Environmental microbiology object of study and applications

Alexander Pearson

The environmental microbiology is the science that studies the diversity and function of microorganisms in their natural environments and the applications of their metabolic capacities in bioremediation processes of contaminated soils and waters. It is usually divided into the disciplines of: microbial ecology, geomicrobiology and bioremediation.

Microbiology (mikros: small, bios: lifetime, logos: study), studies in an interdisciplinary way a wide and diverse group of microscopic unicellular organisms (from 1 to 30 µm), visible only through the optical microscope (invisible to the human eye).

Figure 1. On the left: optical microscope, an instrument that allows micro-organisms to be viewed under magnification (Source: https://pxhere.com/es/photo/1192464). Right: electron micrograph of widely distributed naturally occurring bacteria of the genus Pseudomonas (By: CDC, Courtesy: Public Health Image Library).

Organisms grouped together in the field of microbiology are dissimilar in many important respects and belong to very different taxonomic categories. They exist as isolated or associated cells and can be:

  • Major prokaryotes (unicellular organisms without a defined nucleus), such as eubacteria and archaebacteria.
  • Simple eukaryotes (single-celled organisms with defined nuclei), such as yeasts, filamentous fungi, microalgae, and protozoa.
  • Viruses (which are not cellular, but are microscopic).

Microorganisms are capable of carrying out all their vital processes (growth, metabolism, energy generation and reproduction), independently of other cells of the same or different class.

Article index

  • 1 Relevant microbial characteristics
    • 1.1 Interaction with the external environment
    • 1.2 Metabolism
    • 1.3 Adaptation to very diverse environments
    • 1.4 Extreme environments
    • 1.5 Extremophilic microorganisms
  • 2 Molecular biology applied to environmental microbiology
    • 2.1 Isolation and microbial culture
    • 2.2 Molecular biology tools
  • 3 Areas of study of environmental microbiology
    • 3.1 -Microbial ecology
    • 3.2 -Geomicrobiology
    • 3.3 -Bioremediation
  • 4 Applications of environmental microbiology
  • 5 References

Relevant microbial characteristics

Interaction with the external environment

Free-living unicellular organisms are particularly exposed to the external environment. In addition, they have both a very small cell size (which affects their morphology and metabolic flexibility), and a high surface / volume ratio, which generates extensive interactions with their environment..

Due to this, both microbial survival and ecological distribution depend on their capacity for physiological adaptation to frequent environmental variations..


The high surface / volume ratio generates high microbial metabolic rates. This is related to its rapid rate of growth and cell division. In addition, there is a wide microbial metabolic diversity in nature..

Microorganisms can be considered chemical machines, which transform various substances both inside and outside. This is due to its enzymatic activity, which accelerates rates of specific chemical reactions..

Adaptation to very diverse environments

In general, the microbial microhabitat is dynamic and heterogeneous with respect to the type and quantity of nutrients present, as well as their physicochemical conditions..

There are microbial ecosystems:

  • Terrestrial (on rocks and soil).
  • Aquatic (in oceans, ponds, lakes, rivers, hot springs, aquifers).
  • Associated with higher organisms (plants and animals).

Extreme environments

Microorganisms are found in virtually every environment on planet Earth, familiar or not to higher life forms.

Environments with extreme conditions with respect to temperature, salinity, pH and water availability (among other resources), present "Extremophilic" microorganisms. These tend to be mostly archaea (or archaebacteria), which form a primary biological domain differentiated from that of Bacteria and Eukarya, called Archaea..

Figure 2. Habitats of the Extremophilic microorganisms. Left: Hot spring in Yellowstone National Park, where thermophilic microorganisms have been studied (Source: Jim Peaco, National Park Service [Public domain], via Wikimedia Commons). Right: Antarctica, a place where psychrophilic microorganisms have been studied (Source: pxhere.com).

Extremophilic microorganisms

Among the wide variety of Extremophilic microorganisms, there are:

  • Thermophiles: showing optimal growth at temperatures above 40 ° C (inhabitants of thermal springs).
  • Psychrophiles: optimal growth at temperatures below 20 ° C (inhabitants of places with ice).
  • Acidophilic: of optimal growth under conditions of low pH, close to 2 (acidic). Present in acidic hot springs and underwater volcanic crevices.
  • Halophiles: requiring high concentrations of salt (NaCl) to grow (as in brines).
  • Xerophiles: able to withstand drought, that is, low water activity (inhabitants of deserts such as Atacama in Chile).

Molecular biology applied to environmental microbiology

Microbial isolation and culture

To study the general characteristics and metabolic capacities of a microorganism, it must be: isolated from its natural environment and kept in pure culture (free of other microorganisms) in the laboratory.

Figure 3. Microbial isolation in the laboratory. Left: filamentous fungi growing on solid culture medium (Source: https://www.maxpixel.net/Strains-Growing-Cultures-Mold-Petri-Dishes-2035457). Right: isolation of a bacterial strain by the depletion seeding technique (Source: Drhx [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], from Wikimedia Commons).

Only 1% of the microorganisms existing in nature have been isolated and cultivated in the laboratory. This is due to the lack of knowledge of their specific nutritional requirements and the difficulty of simulating the vast variety of existing environmental conditions..

Molecular Biology Tools

The application of molecular biology techniques to the field of microbial ecology has made it possible to explore the existing microbial biodiversity, without the need for its isolation and cultivation in the laboratory. It has even made it possible to identify microorganisms in their natural microhabitats, that is,, in situ.

This is particularly important in the study of Extremophilic microorganisms, whose optimal growth conditions are complex to simulate in the laboratory..

On the other hand, recombinant DNA technology with the use of genetically modified microorganisms has allowed the elimination of polluting substances from the environment in bioremediation processes..

Study areas of environmental microbiology

As initially indicated, the different areas of study of environmental microbiology include the disciplines of microbial ecology, geomicrobiology, and bioremediation..

-Microbial ecology

Microbial ecology fuses microbiology with ecological theory, through the study of the diversity of microbial functional roles in their natural environment.

Microorganisms represent the largest biomass on planet Earth, so it is not surprising that their ecological functions or roles affect the ecological history of ecosystems..

An example of this influence is the appearance of aerobic life forms thanks to the accumulation of oxygen (Otwo) in the primitive atmosphere, generated by the photosynthetic activity of cyanobacteria.

Research fields of microbial ecology

Microbial ecology is transversal to all the other disciplines of microbiology, and studies:

  • Microbial diversity and its evolutionary history.
  • Interactions between microorganisms in a population and between populations in a community.
  • Interactions between microorganisms and plants.
  • Phytopathogens (bacterial, fungal and viral).
  • Interactions between microorganisms and animals.
  • Microbial communities, their composition and succession processes.
  • Microbial adaptations to environmental conditions.
  • The types of microbial habitats (atmosphere-ecosphere, hydro-ecosphere, litho-ecosphere and extreme habitats).


Geomicrobiology studies the microbial activities that affect terrestrial geological and geochemical processes (biogeochemical cycles).

These occur in the atmosphere, hydrosphere and geosphere, specifically in environments such as recent sediments, bodies of groundwater in contact with sedimentary and igneous rocks, and in the weathered earth's crust..

It specializes in microorganisms that interact with minerals in their environment, dissolving, transforming, precipitating them, among others..

Geomicrobiology research fields

Geomicrobiology studies:

  • Microbial interactions with geological processes (soil formation, rock breakdown, synthesis and degradation of minerals and fossil fuels).
  • The formation of minerals of microbial origin, either by precipitation or by dissolution in the ecosystem (for example, in aquifers).
  • Microbial intervention in biogeochemical cycles of the geosphere.
  • Microbial interactions that form unwanted clumps of microorganisms on a surface (biofouling). These biofouling can cause deterioration of the surfaces they inhabit. For example, they can corrode metal surfaces (bio-corrosion).
  • Fossil evidence of interactions between microorganisms and minerals from their primitive environment.

For example, stromatolites are stratified fossil mineral structures from shallow waters. They are made up of carbonates, coming from the walls of primitive cyanobacteria.

Figure 4. On the left: fossil stromatolites in shallow waters (Left photo source: https://es.wikipedia.org/wiki/Archivo:StromatolitheAustralie2.jpeg). Right: detail of the stromatolites (Right photo source: https://es.m.wikipedia.org/wiki/Archivo:StromatoliteUL02.JPG).


Bioremediation studies the application of biological agents (microorganisms and / or their enzymes and plants), in processes of recovery of soils and water contaminated with substances dangerous to human health and the environment..

Figure 5. Oil contamination in the Ecuadorian Amazon rainforest. Source: Ecuadorian Chancellery [CC BY-SA 2.0 (https://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

Many of the environmental problems that currently exist can be solved with the use of the microbial component of the global ecosystem..

Bioremediation research fields

Bioremediation studies:

  • The microbial metabolic capacities applicable in environmental sanitation processes.
  • Microbial interactions with inorganic and xenobiotic pollutants (toxic synthetic products, not generated by natural biosynthetic processes). Among the most studied xenobiotic compounds are halocarbons, nitroaromatics, polychlorinated biphenyls, dioxins, alkylbenzyl sulfonates, petroleum hydrocarbons and pesticides. Among the most studied inorganic elements are heavy metals.
  • The biodegradability of environmental pollutants in situ and in laboratory.

Applications of environmental microbiology

Among the many applications of this vast science, we can cite:

  • The discovery of new microbial metabolic pathways with potential applications in commercial value processes.
  • Reconstruction of microbial phylogenetic relationships.
  • Analysis of aquifers and public drinking water supplies.
  • Dissolution or leaching (bioleaching) of metals in the medium, for their recovery.
  • Biohydrometallurgy or biomining of heavy metals, in bioremediation processes of contaminated areas.
  • Biocontrol of microorganisms involved in the biocorrosion of radioactive waste containers dissolved in underground aquifers.
  • Reconstruction of primitive terrestrial history, the palaeoenvironment and primal life forms.
  • Construction of useful models in the search for fossilized life on other planets, such as Mars.
  • Sanitation of areas contaminated with xenobiotic or inorganic substances, such as heavy metals.


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  3. McKinney, R. E. (2004). Environmental Pollution Control Microbiology. M. Dekker. pp 453.
  4. Prescott, L. M. (2002). Microbiology. Fifth edition, McGraw-Hill Science / Engineering / Math. pp 1147.
  5. Van den Burg, B. (2003). Extremophiles as a source for novel enzymes. Current Opinion in Microbiology, 6 (3), 213-218. doi: 10.1016 / s1369-5274 (03) 00060-2.
  6. Wilson, S. C., and Jones, K. C. (1993). Bioremediation of soil contaminated with polynuclear aromatic hydrocarbons (PAHs): A review. Environmental Pollution, 81 (3), 229-249. doi: 10.1016 / 0269-7491 (93) 90206-4.

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