Ore Deposits Formed by Biochemical Activity

The biosphere is a unique feature of the earth.  It includes the boundary zone where the lithosphere, atmosphere and hydrosphere meet.  The important turning points in the evolution of the biosphere are intimately related with the formation of important mineral deposits.

The oxygen poor atmosphere of the earth between 3.0 to 1.0 Ga, promoted the dissolution of many metals, mainly iron and manganese, from continental areas.  These were contributed to the seas which came to have a high dissolved content of metals.  The appearance of the first living organisms in the oceans, viz., prokaryotes, blue bacteria and algae resulted in an increase in the dissolved O2 concentration, which in turn led to the precipitation of iron in the form of ferric oxides, producing the world’s most important iron ore deposits – the BIFs.

Organic evolution led to the emergence of flora on the shores which produced the abundant biomass which contributed to the extensive development of different kinds of soils in humid and temperate climates as also to serve as the raw material for coal formation.  The remnants of first terrestrial plants in the littoral zones gave rise to the development of the most important fossil fuel resource – the world-wide Carboniferous (360-300 my) coal deposits.

In several places, and at several times during the geological past, marine evolution was interrupted by events when the level of dissolved oxygen in sea water was dramatically reduced.  These periods, known as periods of anoxia, witnessed mass extinctions of marine life, as a consequence of which organic matter accumulated in sediments,  to be later converted to hydrocarbons.  Such periods of mass extinctions mark the ends of the main epochs in earth’s history (eg the Paleozoic-Mesozoic boundary) and are important moments of evolution.  The increased organic content in sediments can act s a geochemical barrier to induce sulfide precipitation by maintaining a low Eh reducing environment for any metal-bearing solutions.  Such anoxic sedimentation frequently resulted in sulfide enrichment in sediments giving rise to important ore deposits of the Kupferschiefer type (Germany and Poland).

The first step in the formation of hydrocarbons is the biological decomposition of proteins, lipids and carbohydrates in the organic matter to form kerogene, a primitive hydrocarbon species.  This is followed by a long process of maturation during which the organic matter is cracked into smaller and smaller molecules


Microbes interact with metals and minerals in natural environments, altering their physical and chemical state.  They can affect dissolution of minerals as well as their precipitation from solutions.  As such they play an important role in the genesis of mineral deposits.

The term biomineralization represents the collective processes by which organisms form minerals -- a widespread phenomenon mediated by bacteria, protists (organisms made up of single or multiple cells which all contain a nucleus enclosed by a membrane), fungi, plants and animals. Most biominerals are calcium carbonates, silicates and iron oxides or sulfides.  Biomineralization is itself an important interdisciplinary research area, and one that overlaps with Geomicrobiology, which involves the role of microbes in geological processes. 

Microbes are capable of mediating metal and mineral precipitation, e.g. by metabolite production, by changing the physico-chemical environmental conditions around the biomass, and also by the indirect release of metal-precipitating substances from other activities, such as production of phosphate from organic decomposition or phosphate mineral solubilization by stromatolites. Stromatolites were very abundant on the earth in Precambrian times.  The Precambrian stromatolitic phosphorites of Rajasthan, Tamil Nadu and Uttarakhand are examples of biochemically precipitated phosphates.  The earliest stromatolite of confirmed microbial origin dates to 2.724 billion years ago.

Many microbes can attack silicates, thus playing a role in the leaching of silica (leading to the residual concentration of other constituents), genesis of clay minerals, and in soil and sediment formation. Microbe–clay mineral interactions are also important in soil evolution.

Many different metallic minerals form as a direct or indirect result of microbial activity.  Examples include various carbonates, phosphates, oxides and sulfides.  Microbial cell walls, outer layers, and exopolymers can sorb, bind or entrap many soluble and insoluble metal species as well as clay minerals, colloids, oxides, etc. which also have significant metal-sorption properties. Redox transformations are also widespread in microbial metabolism.

Manganese-oxidizing and -reducing bacteria play an important role in the manganese cycle in freshwater and marine environments.  manganese-reducing microbes may mobilize oxidized or fixed manganese, releasing it into the aqueous phase.  Manganese-oxidizing bacteria may form oxideswhich may be deposited as concretions formed around sediment grains, pebbles, mollusc shells, coral fragments, or other debris.  Manganese oxide phases have high sorption capacities for numerous metal cations (e.g. Ni, Zn, Cu, Co, Mn, Pb and Cd), and also serve as strong oxidants for inorganic [e.g. As(III) to As(V); Cr(III) to Cr(IV)] and organic compounds such as humic substances

Microbial reduction of manganese oxides may also lead to the formation of manganous carbonate. Ferromanganese nodules on parts of the ocean floor are inhabited by manganese-oxidizing and -reducing bacteria, and these are likely to contribute to nodule formation. 

Many bacteria can precipitate and deposit Fe(III) oxides and hydroxides (e.g. FeOOH, Fe3O4) around their cells by enzymic, e.g. Gallionella sp., and non-enzymic processes, e.g. Leptothrix sp.

Most non-ferrous sulfides are formed abiotically but some sedimentary deposits are of biogenic origin. Sulfate reducing bacteria play an important role in some sedimentary environments promoting the formation of certain sulfide minerals, especially iron pyrite (FeS2).  Microbial sulfide deposits result from the generation of H2S, usually from bacterial reduction of sulfate.

Examples of important groups of microbes directly involved in geochemical transformations include iron-oxidizing and -reducing bacteria, manganese-oxidizing and -reducing bacteria, sulfate-reducing bacteria, sulfur-oxidizing and -reducing bacteria, and many other prokaryotes (organisms made up of cells that lack a cell nucleus or any membrane-encased organelles) and eukaryotes (organisms made up of cells that possess a membrane-bound nucleus) that can form or degrade silicates, carbonates, phosphates and other minerals.


Biochemical deposits are created when organisms use materials dissolved in air or water to build their tissue. Examples include:

  • Most types of limestone are formed from the calcareous skeletons of organisms such as corals, mollusks, and foraminifera.
  • Coal which forms as plants remove carbon from the atmosphere and combine with other elements to build their tissue.
  • Deposits of chert formed from the accumulation of siliceous skeletons from microscopic organisms such as radiolaria and diatoms.

Some biochemical processes, like the activity of bacteria, can affect minerals in a rock and are therefore seen as part of diagenesis. Fungi and plants (by their roots) and various other organisms that live beneath the surface can also influence diagenesis.

Burial of rocks due to ongoing sedimentation leads to increased pressure and temperature, which stimulates certain chemical reactions. An example is the reactions by which organic material becomes lignite or coal. When temperature and pressure increase still further, the realm of diagenesis makes way for metamorphism, the process that forms metamorphic rock.

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