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An aerated lagoon or aerated basin is a holding and/or treatment pond provided with artificial aeration to promote the biological oxidation of wastewaters. There are many other biological processes for treatment of wastewaters, for example activated sludge, trickling filters, rotating biological contactors and biofilters.

Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms. The largest and most complex marine forms are called seaweeds. They are photosynthetic, like plants, and "simple" because they lack the many distinct organs found in land plants.

Amoeba (sometimes amœba or ameba, plural amoebae) is a term used either to describe protists that move by crawling via pseudopods, or to refer to a genus that includes species that move by this mechanism.

Anaerobic lagoons are used to dispose of animal waste, particularly that of cows and pigs. The waste is washed into the lagoon by flushing the animal pens with water.

Attempts to control disease in the field by the use of soil amendments containing mutually beneficial microorganisms.

Many different soil microorganisms are responsible for nutrient recycling (for one, through decomposing plant residues) and other soil building and maintaining activities. Mixed culture of beneficial microorganisms such as photosynthetic bacteria (Rhodopseudomonas sp) lactic acid bacteria (lactobacillus sp.), yeast (saccharomyces sp.) and fermenting fungi can positively improve the soil fertility as well as plant productivity.

One way by which the pathogenic disease causing organisms can be indirectly suppressed is through the addition of organic matter to mineral soils. In addition to improving tilth, aeration and drainage of soils where organic matter is incorporated, more subtle effects occur at the microscopic level which benefit landscape plants. Organic matter addition enhances population levels of beneficial soil microorganisms

Bioaugmentation is the introduction of a group of natural microbial strains or a genetically engineered variant to treat contaminated soil or water. Usually the steps involve studying the indigenous varieties present in the location to determine if biostimulation is possible. Bioaugmentation is commonly used in municipal wastewater treatment to restart activated sludge bioreactors.

Bioconversion has two meanings in Biology. The first one is also known as biotransformation and is the use of microorganisms to carry out a chemical reaction that is more costly or not feasible nonbiologically. The second is the conversion of organic materials, such as plant or animal waste, into usable products or energy sources by biological processes or agents, such as certain microorganisms or enzymes.

Biodigester is simply the act of anaerobic digestion in a series of processes in which microorganisms break down biodegradable material in the absence of oxygen. As part of an integrated waste management system, anaerobic digestion reduces the emission of landfill gas into the atmosphere. It is widely used to treat wastewater sludges and organic waste because it provides volume and mass reduction of the input material.

The fertilizers are used to improve the fertility of the land using biological wastes, hence the term biofertilizers, and biological wastes do not contain any chemicals which are detrimental to the living soil. They are extremely beneficial in enriching the soil with mutually beneficial microorganisms, which produce organic nutrients for the soil and help combat diseases.

Bioprospecting is a more positive term more commonly used by supporters of commercialization of traditional medicines.

Biostimulation involves the modification of the environment to stimulate existing bacteria capable of bioremediation. This can be done by addition of various forms of rate limiting nutrients and electron acceptors, such as phosphorus, nitrogen, oxygen, or carbon (e.g. in the form of molasses). Additives are usually added to the subsurface through injection wells, although injection well technology for biostimulation purposes is still emerging. Removal of the contaminated material is also an option, albeit an expensive one.

Biotreatment is the processing of waste or hazardous substance using living organisms such as bacteria, fungi or protozoa. It is an environmentally friendly, relatively simple and cost-effective alternative to physico-chemical clean-up options.

Bokashi (Japanese for "fermented organic matter") is a method of intensive composting. It can use an aerobic or anaerobic inoculation to produce the compost. Once a starter culture is made, it can be re-used, like yogurt culture. Since the popular introduction of effective microorganisms (EM), Bokashi is commonly made with only molasses, water, EM, and wheat bran.