Sewage (the waste water from towns and cities) is treated in sewage treatment plants (STPs) mainly with the help of heterotrophic microbes. Primary treatment is a physical process in which floating and suspended solids are removed by sequential filtration and sedimentation, forming primary sludge; the liquid part is the primary effluent. Secondary (biological) treatment is where aerobic microbes are grown as flocs and consume the organic matter in the effluent, greatly reducing its BOD (biochemical oxygen demand); the microbial mass then settles as sludge, part of which is digested by anaerobic bacteria to produce biogas.

Biogas is a mixture of gases (mainly methane, along with carbon dioxide and hydrogen sulphide) produced by the anaerobic breakdown of organic waste such as cattle dung (gobar) and plant material; it is used as a fuel for cooking and lighting. It is produced by a group of anaerobic bacteria called methanogens (for example, Methanobacterium), which are also present in the rumen of cattle and in anaerobic sludge. The biogas plant used to make it is commonly called a gobar gas plant.

Biofertilizers are living organisms (microbes) that enrich the nutrient quality of the soil, mainly by fixing atmospheric nitrogen or making phosphorus available; examples include the bacterium Rhizobium (in root nodules of legumes), cyanobacteria (blue-green algae) and mycorrhiza (a fungus-root association). Biocontrol agents are organisms used to control plant diseases and pests biologically, instead of chemical pesticides; examples include the bacterium Bacillus thuringiensis (used against insect larvae), the ladybird beetle (which eats aphids) and the fungus Trichoderma.