Microorganisms are found throughout an oil production system, from the deep subsurface of the reservoir rock to the production hardware of pipelines and extraction apparatus above ground. The problems associated with their presence are equally diverse yet can often be considered together. Members of the sulphate reducing bacteria (SRB) are responsible for the majority of the bacterial nuisance in oil production and their presence and growth in a system will often result in a combination of problems.

 
Left picture- Oilfield SRB; Middle and right picture- Pitting corrosion

Corrosion  of metal, particularly steel, costs the industry millions of dollars in replacement pipelines and prevention methods. Iron is readily oxidised, its electrons removed, wherever it is in contact with an aqueous environment. The corrosion process can be significantly enhanced by the presence of microorganisms via a variety of mechanisms. For example, SRB that grow as biofilm clusters on metal surfaces establish localised zones with steep electron gradients, speeding electron transfer and hence corrosion.

SRB directly produces Hydrogen sulphide(H2S). This hazardous gas, a respiratory inhibitor, is volatile and toxic.  It is not only a danger to production workers but is also soluble in crude oil causing it to become 'sour'. Oil contaminated with high concentrations of hydrogen sulphide is considered sour because such oil must be treated before it can be burnt to prevent emissions of toxic sulphur compounds to the atmosphere where they are responsible for acid rain. Such treatment is a considerable expense to add to extraction costs and therefore undesirable. Should a well become (economically) too sour a production company will close it rather than bear the added costs of cleaning the oil.

Occasionally a pristine reservoir will be found to be sour immediately upon oil extraction; this is due to thermal decomposition of sulphur compounds or earlier bacterial activity during reservoir maturation. However, more commonly a reservoir will gradually become sour during its production lifetime due to the actions of SRB. This souring occurs because the oil extraction process alters conditions within the reservoir. Drilling down into the subsurface contaminates the deep environment with bacteria that are present at the surface and in shallower rock. It also involves the use of drilling muds to cool and lubricate drilling equipment. Oil based muds often contain biodegradable diesel grade hydrocarbons which are introduced to the reservoir. The onset of secondary oil production is due to a lack of pressure in the reservoir; seawater is pumped down into the reservoir to increase pressure and drive more oil out. Introduced with seawater are high concentrations of sulphate and even more immigrant microorganisms despite employment of biocides and filtration. The seawater also cools the reservoir where it enters it, resulting in a near well bore environment very different to that before human intervention. This environment can be ideal for the proliferation of SRB and results in sulphide biogenesis as bacteria reduce sulphate from the seawater in order to respire.

Although souring has been indisputably proven, the prediction of its extent and timing is notoriously difficult. Mathematical modelling of reservoir souring is needed in order to allow decisions such as materials of construction for new fields.

Microbial Benefits to the Oil Industry
There are numerous functions which bacteria can perform to aid the oil extraction process. Many bacteria produce helpful metabolic by-products such as acids, which can dissolve carbonate rock releasing adhered oil from surfaces and improve the overall porosity and permeability in the formation. Produced gases can increase reservoir pressure and release trapped oil. Carbon dioxide also dissolves in oil and helps with its physical displacement. Certain by-products act as surfactants, reducing interfacial tensions between rock and oil, and creating oil/ water emulsions that are more mobile. Biopolymers give bacterial biofilm their adhesive, plugging property that, while being the cause of formation plugging can be a problem but if carefully managed could improve oil recovery. Bacteria are transported through reservoirs primarily by fluid movement and therefore follow the high permeability paths between an injection well and a production well. Some bacteria will attach to rocks in this zone and reservoir engineers may wish to stimulate their growth by nutrient addition. This nutrient will cause biofilm to grow selectively in the high permeability zones, a benefit to oil recovery because such zones are swept clear of oil at an early stage. Waterflood will then be diverted by the biofilm into less permeable zones where oil still remains so improving water sweep.

Certain bacteria can also degrade hydrocarbons both with and without the presence of oxygen. Hence, there is a possibility of using bacteria to reduce viscosity of heavy oils in reservoirs while removing sulphur from oil. Topside (above ground) desulphurisation is carried out by bacteria today but the down hole (in the reservoir) application still eludes the industry.