Biogeotechnology and environment

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Biogeotechnology and environment
Tomsk Polytechnic University

• Maxim P. Chubik, Ph.D
• Geoecology and Geochemistry Department

Tomsk, 2008
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Plan

• Definitions of biogeotechnology
• Bioleaching
• Bioleaching of ore tailings
• Bioremediation and phytoremediation
• Oil contamination and pathogenic bacteria

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Key words

• microorganisms
• ores
• tailings
• plants
• pollutants
• environment
• soil biota
• oil contamination
• pathogenic effect
• soil-borne infections
• epidemiological situation

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• Biogeotechnology means any technological
  application that uses living organisms to solve
  geological problems

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• Biogeotechnology is applied biotechnology focuses
  on using plants and human-made structures to
  control erosion, protect slopes, and restore
  environmental quality

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• Biogeotechnology is an application of geochemical
  activity of microorganisms in the mining industry
• Microbial Geotechnology is a branch of
  geotechnical engineering that deals with the
  applications of microbiological methods to
  geological materials used in engineering

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Biogeotechnology is the modern multidisciplinary
integration of different sciences and engineering
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Main directions of biogeotechnology

• Bioleaching of metals
• Application of bacteria oxidize methane for
  decrease of methanic concentration in a coal seam
  and coal mines
• Removal a sulfur-containing compounds from coals
• The use of microorganisms for increase of
  secondary oil extraction

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There are even the conceptions
Biohydrometallurgy or Biomining. Bioleaching play
key role in these branches of geology and
biotechnology.
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• Bioleaching is a hydrometallurgical process where
  mobilization of metal takes place from solid
  phase to liquid through microbial activity
• Bioleaching is the extraction of specific metals
  from their ores through the use of microorganisms

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• These microorganisms actually gain energy by
  breaking down minerals into their constituent
  elements.
• Bioleaching by microorganisms takes place
  owing to destruction of a crystal lattice of
  minerals, composing solid. Microorganisms take
  elements necessary for feeding and construction
  of a cell from a crystal lattice.
• This shakes of a lattice are causes the
  destruction of a mineral.

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History

• Hydrometallurgical leaching of copper from ore
  and its precipitation from the resultant
  solutions with metallic iron is an ancient
  technology. The Chinese practiced a form of this
  technology as far back as 100 200 BC.
  Historical records indicate that copper ore
  leaching was also known in Europe and Asia, at
  least as far back as the second century.
• The Moors during their conquest of Spain appear
  to have instituted heap leaching at the Rio Tinto
  mines. By 1752, the Spanish had developed a
  process of copper leaching from partially roasted
  ore at Rio Tinto.
• The role that microorganisms play in this process
  was demonstrated only in 1947 when Colmer and
  Hinkle isolated from acid mine waters bacteria
  belonging to the Thiobacillus genus.
• In the early 1960s uranium mine operators found
  that the mine waters were acidic in nature and
  also contained soluble uranium.
  Thiobacillus ferrooxidans was also found to be
  present in these mine waters. This confirmed the
  active catalytic role of this iron oxidizer in
  solubilisation of uranium from the ores.
• In situ leaching was developed in the late 1960s
  in the Soviet Union.

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• Traditional extractions involve many
  expensive steps such as roasting and smelting,
  which require sufficient concentrations of
  elements in ores. However, low concentrations are
  not a problem for bacteria because they simply
  ignore the waste which surrounds the metals.
• A bioleaching is the most acceptable manner
  of processing of ores since it does not require
  elaboration of mining complexes and allows
  increasing the source of raw materials along with
  providing integrated approach to metals
  extraction. In terms of economy and environmental
  protection, biotechnological methods are more
  sufficient than chemical methods used for
  processing of ores.

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The need for new biogeotechnological methods
arises from recent trends in the mining industry
due to

• Continued depletion of high grade mineral
  resources
• The resulting tendency for mining to be extended
  deeper underground
• The rising cost of high amount of energy required
  in the traditional methods
• The growing awareness of environmental problems

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Some advantages associated with bioleaching

• The use of naturally occurring key components
  microorganisms, water and air
• Simple to operate and maintain
• Low pressure and temperature process
• Capital costs are significantly lower than those
  of the traditional processes
• Environmental friendly process

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• Bioleaching is more eco-friendly than
  traditional extraction methods such as roasting
  and smelting.
• Less landscape damage occurs, since the
  bacteria involved grow naturally, and the mine
  and surrounding area can be left relatively
  untouched. As the bacteria breed in the
  conditions of the mine, they are easily
  cultivated and recycled.

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Some microorganisms are used in the bioleaching

• Acidithiobacillus ferrooxidans
• Acidithiobacillus thiooxidans
• Acidithiobacillus caldus
• Leptospirillum ferrooxidans
• Sulfobacillus thermosulfidooxidans
• Acidianus infernus
• Sulfolobus acidocaldarius
• Desulfovibrio desulfuricans
• Desulfobacter multivorans

• Desulfovibrio vulgaris
• Bacillus subtilis
• Pseudomonas putida
• Pseudomonas dechromaticans
• Aspergillus oryzae
• Aspergillus niger
• Penicillium simplicissimum
• Candida utilis
• Chlorella pyrenoidosa

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chemolithotrophic bacteria
Acidithiobacillus thiooxidans
Leptospirillum ferrooxidans
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heterotrophic bacteria
Bacillus subtilis
Pseudomonas putida
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fungi
Aspergillus niger
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water-plants
Chlorella pyrenoidosa
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Acidithiobacillus ferrooxidans formerly known as
Thiobacillus ferrooxidans

• The principal bacteria which play the most
  important role in solubilising sulfide minerals
  at moderate temperatures are species of the genus
  Acidithiobacillus. These are gram negative rods
  with rounded ends. Most species are mesophilic
  (having an ideal growth temperature of 20-45C)
  and acidophilic.
• Acidithiobacillus ferrooxidans is
  chemolithoautotrophs, which means that carbon
  dioxide is the only source of carbon and they
  derive their energy from chemical transformation
  of inorganic matter or ferrous iron available in
  the form of pyrite in ores.
• All Acidithiobacilli oxidize sulfur or sulfur
  compounds to sulphate or sulphuric acid.
  Acidithiobacillus ferrooxidans can oxidize
  hydrogen sulphide, thiosulphate or elemental
  sulphur.

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• Acidithiobacillus ferrooxidans catalyse the
  breakdown of the mineral arsenopyrite (FeAsS) by
  oxidising the sulfur and metal to higher
  oxidation states whilst reducing dioxygen by H2
  and Fe3.
• This allows the soluble products to dissolve
• FeAsS(s) ? Fe2(aq) As3(aq) S6(aq)

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• Bioleaching of metals can be carried out in
  stirred tanks or constructed heaps and dumps.
• There is In situ leaching. In this technique the
  ore is not moved from its geological setting with
  the advantage that excavating costs can be saved.

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• Usually exactly heap and dump leaching use for
  low-grade ores and ore tailings.
• In general ore mining and processing yearly
  produce billions of tons of mineral tailings,
  creating a disposal problem due to continued
  weathering and dissolution, and causing numerous
  health and environmental problems downstream from
  the point source pollution.

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Objective

• The objective for our research was investigation
  of the changes taking place in phosphorite
  tailings of Djeroy-Syrdaryan deposit, Uzbekistan,
  under influence of microorganisms because the
  attempt to cause phosphorites destruction by
  means of microorganisms in order to increase
  phosphorus in soluble fraction is a new and
  poorly studied direction.
• These tailings constitute an environmental
  problem that needs experimental data to support
  the development of management and control
  strategies.

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The assays of ore tailings and draining water
were investigated by the following methods of
analysis

• general
• chemical
• roentgenhgase
• analytical
• microbiological

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Three different groups of microorganisms were
obtained during microbiological analysis and they
were used for farther experiments

• native microflora (all microorganisms of ore
  tailings and draining water)
• Acidithiobacillus thioparus
• non-differentiated microorganisms growing on
  Belkanovskaya medium

Acidithiobacillus thioparus
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Three series of experiments were aimed at
definition of influence of defining groups of
bacteria in tailings and draining water

• Series 1. The study of ore automicroflora
  destruction effect
• The sample of ore tailings was overwhelmed
  Lualikova medium. In this series the leaching
  solution was sterile, and the sample of tailings
  was non-sterile. As control sample we used the
  sterile sample of tailings in a distilled water,
  cultured on Lualikova medium.
• Series 2. The investigation of effect of
  Acidithiobacillus thioparus
• The samples of ore tailings were overwhelmed
  Bayarink medium. As control sample we used the
  sterile sample of tailings in a distilled water,
  cultured on Bayarink medium. In the experimental
  and control variants of this series the leaching
  solution and the ore tailings were sterile.
• Series 3. The investigation of effect of
  non-differentiated microorganisms growing on
  Belkanovskaya medium
• The samples of the ore tailings was
  overwhelmed Belkanovskaya medium. As control
  sample we used the sterile sample of tailings in
  a distilled water, cultured on Belkanovskaya
  medium. In the experimental and control variants
  of this series the leaching solution and the ore
  were sterile.

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Composition of mediums (grams per litre)

• Lualikova medium (NH4)2SO4 0,5 KCl 0,05
  humic compounds of natural water 20.
• Bayarink medium Na2S2O3 5 NH4Cl 0,1 NaHCO3
  1 Na2HPO4 0,2 MgCl2 0,1.
• Belkanovskaya medium (NH4)2SO4 0,5 K2SO4
  0,1 NaCl 0,1 saccharose 15.
• We did not add soluble phosphates in the mediums
  since it was supposed, that a phosphoric feed
  will be realized owing to phosphates leached from
  the samples of ore tailings.

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• According to the analysis all series of the
  experiment have shown positive result for
  influence on tailings minerals structure. As a
  whole, the activity of microbial cultures stays
  the same, but significantly differs under the
  influence on minerals.

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Concentration of phosphorus in the liquid phase
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• In the near future we plan identification of the
  microorganisms growing on Belkanovskaya medium
  along with thorough study of such mechanisms and
  their role in obtaining microorganisms on the
  tailings.
• These microorganisms can find application in
  manufacture, since they show good leaching
  results do not require additional costs for
  alimentation and clearing of ore tailings.
• We also intend to choose a samples of other
  tailings for further research.

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• To sum up, the bioleaching of waste products
  represents economic gain. Besides, such approach
  will promote faster and effective contribution in
  natural geochemical circulation of a waste
  products obtained by enrichment of ore.
• Bioleaching is the most acceptable method of
  extraction and processing of ores or their
  tailings. However there are other fields in
  modern biogeotechnology solving problems are
  associated with the effects of extraction of
  mineral products.

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Phytoremediation is the use of living green
plants for reduction and removal of contaminants
from contaminated soil, water and sediments
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• Phytoremediation is an energy efficient method of
  remediating sites with low to moderate levels of
  contamination and it can be used in conjunction
  with other more traditional remedial methods as a
  finishing step to the remedial process.
• The plants absorb contaminants through the root
  system and store them in the root biomass or
  transport them up into the stems and leaves.
• A living plant may continue to absorb
  contaminants until it is harvested. After harvest
  a lower level of the contaminant will remain in
  the soil, so the growth and harvest cycle must
  usually be repeated through several crops to
  achieve a significant cleanup. After the process,
  the cleaned soil can support other vegetation.

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Phytoremediation advantages

• phytoremediation costs are much less than
  traditional processes
• plants can be easily monitored to ensure proper
  growth
• valuable metals can be reclaimed and reused
  through phytoremediation
• the least destructive method of remediation
  because it utilizes natural organisms
• preserves the natural state of the environment
• phytoremediation has the ability to clean old
  contaminated sites

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Phytoremediation disadvantages

• phytoremediation is confined to the area covered
  by the depths of the roots
• slower than traditional processes
• leeching of contaminants into groundwater cannot
  be fully prevented by plant based remediation
  systems
• danger of bioaccumulation of contaminants from
  primary to secondary consumers in the food chain

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Examples of phytoextraction from soils

• Arsenic, using the Sunflower or the Chinese Brake
  fern
• Cadmium and zinc, using Alpine pennycress
• Lead using Indian Mustard or Ragweed
• Uranium using Sunflowers
• Mercury, selenium and organic pollutants have
  been removed from soils by transgenic plants
  containing genes for bacterial enzymes

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• Although generally this process has been tried
  more often for extracting heavy metals than for
  organics.
• Problems with organic waste products to solve
  bioremediation technologies.

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Bioremediation is any process that uses
microorganisms to return the environment altered
by contaminants to its original condition
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• By definition, bioremediation is the use of
  living organisms to detoxify the environmental
  contaminants into less toxic forms. Contaminant
  compounds are transformed by living organisms
  through reactions that take place as a part of
  their metabolic processes. For bioremediation to
  be effective, microorganisms must enzymatically
  attack the pollutants and convert them to
  harmless products.
• The microorganisms may be indigenous to a
  contaminated area or they may be isolated from
  elsewhere and brought to the contaminated site.
• Most bioremediation systems are run under aerobic
  conditions, but running a system under anaerobic
  conditions may permit microbial organisms to
  degrade otherwise resistant molecules.

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• Bioremediation techniques are typically more
  economical than traditional methods such as
  incineration, and some pollutants can be treated
  on site, thus reducing exposure risks for
  clean-up personnel, or potentially wider exposure
  as a result of transportation accidents.
• Since bioremediation is based on natural
  attenuation the public considers it more
  acceptable than other technologies.
• Bioremediation is an option that offers the
  possibility to destroy or render harmless various
  contaminants using natural biological activity.
  As such, it uses relatively low-cost,
  low-technology techniques, which generally have a
  high public acceptance and can often be carried
  out on site.

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Like other technologies, bioremediation has
limitations

• Some contaminants, such as chlorinated organic or
  high aromatic hydrocarbons, are resistant to
  microbial attack.
• Contaminants are degraded either slowly or not at
  all, hence it is not easy to predict the rates of
  clean-up for a bioremediation exercise.
• There are no rules to predict if a contaminant
  can be degraded.

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Some contaminants potentially suitable for
bioremediation
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• The control and optimization of bioremediation
  and phytoremediation processes is a complex
  system of many factors.
• Besides contamination of soils with organic
  compounds is a problem often associated with the
  processing and distribution of crude and refined
  petroleum hydrocarbons.

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The influence of oil contamination on a soil
pathogenic microbiota
The view of oil-contaminated site in Western
Siberia
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Some byproducts of petroleum extraction and
manufacturing

• bitumen
• gasoline
• kerosene
• mining brine solutions

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The soil biota includes

• Megafauna size range 20 mm upwards, e.g. moles,
  rabbits, and rodents.
• Macrofauna size range 2-20 mm, e.g. woodlice,
  spiders, earthworms, beetles, centipedes, slugs,
  snails, ants.
• Mesofauna size range 100 micrometre-2 mm, e.g.
  tardigrades, mites and springtails.
• Microfauna and Microflora size range 1-100
  micrometres, e.g. yeasts, bacteria, fungi,
  protozoa, roundworms.

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Among these organisms, bacteria play key roles in
maintaining a life of soil

• Every gram of soil contains at least a million of
  these tiny one-celled organisms. These microbes
  are able to perform an extremely wide range of
  chemical transformations.
• Some species of bacteria are able to degrade
  pollutants while other species, particularly
  bluegreen algae, are able to fix nitrogen.
• In general, bacteria are the organisms that are
  mainly responsible for transforming inorganic
  constituents from one chemical form to another.

A soil particle with microorganisms
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• Many soil-dwelling bacteria are pests, often
  causing diseases of plants, animals and human.
• Soil-borne infections such as a tetanus,
  listeriosis and anaerobic gas infection or, less
  dangerous, dysentery and pseudotuberculosis may
  cause serious systemic diseases, often in
  individuals with impaired immunity.

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Soil-borne diseases of public health importance

• Protozoa
• Naegleria, acanthamoeba, cyclospora,
  cryptosporidia
• Fungi
• Histoplasmosis, coccidioidomycosisblastomycosi
  s, chromoblastomycosis, sporotrichosis
• Roundworms
• Hookworm, CLM, VLM, strongyloidiasis,
  baylisascariasis
• Bacteria
• Tetanus, melioidosis, leptospirosis,
  listeriosis, staphylococcal scalded skin syndrome

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• A microbiota of contaminated soil can alter a
  different characteristics, including virulence,
  after contact with pollutants. For instance,
  pathogens reserving in a soil may be modifed
  after contact with crude oil.
• Also a virulence and other characteristics of
  pathogenic bacteria can be changed after
  finishing of bioremediation and phytoremediation
  process.

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Our goals

• To use the microbiological framework to study the
  invasion, persistence, variability and other
  biological, physiological and biochemical
  characteristics of pathogenic microorganisms in a
  changing soil.
• To analyse the role of anthropogenic oil
  contamination in dynamics of development of
  epidemiological diseases.

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• We are conducting this examination in the lab
  conditions on the test-tubes with bacterial
  culture and various concentrations of crude oil,
  since in the initial stage of our research we are
  trying to determine which parameters of soil
  microbes are being changed under the influence of
  this type of pollutant.

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Our main goal

• The formation of system for prognostication of
  epidemiological situation in areas with high
  level of anthropogenic soil contamination and in
  the contaminated territories have been returned
  to its original condition as a result of the
  bioremediation or phytoremediation measures

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Staphylococcus aureus

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Staphylococcus aureus is a Gram-positive
spherical bacteria, which appears as grape-like
clusters when viewed through a microscope and has
large, round, golden-yellow colonies, when grown
on agar.

aureus means "golden" in Latin
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• Staphylococcus aureus, the most common cause of
  staph infections such as boils, abscesses,
  pneumonia and sepsis.
• As a rule, spread of Staphylococcus aureus is
  through human-to-human contact, but environmental
  bacterial contamination (including soil
  contamination), also play enough important role.
• The choice of this bacterial species is
  associated with the presence of the many apparent
  pathogenic features in staphylococcus.

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Pathogenic features of Staphylococcus aureus

• surface proteins that promote colonization of
  host tissues (SEA-G, Staphylokinase)
• invasins that promote bacterial spread in tissues
  (leukocidin, hyaluronidase)
• surface factors that inhibit phagocytic
  engulfment (Protein A)
• biochemical properties that enhance their
  survival in phagocytes (catalase production)
• immunological disguises (Protein A, coagulase,
  clotting factor)
• membrane-damaging toxins that lyse cell membranes
  (hemolysins, leukotoxin, ß-toxin)

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The volume of liquid phase of rabbit plasma after
collective incubation with bacterial culture of
S. aureus which have been cultivated with
different concentrations of crude oil (Coagulase
Test)
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• In the near future we plan to use an artificial
  soil model for detail examination parameters of
  soil microbes.
• We also intend to analyse the reaction of soil
  pathogenic microbiota with various oil byproducts.

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Conclusions

• The mining industry is constantly seeking new and
  more practical and environmental friendly
  technologies. Therefore biogeotechnology occupies
  an increasingly important place among the
  available mining technologies. Today it is no
  longer a promising technology but the actual
  alternative for solving various mining and
  geological problems.
• The biogeotechnology has obvious environmental
  and medical applications.

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