Aerobic microbes degrade the pollutants in the presence of oxygen. They mainly degrade pesticides and hydrocarbons. Pseudomonas putida is a genetically engineered microorganism (GEM). Ananda Mohan Chakrabarty obtained patent for this recombinant bacterial strain. It is multiplasmid hydrocarbon-degrading bacterium which can digest the hydrocarbons in the oil spills.
Nitrosomonas europaea is also capable of degrading benzene and a variety of halogenated organic compounds including trichloroethylene and vinyl chloride. Ideonella sakaiensis is currently tried for recycling of PET plastics. These bacteria use PETase and MHETase enzymes to breakdown PET plastic into terephthalic acid and ethylene glycol.
Anaerobic microbes degrade the pollutants in the absence of oxygen. Dechloromonas aromatica has the ability to degrade benzene anaerobically and to oxidize toluene and xylene. Phanerochaete chrysosporium an anaerobic fungus exhibits strong potential for bioremediation of pesticides, polyaromatic hydrocarbons, dyes, trinitrotoluene, cyanides, carbon tetrachloride, etc., Dehalococcoides species are responsible for anaerobic bioremediation of toxic trichloroethene to nontoxic ethane. Pestalotiopsis microspora is a species of endophytic fungus capable of breaking down and digesting polyurethane. This makes the fungus a potential candidate for bioremediation projects involving large quantities of plastics.

Biogas is a mixture of different gases produced by the breakdown of organic matter in the absence of oxygen. Biogas can be produced from raw materials such as agricultural wastes, manure, municipal wastes, plant material, sewage, food waste, etc., Biogas is produced under the anaerobic condition when the organic materials are converted through microbiological reactions into gas and organic fertilizer. Biogas primarily consists of methane (63 percent), along with CO₂ and hydrogen. Methane-producing bacteria are called methanogens and one such common bacterium is Methanobacterium. Biogas is devoid of smell and bums with a blue flame without smoke. The Methanogens are also present in anaerobic sludge and rumen of cattle. In the rumen, these bacteria help in the breakdown of cellulose. The excreta of cattle called dung is commonly called "Gobar". Gobar gas is generated by the anaerobic decomposition of cattle dung. It consists of methane, CO₂ with some hydrogen, nitrogen and other gases in trace amounts.
In a biogas plant, anaerobic digestion is carried out in an airtight cylindrical tank known as digester. It is made up of concrete bricks and cement or steel. Bio-wastes are collected and a slurry of dung is fed into this digester. It has a side opening into which organic materials for digestion are incorporated for microbial activity. Anaerobic digestion is accomplished in three stages: solubilisation, acidogenesis, and methanogens. The outlet is connected to a pipe to supply biogas. The slurry is drained through another outlet and is used as fertilizer. Biogas is used for cooking and lighting. The technology of biogas production was developed in India mainly due to the efforts of the Indian Agricultural Research Institute (IARl) and Khadi and Village Industries Commission (KVIC).

Sewage treatment is usually performed in the following three stages

Primary treatment: Primary treatment involves the physical removal of solid and particulate organic and inorganic materials from the sewage through filtration and sedimentation. Floating debris is removed by sequential filtration. Then the grit (soil and small pebbles) are removed by sedimentation. All solids that settle form the primary sludge and the supernatant forms the effluent. The effluent from the primary settling tank is taken for secondary treatment.
Secondary treatment or biological treatment: The primary effluent is passed into large aeration tanks where it is constantly agitated mechanically and air is pumped into it. This allows vigorous growth of useful aerobic microbes into floc (masses of bacteria associated with fungal filaments to form mesh like structures). While growing, these microbes consume the major part of the organic matter in the effluent. This significantly reduces the BOD (Biochemical oxygen demand or Biological oxygen demand). BOD refers to the amount of the oxygen that would be consumed, if all the organic matter in one litre of water were oxidized by bacteria. The sewage water is treated till the BOD is reduced. The greater the BOD of the waste water more is its polluting potential. Once the BOD of sewage water is reduced significantly, the effluent is then passed into a settling tank where the bacterial "floes" are allowed to sediment. This sediment is called activated sludge. A small part of activated sludge is pumped back into the aeration tank to serve as the inoculum. The remaining major part of the sludge is pumped into large tanks called anaerobic sludge digesters. Here, the bacteria which grow anaerobically, digest the bacteria and the fungi in the sludge. During this digestion, bacteria produce a mixture of gases such as methane, hydrogen sulphide and CO₂. These gases form biogas and can be used as a source of energy.
Tertiary treatment: Tertiary treatment is the final process that improves the quality of the waste water before it is reused, recycled or released into natural water bodies. This treatment removes the remaining inorganic compounds and substances, such as nitrogen and phosphorus. UV is an ideal disinfectant for wastewater since it does not alter the water quality - except for inactivating microorganisms. UV is a chemical free process that can completely replace the existing chlorination system and also inactivates chlorine-resistant microorganisms like Cryptosporidium and Giardia.

Microbes used for production of chemicals like organic acids and enzymes. Examples of organic acid producers are Aspergillus niger for citric acid, Acetobacter aceti for acetic acid, Rhizopus oryzae for fumaric acid, Clostridium butyricum for butyric acid and Lactobacillus for lactic acid.
Yeast (Saccharomyces cerevisiae) and bacteria are used for commercial production of enzymes. Lipases are used in detergent formulations and are used for removing oily stains from the laundry. Bottled juices are clarified by the use of pectinase, protease, and cellulase. Rennet can also be used to separate milk into solid curds for cheese making. Streptokinase produced by the bacterium Streptococcus and genetically engineered Streptococci are used as "clot buster" for removing clots from the blood. vessels of patients who have undergone myocardial infarction.
Cyclosporin A, an immunosuppressant used in organ transplantation is produced from the fungus Trichoderma polysporum. It is also used for its anti-inflammatory, anti-fungal, and anti-parasitic properties. Statins produced by the yeast Monascus purpureus have been used to lower blood cholesterol levels. It acts by competitively inhibiting the enzyme responsible for the synthesis of cholesterol. Recombinant human insulin has been produced predominantly using E. coli and Saccharomyces cerevisiae for therapeutic use in human.

(i) Biogas is a mixture of different gases produced by the breakdown of organic matter in the absence of oxygen. Biogas can be produced from raw materials such as agricultural wastes, manure, municipal wastes, plant material, sewage, food waste, etc.,
(ii) The excreta of cattle called dung is commonly called "Gobar'. Gobar gas is generated by the anaerobic decomposition of cattle dung. It consists of methane, CO₂ with some hydrogen, nitrogen and other gases in trace amounts.
(iii) In a biogas plant, anaerobic digestion is carried out in an air tight cylindrical tank known as digester (Fig.). It is made up of concrete bricks and cement or steel. Bio-wastes are collected and slurry of dung is fed into this digester. It has a side opening into which organic materials for digestion are incorporated for microbial activity. Anaerobic digestion is accomplished in three stages: solubilisation, acidogenesis and methanogenisis. The outlet is connected to a pipe to supply biogas. The slurry is drained through another outlet and is used as fertilizer. Biogas is used for cooking and lighting.