Petroleum microbiology is a branch of

microbiology Microbiology () is the scientific study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, bacteriology, prot ...

that deals with the study of

microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

s that can metabolize or alter crude or refined

petroleum Petroleum, also known as crude oil, or simply oil, is a naturally occurring yellowish-black liquid mixture of mainly hydrocarbons, and is found in geological formations. The name ''petroleum'' covers both naturally occurring unprocessed crud ...

products. These microorganisms, also called hydrocarbonoclastic microorganisms, can degrade hydrocarbons and, include a wide distribution of bacteria,

methanogenic Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. Organisms capable of producing methane for energy conservation have been identified only from the Domain (biology), domai ...

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

, and some

fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...

. Not all hydrocarbonoclasic microbes depend on hydrocarbons to survive, but instead may use petroleum products as alternative carbon and energy sources. Interest in this field is growing due to the increasing use of

bioremediation of oil spills Bioremediation of petroleum contaminated environments is a process in which the biological pathways within microorganisms or plants are used to degrade or sequester toxic hydrocarbons, heavy metals, and other volatile organic compounds found within ...

Applications

Bioremediation

Bioremediation of oil contaminated soils, marine waters and oily sludges ''in situ'' is a feasible process as hydrocarbon degrading microorganisms are ubiquitous and are able to degrade most compounds in petroleum oil. In the simplest case, indigenous microbial communities can degrade the petroleum where the spill occurs. In more complicated cases, various methods of adding nutrients, air, or exogenous microorganisms to the contaminated site can be applied. For example, bioreactors involve the application of both natural and additional microorganisms in controlled growth conditions that yields high biodegradation rates and can be used with a wide range of media. Crude oils are composed of an array of chemical compounds, minor constituents, and trace metals. Making up 50-98% of these petroleum products are hydrocarbons with saturated, unsaturated, or aromatic structures which influence their biodegradability by hydronocarbonclasts. The rate of uptake and biodegradation by these hydrocarbon-oxidizing microbes not only depend on the chemical structure of the substrates, but is limited by biotic and abiotic factors such as temperature, salinity, and nutrient availability in the environment.

''Alcanivorax borkumensis''

A model microorganism studied for its role in bioremediation of oil-spill sites and hydrocarbon catabolism is the alpha-proteobacteria ''

Alcanivorax ''Alcanivorax'' is a genus of alkane-degrading marine bacteria Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas ...

'', which degrades aliphatic alkanes through various metabolic activities. ''

Alcanivorax borkumensis ''Alcanivorax borkumensis'' is an alkane-degrading marine bacterium which naturally propagates and becomes predominant in crude-oil-containing seawater when nitrogen and phosphorus nutrients are supplemented. Description ''A. borkumensis'' is a ...

'' utilizes linear hydrocarbon chains in petroleum as its primary energy source under aerobic conditions. When further supplied with sufficient limiting nutrients such as nitrogen and phosphor, it grows and produces surfactant glucolipids to help reduce surface water tension and enhance hydrocarbon uptake. For this reason, nitrates and phosphates are often commercially added to oil-spill sites to engage quiescent populations of ''A. borkumensis'', allowing them to quickly outcompete other microbial populations and become the dominant species in the oil-infested environment. The addition of rate-limiting nutrients promotes the microbe's biodegrading pathways, including upregulation of genes encoding multiple alkane hydroxylases that oxidize various lengths of linear alkanes. These enzymes essentially remove the problematic hydrocarbon constituents of petroleum oil while ''A. borkumensis'' simultaneously increases synthesis of anionic glucoproteins, which are used to emulsify hydrocarbons in the environment and increase their bioavailability. The presence of crude oil along with appropriate levels of nitrogen and phosphor catalyzes the removal of petroleum either by mechanisms that enhance the efficiency of substrate uptake or by direct biodegradation of aliphatic chains.

Commercial applications

Two well-known oil spills exemplify large scale marine bioremediation applications: In 1989, the Exxon Valdez ran aground, spilling 41.6 million liters of crude oil, and launching one of the first major bioremediation efforts for an oil spill. Cleanup of Alaskan shorelines relied in part on

fertilizer A fertilizer (American English) or fertiliser (British English; see spelling differences) is any material of natural or synthetic origin that is applied to soil or to plant tissues to supply plant nutrients. Fertilizers may be distinct from ...

application to augment bacterial growth. In 2010, the BP ''Deepwater Horizon'' oil spill released 779 million liters of oil into the Gulf of Mexico. This was the largest oil spill of all time and indigenous petroleum microorganisms played a major role in petroleum degradation and cleanup.

Biosurfactants

These are microbial-synthesized surface-active substances that allow for more efficient

microbial biodegradation Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons (e ...

of hydrocarbons in bioremediation processes. There are two ways by which biosurfactants are involved in bioremediation. (1) Increase the surface area of

hydrophobic In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, th ...

water-insoluble substrates. Growth of microbes on hydrocarbons can be limited by available surface area of the water-oil interface.

Emulsifiers An emulsion is a mixture of two or more liquids that are normally immiscible (unmixable or unblendable) owing to liquid-liquid phase separation. Emulsions are part of a more general class of two-phase systems of matter called colloids. Although ...

produced by microbes can break up oil into smaller droplets, effectively increasing the available surface area. (2) Increase the bioavailability of hydrophobic water-insoluble substrates. Biosurfactants can enhance the availability of bound substrates by desorbing them from surfaces (e.g. soil) or by increasing their apparent solubility. Some biosurfactants have low critical micelle concentrations (CMCs), a property which increases the apparent solubility of hydrocarbons by sequestering hydrophobic molecules into the centres of

micelle A micelle () or micella () (plural micelles or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant amphipathic lipid molecules dispersed in a liquid, forming a colloidal suspension (also known as associated collo ...

Oil Recovery

Microbial enhanced oil recovery Microbial enhanced oil recovery (MEOR) is a biological based technology consisting in manipulating function or structure, or both, of microbial environments existing in oil reservoirs. The ultimate aim of MEOR is to improve the recovery of oil ent ...

(MEOR) is a technology in which microbial environments are manipulated to enhance oil recovery. Nutrients are injected ''in situ'' into porous media and indigenous or added microbes promote growth and/or generate products that mobilize oil into producing wells. Alternatively, oil-mobilizing products can be produced by

fermentation Fermentation is a metabolic process that produces chemical changes in organic substrates through the action of enzymes. In biochemistry, it is narrowly defined as the extraction of energy from carbohydrates in the absence of oxygen. In food ...

and injected into the reservoir. Various products and microorganisms are useful in these applications and each will yield different results. The two general strategies for enhancing oil recovery are altering the surface properties of the interface and using

bioclogging Bioclogging or biological clogging is clogging of pore space in soil by microbial biomass; their body and their byproducts such as extracellular polymeric substance (EPS). The microbial biomass blocks the pathway of water in the pore space, forming ...

to change the flow behavior.

Biomass Biomass is plant-based material used as a fuel for heat or electricity production. It can be in the form of wood, wood residues, energy crops, agricultural residues, and waste from industry, farms, and households. Some people use the terms bi ...

biosurfactants Biosurfactant usually refers to surfactants of microbial origin. Most of the biosurfactants produced by microbes are synthesized extracellularly and many microbes are known to produce biosurfactants in large relative quantities. Some are of commerci ...

, biopolymers,

solvents A solvent (s) (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for p ...

, acids, and gases are some of the products that are added to oil reservoirs to enhance recovery. Other resources for this application:

Biosensors

Microbial biosensors identify and quantify target compounds of interest through interactions with the microbes. For example, bacteria may be used to identify a pollutant by monitoring their response to the specific chemical. The biosensor system may simply use bacterial growth as a pollutant indicator, or rely on

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

tic assays wherein a reporter gene is induced by the chemical. Many analytical techniques require expensive treatment of soil samples and/or expensive equipment to detect the presence of pollutants. Bacterial biosensor systems offer the potential for cheap, robust detection systems that are selective and highly sensitive. One developed system uses ''

Pseudomonas fluorescens ''Pseudomonas fluorescens'' is a common Gram-negative, rod-shaped bacterium. It belongs to the ''Pseudomonas'' genus; 16S rRNA analysis as well as phylogenomic analysis has placed ''P. fluorescens'' in the ''P. fluorescens'' group within the genu ...

'' HK44 to quantitatively assay for

naphthalene Naphthalene is an organic compound with formula . It is the simplest polycyclic aromatic hydrocarbon, and is a white crystalline solid with a characteristic odor that is detectable at concentrations as low as 0.08 ppm by mass. As an aromati ...

using

bioluminescence Bioluminescence is the production and emission of light by living organisms. It is a form of chemiluminescence. Bioluminescence occurs widely in marine vertebrates and invertebrates, as well as in some fungi, microorganisms including some b ...

Challenges

Often in the process of degrading a pollutant, a microbe can create intermediates or

byproducts A by-product or byproduct is a secondary product derived from a production process, manufacturing process or chemical reaction; it is not the primary product or service being produced. A by-product can be useful and marketable or it can be consid ...

that are also harmful, sometimes even more harmful than the original substrate. For example, some microbes produce

hydrogen sulfide Hydrogen sulfide is a chemical compound with the formula . It is a colorless chalcogen-hydride gas, and is poisonous, corrosive, and flammable, with trace amounts in ambient atmosphere having a characteristic foul odor of rotten eggs. The unde ...

as a byproduct in the degradation of certain petroleum hydrocarbons and if those gases are not detoxified before escaping the system, they can be released into the atmosphere.

Biodegradation pathways

The pathways of degradation of different petroleum products vary depending on the substrate and the microorganism (i.e. aerobic/anaerobic). Specific degradation pathways of many hydrocarbon compounds can be found on th
University of Minnesota Biocatalysis/Biodegradation Database