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Geomicrobiology is the study of the interactions between microbes and minerals. Geomicrobiology (Geochemical microbiology) is the branch of microbiology that studies the applications of microorganisms in the mining of metals, crude oil and other natural resources from their natural sources or the ground. Microorganisms are currently being exploited in a number of mining and oil recovery activities. They have also been used to prospect for oil, gas and coal in areas deemed to be low in these resources. Microorganisms including bacteria, algae, fungi and protozoa form both beneficial and non-beneficial   associations with other living organisms on the earth’s surface and even below the earth’s surface. These microbes interact via several host-parasite relationships in their bid to exploit the chemical, physical and biological components of the earth’s components.

Microorganisms cause mineral precipitation and dissolution and control the distribution of elements in diverse environments at the surface of the earth as well as below the surface of the earth. And it is worthy of note that mineralogical and geochemical factors exert important controls on microbial evolution and the structure of microbial communities found at both the earth surface and below the earth surface. Microorganisms and the many minerals of the earth are interdependent; and their individual or collaborative activities also contribute the several changes we now see in the environment. Thus the understanding and proper exploitation of these interdependence between minerals and microbes will enable scientists to better control some of the adverse activities of microbial-mineral associations.

Microbes have contributed tremendously to the formation of minerals, their dissolution, and their distribution in the earth’s surface. The field of geomicrobiology concerns the role of microbes and microbial processes in geological and geochemical processes as it pertains to the earth’s surfaces. This branch of microbiology (which is a combination of geology and microbiology) is especially important when dealing with microorganisms in aquifers and public drinking water supplies, as well as in the exploration of metals and other minerals in the earth. Geomicrobiology concerns itself with how microbes eat rocks. Some rock-eating microbes known as extremophiles or geomicrobes co-exist with rock surfaces and other minerals in the earth’s surfaces; and these geomicrobes are vital in several other biological, chemical, physical and/or geochemical processes that occur in the environment (Table 1). Extremophiles are microorganisms that live in areas considered too hostile for other living organisms.

Table 1. Geomicrobes and the metals/minerals they metabolize

Metals/mineralsGeomicrobesBiogeochemical process
Sulphur (S)Sulfate-reducing bacteriaThey use sulfate as an oxidizing agent, reducing it to sulfide.  
Iron (Fe)Acidithiobacillus thiooxidansThey are used in a mining technique such as bioleaching – whereby metals are extracted from their ores through oxidation.  
Manganese (Mn)  Bacillus species and Pseudomonas putidaThey carry out the oxidation of manganese in the soil and fresh water.  
UraniumNitrate dependent Fe(II)-oxidizing microorganismsThey carry out the reduction of uranium under anaerobic conditions with Fe(III) and/or sulfate reduction; and this is usually applicable in aquifers contaminated with uranium from nuclear plants or weapons and fuels.  
Phosphorus (P)Pseudomonas fluorescens, Bacillus caldolyticus, P. stutzeri, E. coli, Agrobacterium tumefaciens, Saccharomyces cerevisiae and RhizobiumThey promote the dissolution of various phosphate minerals (either in their organic or inorganic forms) and make phosphorus available for other vital activities in the ecosystem.

An example of an extremophile is the anaerobic sulfate reducing bacteria, which are known to live in hyper-saline lagoons and other bodies of water with high salt concentrations. Extremophiles live in areas with high salt concentrations. Geomicrobiology is a combination of geology and microbiology; and it studies the impact of microbes on rocks and other solid parts of the environment. Geomicrobiological processes are relevant in many natural environments including aquifers, geological and geochemical processes, extreme environments (acidic, extreme temperatures and saline conditions) and metal ion reduction or extraction. Geomicrobiology can be applied in several processes including but not limited to weathering, precipitation of carbonates and phosphates and nuclear waste disposal.

Weathering is defined as the breaking down of rocks and minerals on the earth’s surface. It plays an important role on the earth ecosystems; weathering is very important for the release of nutrients into the earth’s biosphere as a result of rock dissolution. Water, ice, acids, salt, plants, animals, and changes in temperature are all agents of weathering. During rock dissolution, the bits of rocks and minerals produced are steadily transported away through erosion. Though weathering can be considered to be a strictly physical and chemical process; it is nevertheless affected by the presence of microbial communities and their activities which go on in the earth’s surfaces. Thus microbial weathering is defined as the weathering or rock dissolution that is mainly mediated by microbial activities in the earth’s surfaces. Microbial weathering is usually due to the formation of organic acids and/or the production of metal-chelating siderophores on the surface of rock or minerals.

Siderophores are low-molecular weight iron-chelating compounds synthesized and exported by most microorganisms including fungi and bacteria for the uptake of iron in their environment. Microbes also contribute to the precipitation of carbonates and phosphates in the earth’s rock. The influence of microbes especially bacteria in the precipitation of minerals including carbonates and phosphates is well documented in different natural habitats including aquatic environments and geological systems such as rock formations and aquifers. Microbes especially fungi have also been reported to possess good nuclear waste disposal qualities. Fungi can be very radiation-resistant and can survive and colonize concrete barriers under severe radioactive contamination. Fungal growth has also been observed on the surfaces of structures that have undergone radioactive contamination over several years.

A typical example is the 1986 Chernobyl catastrophe in Russia in which fungal growth was observed on the walls of inner structures built around and within the Chernobyl nuclear plant. Thus, since the safe and long-term storage of both existing and future nuclear wastes is important in protecting the environment in probable nuclear contamination, the physiology of fungi in relation to their innate resistance to radiation is currently being investigated for the future construction of nuclear waste repositories to ensure a sustainable environment for mankind. The fungal genera with such activities include Alternaria, Cladosporium, and Aureobasidium. Microbes require sufficient amount of energy to be able to carry out their different geomicrobiological process; and thus the study of how these organisms acquire and utilize energy (i.e. microbial energetics) is vital in the study of geomicrobiology.

Geomicrobiology is applied in several areas to solve environmental problems. Some of the key areas where geomicrobiology is applied include bioremediation, water and/or borehole drilling, bioleaching and extraction of metals from their ores. Bioremediation is a waste management technique that involves the use of organisms to remove or neutralize pollutants from a contaminated site. It is the biological treatment that uses naturally occurring organisms like microorganisms to break down hazardous substances into less toxic or non toxic substances in the environment. Some contaminants such as copper and lead however, cannot be easily treated by bioremediation using microorganisms. But oil spillage has been controlled with the use of microbes that has high affinity for oil. Pseudomonas species are commonly used in bioremediation activities especially in the control of oil spillage.

Bioleaching is the extraction of metals from their ores through the use of living organisms especially microbes.Bioleaching is applied in the recovery of metals such as copper, zinc, lead, arsenic, antimony, nickel, molybdenum, gold, silver, and cobalt from their natural states (i.e. ores).Bioleaching can involve numerous ferrous iron oxidizing bacteria and sulfur oxidizing bacteria, including Acidithiobacillus ferrooxidans (formerly known as Thiobacillus ferrooxidans) and Acidithiobacillus thiooxidans (formerly known as Thiobacillus thiooxidans). As a general principle, iron III ions (Fe3+) ions are used to oxidize the ore; and this step is entirely independent of any microbial action. The role of iron-oxidizing bacteria in the extraction of iron from their ores is the further oxidation of the ore; and these microbes also helps in the regeneration of the chemical oxidant Fe3+ from iron II ions (Fe2+). For example, bacteria catalyze the breakdown of the mineral pyrite (FeS2) by oxidizing the sulfur and metal (in this case ferrous iron, (Fe2+) using oxygen. This yields soluble products that can be further purified and refined to yield the desired metal.

Further reading

Jee C and Shagufta (2007). Environmental Biotechnology. APH Publishing Corporation, Darya Ganj, New Delhi, India.

Latha C.D.S and Rao D.B (2007). Microbial Biotechnology. First edition. Discovery Publishing House (DPH), Darya Ganj, New Delhi, India.

Maier R.M, Pepper I.L. and Gerba C.P (2000). Environmental Microbiology. Academic Press, San Diego.

Mishra B.B, Nanda D.R and Dave S.R (2009). Environmental Microbiology. First edition. APH Publishing Corporation, Ansari Road, Darya Ganj, New Delhi, India.

Paul E.A (2007). Soil Microbiology, ecology and biochemistry. 3rd edition. Oxford: Elsevier Publications, New York.

Pelczar M.J., Chan E.C.S. and Krieg N.R. (2003). Microbiology of Soil.  Microbiology, 5th Edition. Tata McGraw-Hill Publishing Company Limited, New Delhi, India.

Pepper I.L and Gerba C.P (2005). Environmental Microbiology: A Laboratory Manual. Second Edition. Elsevier Academic Press, New York, USA. 

Roberto P. Anitori (2012). Extremophiles: Microbiology and Biotechnology. First edition. Caister Academic Press, Norfolk, England.

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