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BIOMINING - One of the marvels of Biotechnology of present

day for environment-friendly mining and mineral processing

By: Partha Das Sharma

Biohydrometallurgy can be defined as the field of applications resulting from the control
of natural (biochemical) processes of interactions between microbes and minerals to
recover valuable metals. Many biotechnology-derived processes use microorganisms to
help ease the usage of harmful chemicals in various industrial processes. The mining
industry uses microorganisms and their natural ability to digest, absorb, and change the
quality of different chemicals and metals, to refine ores. Microorganisms have been
introduced to various areas of the mining industry with phenomenal success. Advances in
biotechnology have permitted the extraction of metals from low-grade ores, improved
recovery rates at operations, and reduced operating costs.

Biomining is an application of biotechnology in recovery of various minerals from ore.
Biomining is defined as extracting mineral ores or enhancing the mineral recovery from
mines using microorganisms instead of traditional mining methods. Copper was the first
metal extracted using microorganisms in the ancient past in the Mediterranean region.
Biomining is becoming popular because it is cheap, reliable, efficient, safe, and
environmentally friendly, unlike traditional mining methods. The efficiency of bio-
mining can be increased either by finding suitable strains of microorganisms or by
genetically modifying existing microorganisms, made possible due to rapid advances in
the field of biotechnology and microbiology. Ores of high quality are rapidly being
depleted and biomining allows environmentally friendly ways of extracting metals from
low-grade ores (ores that have small amounts of valuable metals scattered throughout).

Biomining includes two different chemical processes called bioleaching and

biooxidation. Thus, biomining is an application of biotechnology and is also known as
microbial leaching or alternately, biooxidation.

There are different types of bacteria present in nature that oxidize metal sulfides and
solubilize minerals, thus, helping in their extraction from the ores. It is very important
to select suitable microorganisms to ensure the success of biomining, a process which
requires knowledge of properties of microorganisms, both physiological and biochemical.
Bacteria are found to be the most suitable microorganisms that can be used for extraction
of metals in bio-mining.

Characteristics of the bacteria used in bio-mining:

a. Mineral extraction involves the production of high temperatures so the bacteria should
be able to survive the heat, hence, they should be thermophilic.
b. Bio-mining involves using strong acids and alkalis, hence, bacteria should be
c. Bacteria should produce energy from inorganic compounds, hence, should also be
autotrophic (characteristic of an organism capable of making nutritive organic molecules
from inorganic sources via photosynthesis i.e., involving light energy or chemosynthesis
i.e., involving chemical energy).
d. The bacteria should be able to adhere to the solid surfaces or have the ability to form

Identification of Bacteria Useful for Biomining Operations

There are wide varieties of bacteria with varying capabilities existing on earth, Therefore,
it is essential to identify precisely the types that can perform biooxidation/bioleaching
effectively. Thiobacillus ferrooxidans is a chemophilic, moderately thermophilic
bacteria which can produce energy from oxidation of inorganic compounds like sulfur
and iron. It is the most commonly used bacteria in biomining.

Several other bacteria such as T.thioxidans, Thermothrix thiopara, Sulfolobus

acidocaldarius and S. brierleyi are also widely used to extract various minerals.

Thermothrix thiopara is an extremely thermophilic bacteria that can survive very high
temperatures between 60-75C and is used in extraction of sulfur.
Techniques like genetic engineering and conjugation are used to produce bacteria with
desired characteristics to increase the rate of biooxidation thus increasing the mineral
yield through biomining. It is also important to identify biomining bacteria present in
colonies of other bacteria. Techniques developed for this purpose include: (a)
Immunoflourescence, (b) Dot immunoassay, and (c) Dot-blot hybridization.

(a) Immunofluorescence - This technique is generally used to identify specific

antibodies or antigens present in biological fluids. Fluorescent antibodies are used to
identify biomining bacteria.

(b) Dot Immunoassay - This technique is used to identify ore-adhering bacteria like
T.ferrooxidans and T.thiooxidans. The bacteria are applied in the form of dots on a
nitrocellulose film. Antigen-antibody reaction is carried out on the film and then treated
with a secondary antibody to make the reaction visible by producing a color. The sample
can be approximated by comparison of the test sample with that of a known sample.

(c) Dot-blot Hybridization- This is a DNA based technique to identify biomining bacteria
such as T.ferrooxidans. The bacteria are isolated from samples of ores and soil treated
with sodium dodecyl sulfate (SDS). The cells are disrupted to extract DNA and the
extracted DNA is then purified. The DNA obtained from ore sample is fixed on
nitrocellulose membrane using southern blotting technique. Genetic probes are used to
identify and distinguish various biomining bacteria used in this procedure. The DNA
fragments on the membrane are treated with standard probes.

Minerals are recovered from ores by the microorganisms mainly by two mechanisms: (a)
Oxidation and (b) Reduction.

(a) Oxidation
The microorganisms like T.ferroxidans and T.thioxidans are used to release iron and
sulfur respectively. T.ferroxidans oxidize ferrous ion to ferric ion.

4Fe++ + O2 + 4H+ → Fe+++ + 2H2O

The bacteria attach to the surface of the ore and oxidize by a direct and indirect method.
Direct Method -
In this method the ore is oxidized by the microorganisms due to the direct contact with
the compound.
2FeS2 + 7O2 + 2H2O → 2FeSO4 + 2H2SO4
Indirect Method -
In this method the mineral is indirectly oxidized by an agent that is produced by direct
oxidation. For example, the ferric ion produced by the above reaction is a powerful
oxidizing agent and can release sulfur from the metal sulfides. Thus production of ferric

ion indirectly causes oxidation of metal sulfide resulting in the breaking of the crystal
lattice of the heavy metal sulfide and separating the heavy metal and sulfur.
CuS + Fe+++ → Cu+ + S + Fe++

(b) Reduction -
Bacteria like Desulfovibro desulfuricans play an active role in reduction of sulfates which
results in the formation of hydrogen sulfides.
4H2 + H2SO4 → H2S + 4H2O

1. Stirred Tank Biomining - This method is used for leaching from substrates with high
mineral concentration. Since the method is expensive and time consuming, substrates
with lower concentration are not used for leaching. Copper and refractory gold ores are
well suited for this type of method. Special types of stirred tank bioreactors lined with
rubber or corrosion resistant steel and insulated with cooling pipes or cooling jackets are
used for this purpose.

Thiobacillus is the commonly used bacteria. Since it is aerobic the bioreactor is provided
with an abundant supply of oxygen throughout the process provided by aerators, pumps
and blowers. This is a multi-step process consisting of large numbers of bioreactors
connected to each other. The substrate moves from one reactor to another and in the final
stage it is washed with water and treated with a variety of chemicals to recover the

The name is fairly self-explanatory, as the process requires constructing large aerated
tanks that are generally arranged in a series, so that runoff from one tank serves as raw
material for the next. In this way, the reactor can operate in continuous flow mode, with
fresh ore being added to the first tank while the runoff from the final tank is removed and
treated. The ore to be processed is generally crushed to a very small particle size, to
ensure that the solids remain suspended in the liquid medium. Mineral nutrients in the
form of (NH4)2SO4 and KH2PO4 are also added to the tanks to ensure maximal microbial
density is maintained.

Due to the extremely high cost of stirred tank reactors, they are only used for highly
valuable materials. For gold extraction for example, this technique is usually used when
the ore body contains high concentrations of arsenopyrite (AsFeS).

2. Bioheaps - Bioheaps are large amounts of low grade ore and effluents from extraction
processes that contain trace amounts of minerals. Such effluents are usually stacked in
large open space heaps and treated with microorganisms to extract the minerals. Bioheaps
are also called biopiles, biomounds and biocells. They are also used for biodegradation of
petroleum and chemical wastes. The low grade ores like refractory sulfide gold ore and
chalocite ore (copper) are crushed first to reduce the size then treated with acid to
promote growth and multiplication of chemophilic bacteria. The crushed and acid-treated
ore is then agglomerated so that the finer particles get attached to the coarser ones, and
then treated with water or other effluent liquid. This is done to optimize moisture content
in the ore bacteria that is inoculated along with the liquid. The ore is then stacked in large
heaps of 2-10 feet high with aerating tubes to provide air supply to the bacteria thus
promoting biooxidation.

Advantages of using bioheaps are that they are: (a) cost effective, (b) of simple design
and easy to implement, and (c) very effective in extracting from low concentration ores.

Disadvantages of using bioheaps are that they: (a) are time consuming (takes about 6-24
months), (b) have a very low yield of mineral, require a large open area for treatment,
have no process control, (c) are at high risk of contamination, and (d) have inconsistent
yields because bacteria may not grow uniformly in the heap.

3. In-situ Bioleaching - In this method the mineral is extracted directly from the mine
instead of collecting the ore and transferring to an extracting facility away from the site
of the mine. In-situ bio-mining is usually done to extract trace amounts of minerals
present in the ores after a conventional extraction process is completed. The mine is
blasted to reduce the ore size and to increase permeability and is then treated with water
and acid solution with bacterial inoculum. Air supply is provided using pipes or shafts.
Biooxidation takes place in-situ due to growing bacteria and results in the extraction of
mineral from the ore.


Success of biomining and efficiency in recovery of minerals depends on various factors

some of which are discussed below.

(a) Choice of Bacteria - This is the most important factor that determines the success of
bioleaching. Suitable bacteria that can survive at high temperatures, acid concentrations,
high concentrations of heavy metals, remaining active under such circumstances, are to
be selected to ensure successful bioleaching.

(b) Crystal Lattice Energy - This determines the mechanical stability and degree of
solubility of the sulfides. The sulfide ores with lower crystal lattice energy have higher
solubility, hence, are easily extracted into solution by the action of bacteria.

(c) Surface Area - Rate of oxidation by the bacteria depends on the particle size of the
ore. The rate increases with reduction in size of the ore and vice-versa.

(d) Ore Composition - Composition of ore such as concentration of sulfides, amount of

mineral present, and the extent of contamination, has direct effect on the rate of bio-

(e) Acidity - Biooxidation requires a pH of 2.5-3 for maximum results. The rate of
biooxidation decreases significantly if the Ph is not in this range since the activity of
acidophilic bacteria is reduced.

(f) Temperature - The bacteria used in biomining are either mesophilic or thermophilic.
Optimum temperature is required for biooxidation to proceed at a fast rate. Optimum
temperature range for a given bacteria is between 25-35° C depending on the type of ore
being selected. The rate of biooxidation is reduced significantly if the temperature is
above or below the optimum temperature.

(g) Aeration - The bacteria used in biomining are aerobic thus require an abundant supply
of oxygen for survival and growth. Oxygen can be provided by aerators and pipes.
Mechanical agitation is also an effective method to provide continuous air supply
uniformly and also to mix the contents.

(h) Solid-liquid Ratio - The ratio of ore/sulfide to the leach solution (water + acid
solution + bacteria inoculum) should be maintained at optimum level to ensure that
biooxidation proceeds at maximum speed. The leach solution containing leached
minerals should be removed periodically and replaced with new solution.

(i) Surfactants - Adding small amounts of surfactants like Tween 20 to the leaching
process increases the rate of biooxidation of minerals from sulfide ores. The surfactants
decrease the surface tension of the leach solution, thus, wetting the ore and resulting in
increased bacterial contact which ultimately increases the rate of biooxidation.


(a) Biomining of Copper - Copper was the first metal extracted by bioleaching. It is the
metal most commonly extracted from oxide ores by this method. In the United States,
alone, about 11% of copper is produced from low grade ores by bioleaching technique
every year. Copper is available in mines across the world in more than 350 types of ores,
but it is mainly present along with sulfur. Copper from low-grade ores like copper sulfide
minerals is most commonly extracted by biooxidation since it is not economically viable
to use conventional metallurgical techniques.

(b) Biomining of Gold - Biooxidation of refractory gold ores to extract gold is carried
out by a commercial procedure called BIOX developed by GENCOR S.A Ltd
Johannesburg South Africa in an effort to replace existing procedures which posed severe
pollution problems. The BIOX process had several advantages over existing procedures
including lower cost.

(c) Microbially Enhanced Oil Recovery (MEOR) - Recent technological developments

have helped to make possible the recovery of oil. Using microorganisms is one such
technique to improve the recovery process hence called “microbially enhanced oil
recovery” (MEOR). It was discovered in 1926 that microorganisms can be used in the
petroleum industry to enhance oil recovery, but the concept became popular only after the
1950s. Microbes can enhance the recovery of petroleum products directly or indirectly.


Although mining is one of humankind's oldest activities, the techniques used to extract
minerals haven't changed substantially for centuries. Ores are dug from the earth,
crushed, then minerals such as copper and gold are extracted by extreme heat or toxic
chemicals. The environmental and health effects of traditional mining technologies have
been deleterious.

In the past few years, the mining industry has been turning to a more efficient and
environmentally salubrious method for extracting minerals from ores: microorganisms

that leach them out. Using a bacterium such as Thiobacillus ferooxidans to leach copper
from mine tailings has improved recovery rates and reduced operating costs. Moreover, it
permits extraction from low grade ores - an important consideration in the face of the
depletion of high grade ores.

Thiobacillus ferooxidans, which is naturally present in certain sulfur-containing

materials, gets energy by oxidizing inorganic materials, such as copper sulfide minerals.
This process releases acid and an oxidizing solution of ferric ions, which can wash out
metals from crude ore. Poor quality copper ore, which is bound up in a sulfide matrix, is
dumped outside a mine and treated with sulfuric acid to encourage the growth of T.
ferooxidans. As the bacteria chew up the ore, copper is released and collected in solution.
The sulfuric acid is recycled.

Currently 25% of all copper worldwide, worth more than $1 billion annually, is produced
through bioprocessing. This ranks it as one of the most important applications of
biotechnology today. Bioprocessing is also being used to economically extract gold from
very low grade, sulfidic gold ores, once thought to be worthless.

To increase the efficiency of biomining, the search is on for bacterial strains that are
better suited to large-scale operations. Bioprocessing releases a great deal of heat, and
this can slow down or kill the bacteria currently being used. Researchers are turning to
heat-loving thermophilic bacteria found in hot springs and around oceanic vents to solve
this problem. These bacteria thrive in temperatures up to 100 degrees Celsius or higher
and could function in a high temperature oxidative environment.

Another effort is underway to find - or genetically engineer - bacterial strains that can
stand up to heavy metals such as mercury, cadmium, and arsenic, which poison microbes
and slow the bioprocessing. Some microbes have enzymes that protect their basic
activities from heavy metals or pump them out. If genes that protect microbes from heavy
metals can be identified, resistant strains might be engineered. In any event, biomining is
now at the top of mining technology, and future development of the technology appears


Biomining is the sustainable, biotechnological process utilizing microorganisms to
remove metals from sulfide mineral ores and concentrates. The development of
biomining has progressed from poorly designed dumps to highly engineered heaps and
stirred tank reactors in an industrially important biotechnological process. The release of
metals from sulfide minerals is catalyzed by iron oxidizing acidophilic (optimum pH for
growth <3) microorganisms that act in consortia with heterotrophic and sulfur oxidizing
acidophiles in a mixed culture. The microorganisms catalyze metal release by
regenerating ferric iron that oxidizes the mineral sulfide bond to produce metals and
reduced inorganic sulfur compounds. The other microorganisms in the mixed culture may
oxidize the reduced inorganic sulfur compounds to sulfuric acid that is the source of the
acid in these environments.

Now, tremendous improvements in biomining are expected with continued research in
identifying bacterial strains better suited for individual applications and large-scale
operations as well as in the genetic engineering of bacterial strains that can stand up to
high temperature processes and heavy metals such as arsenic, mercury, or cadmium.
Biomining has become one of the premier mining technologies, and the future appears
bright. The potential applications of biotechnology to mining and processing are
countless. Some examples of past projects in biotechnology include a biologically
assisted in situ mining program, biodegradation methods, passive bioremediation of acid
rock drainage, and bioleaching of ores and concentrates. Research often results in
technology implementation for greater efficiency and productivity or novel solutions to
complex problems. Additional capabilities include the bioleaching of metals from sulfide
materials, phosphate ore bioprocessing, and the bioconcentration of metals from
solutions. One project recently under investigation is the use of biological methods for
the reduction of sulfur in coal-cleaning applications. From in situ-mining to mineral
processing and treatment technology, biotechnology provides innovative and cost-
effective industry solutions.




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