 1970s, but the area is now experiencing renewed interest, funding, and revival by the exploitation of fast-progressing genomics and bioengineering techniques.

This article addresses the relevance and potential of biotechnology applications to the energy industry, envisioning the areas where biotechnology science progress might affect present and future business.

Black Energy: Oil, Gas, and Bugs

Oil and gas have been part of this planet for so long that the smallest living cells on the surface and in the deep biosphere have evolved ways to feed on them and gain energy, however unpalatable the ingredients might be. Bacterial degradation of crude oil in the reservoir is the cause of the poor quality of oil found in many areas, from the Canadian tar sands to offshore fields. Some of the biochemical pathways of oil hydrocarbon transformation are known, but many remain to be clarified, including mechanisms that might be in action in the reservoirs where temperature is compatible with bacterial life. Recent indications support the possibility of in-situ bioconversion processes of oil to methane and maybe even to other gaseous hydrocarbons. In similar ways to biological conversion of some types of coal to methane, exploitation and acceleration of the natural phenomena could be an interesting alternative to other traditional technologies of energy recovery from difficult sources.

DNA technology applied to environmental microbiology has evolved in the past decade, providing new methods to shed light on the ways microorganisms affect the environment in which they live. Metagenomics is the branch of this technology which describes the groups of genes and related enzymes at play in that environment, expressed by associations of bacteria that depend on each other and on the environmental conditions to survive and replicate. The study of such aggregates of genes and enzymes is at the basis of an understanding of the many reactions that could or could not take place in that environment. If applied to the yet obscure and poorly known oil-bearing environment inhabited by microorganisms, this technology will help in clarifying the type of microorganisms that survive there and that might be exploited.

But which type of reaction could actually help, if encouraged and supported through environmental engineering, to enhance energy recovery from the reservoirs? Controlled conversion to methane or to other gases is one possibility. Synthesis of biosurfactants stimulated by the addition of nutrients or ions might be another; the technical options will depend largely on the type of environment itself (i.e., type of rock, physical and chemical parameters, water accessibility, and the presence
of biocatalysts).

Environmental engineering applied to processes of bioremediation shares common aspects and uncertainties with any technology aimed at the management of the subsurface biosphere and might provide insight into the advantages and pitfalls of this approach, especially where sound knowledge on the biocatalyst at play is available. A practical example of this type of application is the experimental use of nitrate to prevent souring by modifying bacterial populations in reservoirs, inducing selective growth and activity of bacteria that in these conditions counteract and control the hydrogen sulfide-producing bacteria. In this case, the most commonly found H2S-producing and -consuming bacteria in reservoirs have been identified and could be recognized and monitored.

Research projects and initiatives currently active in the area of reservoir microbiology are focused mainly on the difficult task of extracting energy in a clean and efficient way from tar sands and heavy oil deposits in Canada and South America, while other projects involve oil reservoir bacterial metagenomic and microbial enhanced oil recovery. While the first practical results from these efforts might be forthcoming in the next 2 decades, first evidence supports the approach. Groundbreaking work on anaerobic hydrocarbon bioconversions has been conducted at the Max Planck Inst. and in the U.S., while Larter’s and I. Head’s groups at Newcastle, U.K., and now in Canada, are at the forefront in the area where discovery and application to the energy industry feed each other and progress together.

Our own analysis of bacterial DNA extracted from rock cores from degraded oil reservoirs supports the notion that bacteria live in reservoirs at the interface between oil and water, and the genetic information can be processed and function extrapolated from genetic similarities (Fig. 1). The constraints imposed by the often harsh living conditions of this type of environment might determine survival of bacterial consortia composed of few and specialized types, which will be easier to analyze than complex populations, as was found to be the case for the biofilm components characterized from an acidic mine in one of the first applications of this technology, in 2003.

Fig. 1—Uncovering the identity of bacteria living hundreds of meters below the seafloor, at the interface between degraded oil and water. DNA is extracted from the rock, gene-amplified, analyzed by electrophoresis, and sequenced. Band sequences allow recognition of bacterial species possibly involved in oil biodegradation in reservoirs. DNA from bands in the red frame have been sequenced and found to be similar to bacteria degrading oil components.

Biotechnological applications nearer to practical use in the oil industry involve the manufacturing of enzymes or biocatalysts customized to specialized tasks. Commercial enzymes are already in use to degrade biopolymers used in well-stimulation applications, and the rapid development of prokaryotic-diversity mining technologies to find new and sturdy biocatalysts promises fast progress in this field. In particular, two approaches are emerging in the identification and optimization of new catalysts: One relies on techniques of accelerated in-vitro evolution of natural enzymes, based on powerful methods of reiterated mutagenesis and selection, and the other relies on direct functional selection of bacterial activities from extremely diversified natural environments. Recent examples show that in both cases, biocatalysts with superior activities can be isolated. Similarly, progress might be expected in those activities that seek to exploit biological ways to remove from the environment medium-low levels of degradable waste from extraction activities.

Green Energy

The real challenge for biotechnology applied to the quest for clean energy might reside in the development of new processes to produce energy from alternative and renewable sources to help curb the rise in CO2 emissions.

Corn bioethanol and biodiesel production processes, while feasible and commercially available, are still uneconomical unless subsidized or integrated in dedicated circuits, and they compete with food for land use. New processes for the production of biofuels from agricultural waste and “low grade” renewable hydrocarbons are in development and should provide us with better ways to produce energy from cheaper sources than corn sugar and vegetable oils. While biofuel’s production from land products is not predicted to cover more than a fraction of transportation energy needs, this portion could be sizeable. Bioethanol produced in the U.S. is now near 3% of total fuel and predicted to increase 50% in the next year, while major countries in Europe plan to substitute up to 20% of national fuel for transportation with biofuels by 2020, in line with the European vision of bioenergy production and use. Gene modification and metabolic engineering of biocatalysts is at the basis of new processes for the production of biofuels—in fact, superior enzymes and bacterial strains capable of optimally metabolizing biomass-derived hydrocarbons have been developed for the production of bioethanol, and new ones are in development. New, dedicated crops for energy, easy to metabolize into biofuels, are also an interesting object of research and development. The energy industry is looking at research in this field as an opportunity for the future, as testified by the significant investments being made.

Fig. 2—Carbon cycle from sunlight+CO2 to plants to
petroleum from sunlight to plants directly to fuels.

There is something intrinsically elegant in the biological process of capturing and transforming atmospheric carbon and light energy into chemicals that compels mimicry (Fig. 2). Many types of microorganisms populating the sea live on solar energy and carbon from atmospheric carbon dioxide. The (meta)genomes of marine microorganisms, among others, are just starting to be accessed and could possibly be harnessed into new, more efficient microorganisms dedicated to energy production for human use. While several research initiatives focus on strain amelioration and better biofuel productivity for light- and CO2-capturing microorganisms, some prefer to imagine the development of totally new, artificial cells, designed just for this purpose. Toward this aim, Craig Venter’s Synthetic Genomes and the JCV Inst. are funneling financial and intellectual resources. While the tools are being developed for this purpose, success is not guaranteed and the results will probably be long in coming, but the game is worthy.

Francesca de Ferra is a technical manager at the R&D Center of Eni Refining and Marketing Div. of San Donato Milanese in Milano, Italy. She has returned to Italy as a biotechnology expert after earning a PhD degree at State U. of New York on a Fulbright grant, getting post-doctoral training in molecular biology, and holding a position as assistant professor at the Wistar Inst. at the U. of Pennsylvania. Her main research interests at Eni concerned opportunities for industrial exploitation of environmental microbiology in the upstream sector and the research and development of clean processes based on biocatalysis. She currently holds a contract professorship at the U. of Milano in the field of environmental biotechnology and is involved in the development of new processes for the production of biofuels.