What is environmental microbiology?

Environmental biology deals with the study of microorganisms and their interaction with their surroundings. This term itself covers the microbial interactions with water, soil, air, and microbial too.

There is a vast scope of microbiology in various applied sciences such as environmental engineering. Microorganisms are widely used in increasing the quality of food and for the betterment of human beings. Microorganisms can degrade the complex living waste into compost. They can even degrade the pesticides used in agriculture to detoxify their poisonous nature. They can also neutralize the toxic effluent released from the industries.

Clinical microbiology is critical to understand coronavirus disease 2019 (COVID-19). The laboratories are studying the coronavirus globally. It will help in developing drugs and vaccines for this pathogen.

Some species of microorganisms can degrade petrol products so that they do not pollute the marine environment. They are of great importance in the bioleaching of ores. So, the study of environmental microbiology is of great importance.

Microorganism adaptation

Archaea are considered highly adapted to every environment as well as they could thrive well in extreme conditions. Therefore, they are known as extremophiles. 

But, as per the three-domain classification:

  • Bacteria
  • Archaea
  • Eukarya 

They show morphological and structural differences that help in distinguishing them based on phenotypic classification.

Microbiologists believed that the archaea were the type of microbes from which all other life has descended. It is widely accepted that they are the ancestors of eukaryotes due to their similarity to eukaryotes.

The microorganisms are highly adapted to the extreme environment, therefore known as extremophiles. These organisms can survive in acidic, alkaline, and harsh environments.

Microorganisms in water resource

Solid and liquid waste in large quantities causes environmental problems. The biogas is generated from such waste, and slurry is used as compost in agriculture. An alga "Spirulina" is rich in protein and cultivated by using human and animal excreta by the underdeveloped nations to fulfill the nutrient requirement of the population.

The waste from factories after treatment with microorganisms proved beneficial for irrigation purposes. It reduces waste along with maintaining a sustainable environment. Nowadays, research institutes are using garbage to produce electricity. The "hog" fuel which is generated by burning wood and bark mixture is a new fuel combustion technology used by the United States. The large size bioreactors which are made up of steel are used to produce hog fuel for generating electricity and the exhausted heat is used in the manufacturing operations as process steam.

Microorganisms in organic compost

For improving the growth of plants, compost is added, which is a mixture of decayed organic matter along with some manure. For compost formation, the residues of plants together with the dung of animals, especially the cattle, cows are left for a certain period. This mixture is covered with loose mud, this compost that consists of lignin, cellulose, pectin undergoes several chemical reactions under aerobic conditions to produce organic fertilizer.  The microbes include Penicillium, Trichoderma, Aspergillus species that improve the quality of the compost.

Vermicomposting is a procedure that also involves invertebrates such as earthworms for composting organic matter. The primary environmental microorganisms involved in vermicomposting along with earthworms are bacteria, actinomycetes, and fungi.

Microorganism involved in biogas production

To meet the increasing demand of the population, there is a need to encourage the installation of biogas plants to follow the sustainable use of resources. Anaerobic digestion utilizing microbial communities involves three steps:

  1. Solubilization
  2. Acidogenesis
  3. Methanogenesis

Among the three steps, the most important step is the last one "Methanogenesis"- Production of methane occurs with the help of methanotrophs include M. barkerii, M. bryantii, M. thermoautotrophicum, M. arboriphilus.

Microbial communities in sewage (wastewater treatment)

Sewage is the wastewater consisting of human excreta along with washed and used water. The bio-solids present in sewage water contains 95.5% water with 0.1 to 0.5% organic and inorganic materials. Sewage water has a rich microbial diversity consisting of fungi, bacteria, amoebae, nematodes, algae. The common bacteria are coliform (E.coli). The other pathogens are also present that can cause cholera, dysentery, polio, and typhoid fever.

1) Small scale sewage treatment

There are several methods involved:


This sewage treatment is carried out for domestic purposes in many homes. It is made up of concrete material with pores on the walls, and it remains open from the bottom for sludge collection in huge amounts. Due to a  large collection, a biofilm is formed over the upper surface, and it should be cleaned at regular intervals with strong acid. A dried bacterial culture can be added to this waste for better decomposition of sludge.

Septic tanks

These tanks are common in rural areas where public health services are not present. The tank is present below the ground level and water flows through the inlet pipes and moves out from outlet pipes to a collecting box that opens in the surrounding soil surface area. Through this process, the pathogen is not eliminated, this is because the drinking water supply is kept away from septic tanks.

The microbial diversity present in the tank is mainly anaerobic bacteria that decompose the organic materials into amino acids, glycerol, gases, fatty acids, etc.

2) Large scale sewage treatment

There are several methods involved:

1. Primary treatment

Through this method, 20-30% of organic waste can be removed in the particulate form.

2. Secondary treatment

This treatment is known as biological treatment or microbial degradation. This treatment removes pathogens and 90-95% of the biological oxygen demand (BOD). The microbiome present can be of aerobic or anaerobic nature.

a) Oxidation ponds- These ponds are habitats of algal blooms and coliforms. In this, the degradation is carried out by microbial community that includes Spirulina platensis, Chlorella pyrenoidosa, ellipsoids, etc.

b) Trickling filter- Anaerobic digestion takes place in this treatment that contains a bed with crushed stone, sand, gravel at the bottom of the tank. The organic waste slowly trickles over the rocks of this trickling filter. A revolving sprinkler is present that distributes the liquid over the rock surface. Continous sprinkling creates an environment saturated with oxygen. 

The slimy layer contains a microbial community of bacterial species that includes Beggiatoa alba, Achromobacter species, Pseudomonas, and Flavobacterium.

c) Activated sludge- This is an aerobic treatment where sewage is under the vigorous aeration that creates flocs. These flocs are passed to the settling tank. The microbial ecology present here includes yeast, protozoa, fungi.

The microbiological community contains heterotrophs such as gram-negative bacteria, some filamentous fungi, large filamentous bacteria, yeast, and protozoa. 

d)  Anaerobic digesters- These digesters processed the settled sewage waste and treats the industrial effluents that have high BOD levels. This treatment involves three steps:

  1. Fermentation- The sludge changes into organic acids by several bacterial species of Bacteroides, Eubacterium, Lactobacillus
  2. Acetogenic reaction- The products produced in the first fermentation step is used in this step by acetogenic bacteria that produce products like acetate, and carbon dioxide. 
  3. Methanogenesis-  In this step, the products produced in the second step are used as substrate. The microbial life present here includes Methanococcus, Methanobacterium, Methanogenium, etc.

3. Tertiary Treatment

This treatment aims to remove the non-biodegradable waste, minerals through bioaugmentation, and heavy metals through the bioremediation process. In this process, microbes are used to treat contaminated soil and groundwater. The microbes grow rapidly and use contaminants as a source of energy.

Advantages of environmental microbiology

Environmental science involves several microbes for research purposes along with bioleaching, migration of elements, and other processes. Some advantages include:

Microbial leaching

  • Algae and other non-sporing bacteria including Pseudomonas that are present in excess in the rocks are capable of fixing atmospheric nitrogen. Environmental microbiology emphasizes the use of microbial ecology to deliver fruitful research results.
  • Species of algae and Thiobacillus can liberate up to 20-25% of the carbon that is fixed in nature in its molecular form. The growth and biomass accumulation of the heterotrophs in the Thiobacillus and nitrifying bacteria has been proved beneficial.


It refers to the manual addition of organic archaea or microbes to the bioreactor. This is added to treat sewage or other contaminated materials. In most cases, a microbial population is already present in this environment will but due to bioaugmentation, this population is enriched is very effective in reducing the level of contamination. On adding pre-grown microbial cultures in the bioreactors, its efficacy and efficiency increase. It helps to remove the contaminants more quickly and effectively at a lower cost.


  • Petroleum and its products are considered hydrocarbons. These complex compounds can be cleaved into simpler molecules by microorganisms. Microorganisms use the processed oil and other pollutants.
  • Among the microorganisms, fungi and bacteria take an active part in decomposing oil and oil products. Cyanobacteria, yeast, and bacteria are also involved in the oxidation process of hydrocarbons. Oil is considered a pollutant as it floats on the water surface and forms sticky oil biofilm. The addition of microbial communities in spills can significantly increase the process of bioremediation. Hence, microorganisms associated with environmental microbiology are of much importance in the research field.

In the abatement of pollution

Microbial strains are capable of degrading pollutants. A superbug is developed using a strain of Pseudomonas putida which was genetically engineered. It is capable of converting styrene oil into biodegradable plastic. Environmental science uses Thiobacillus ferrooxidans to the maximum level. It oxidizes sulfur to sulfates which are useful to plants.


It has been defined as a that uses biological activity to reduce the concentration or toxicity of a pollutant. The microbes serve as scavengers in bioremediation. The removal of contamination by microbes from the environment is known as bioremediation.

Microorganisms are used to perform the function of bioremediation Other names used for bioremediation are:- biodegradation, biotreatment, bioreclamation, and bio restoration. Bioremediation is also carried by plants and fungi which is also known as Phytoremediation and Mycoremediation respectively.


To analyze deoxyribonucleic acid (DNA) samples without using pure cultures to study the samples directly isolated from the environment for the qualitative study of the microorganisms. Genomic analysis is different from metagenomic as the former focuses on the complete genome study whereas, metagenomics focuses on the study of an individual or organism genome study isolated directly from the environment. Metagenomics is also very important as it helps in the study of the complete sequences of the community rather than focus on an individual. Metagenomics is very important in the field of microbiology as it helps researchers in studying the microbial communities in their natural habitat.

Context and Applications

The topic is relevant for people pursuing their Bachelor's degree and also Master's degree. Students from the following fields are going to find this topic relevant.

  • Ecology
  • Environmental Microbiology.
  • Earth science

Practice Problems

Q 1. The microflora which is present as a top cover over the trickling filters?

  1. Biofilm
  2. Zoological film
  3. flocs
  4. Geological film


Q 2. Who is the partner of fungus in the lichen association?

  1. Phycobiont 
  2. Mycobiont
  3. Photosymbiont
  4. All of the above


Q 3. Which among the following is the obligatory interaction?

  1. Mutualism
  2. Commensalism
  3. Cooperation
  4. Ammensalism


Q 4. Which treatment uses spraying filters?

  1. Oxidation ponds
  2. Septic tanks
  3. Trickling filters
  4. Anaerobic digesters

Answer-c-Trickling filters

Q 5. Which of the following bacteria helps in changing sludge into organic acids?

  1. Spirulina platensis
  2. Chlorella pyrenoidosa
  3. Eubacterium
  4. Ellipsoids


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