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.

Biotechnology is the use of living organisms, cells or their components (such as enzymes) to make products or processes useful to human beings (for example, medicines, vaccines and improved crops). Recombinant DNA (rDNA) technology, also called genetic engineering, is the technique of combining (joining) DNA from two different sources to form a new recombinant DNA molecule, which is then introduced into a host organism where it expresses the desired character. It is the core technique of modern biotechnology.

The three main tools of recombinant DNA technology are: (1) restriction enzymes (molecular scissors), which cut the DNA at specific recognition sites, and DNA ligase, which joins DNA fragments; (2) cloning vectors (such as plasmids and bacteriophages), which are vehicles used to carry the desired (foreign) DNA into the host cell and help it multiply; and (3) a competent host organism (such as the bacterium E. coli), into which the recombinant DNA is introduced so that it can replicate and express the gene.

Restriction enzymes (restriction endonucleases) are enzymes obtained from bacteria that cut DNA at specific recognition sequences, which are usually palindromic (read the same on both strands). Each restriction enzyme recognises a particular base sequence and cuts the DNA within or near it (for example, EcoRI). They are called molecular scissors because they cut the DNA strands at precise positions, often producing sticky ends that help in joining DNA fragments from different sources during genetic engineering.

A cloning vector is a DNA molecule (commonly a plasmid or a bacteriophage) that is used as a carrier to transfer a desired (foreign) DNA fragment into a host cell and to replicate it there. The essential features of a good cloning vector are: (1) an origin of replication (ori), which enables the vector to replicate inside the host; (2) a selectable marker (such as a gene for antibiotic resistance), which helps to identify and select the host cells that have taken up the vector; and (3) unique restriction (recognition) sites where the foreign DNA can be inserted.

The main steps are: (1) isolation of the desired DNA (gene) and of the vector DNA; (2) cutting both the desired DNA and the vector with the same restriction enzyme to get compatible (sticky) ends; (3) joining (ligation) of the desired DNA into the vector using DNA ligase to form the recombinant DNA; (4) introduction (transformation) of the recombinant DNA into a suitable host cell; and (5) selection and multiplication of the transformed host cells so that the gene is expressed and the desired product is obtained (using a bioreactor and downstream processing).

PCR (polymerase chain reaction) is a technique used to make multiple copies (amplify) of a specific segment of DNA in a test tube (in vitro). It uses primers and a heat-stable DNA polymerase (Taq polymerase from Thermus aquaticus). Its three steps, repeated in cycles, are: (1) denaturation - the DNA is heated to separate the two strands; (2) annealing - the primers bind to the complementary sequences on the single strands at a lower temperature; and (3) extension - Taq polymerase extends the primers to synthesise new strands. Repeating the cycles increases the DNA exponentially.

A bioreactor is a large vessel (often thousands of litres) in which the raw materials are biologically converted into specific products by microbes, plant or animal cells or enzymes, under optimum controlled conditions of temperature, pH, oxygen and so on. The most commonly used type is the stirred-tank bioreactor. Downstream processing refers to all the processes carried out after the product has been formed in the bioreactor, such as separation and purification of the product, and its formulation with preservatives and quality control, before it is marketed as a finished product.

Genetically modified organisms (GMOs) are plants, animals or microbes whose genes have been altered (modified) by genetic engineering to introduce a desired character. Advantages of GM (genetically modified) crops: (1) they can be made more tolerant to abiotic stresses such as cold, drought, salt and heat; (2) they can be made resistant to pests, reducing the need for chemical pesticides (for example Bt cotton); (3) they can have improved nutritional value (biofortification, e.g. golden rice rich in vitamin A) and a longer shelf life; and (4) they can increase crop yield.

Bt cotton is a genetically modified variety of cotton that carries a gene (a cry gene) taken from the soil bacterium Bacillus thuringiensis (Bt). This gene codes for a protein (the Bt toxin) that is toxic to certain insect pests such as the cotton bollworm. The toxin is produced as an inactive protoxin (crystal), which, when eaten by the insect, is activated in the alkaline gut of the insect, binds to the gut cells and kills the insect. Thus Bt cotton is protected from the pest without using chemical insecticides.

Human insulin is produced by recombinant DNA technology (the product is called Humulin). Insulin consists of two short polypeptide chains, A and B, joined by disulphide bonds. In the method developed by the company Eli Lilly, the DNA sequences coding for the A and B chains were prepared and introduced separately into the bacterium E. coli; the bacteria produced the two chains separately. These chains were then extracted and joined together by disulphide bonds to form functional human insulin. This insulin is identical to human insulin and does not cause the allergies that animal insulin sometimes did.

Gene therapy is a collection of methods that allow the correction of a gene defect that has been diagnosed in a person; a normal (healthy) functional gene is introduced into the individual (or embryo) to replace or compensate for the non-functional defective gene, so that the normal function is restored. The first clinical gene therapy was given in 1990 to a girl suffering from adenosine deaminase (ADA) deficiency, a disorder of the immune system, in which functional ADA genes (in her lymphocytes) were introduced into her body.

Transgenic animals are animals whose DNA has been altered (manipulated) to carry and express an extra (foreign) gene from another organism. Uses: (1) they are used to study how a gene contributes to the development of a disease and to study normal physiology (for example, transgenic mice used to study diseases); (2) they are used to produce useful biological products, such as human proteins in their milk (for example, a transgenic cow producing human alpha-lactalbumin); and (3) they are used for testing the safety of vaccines and the toxicity of chemicals.

Biopiracy is the unauthorised use and exploitation of the bio-resources (plants, animals and microbes) and the traditional knowledge of a country or community by other organisations or nations, usually without proper permission or fair payment (for example, patenting the medicinal use of a plant known traditionally in India). The GEAC (Genetic Engineering Appraisal Committee) is an Indian government body that makes decisions regarding the validity and safety of genetically modified (GM) research and the safety of introducing GM organisms for public use.

Population density is the number of individuals of a population present per unit area or volume at a given time. Natality (birth rate) is the number of births (new individuals added to the population) per unit time. Mortality (death rate) is the number of deaths (individuals lost from the population) per unit time. A population grows when natality and immigration exceed mortality and emigration.

Exponential (geometric) growth occurs when resources (food, space) are unlimited; the population grows without any check and its growth curve is J-shaped. Logistic growth occurs when resources are limited; the population grows slowly at first, then rapidly, and finally slows down and levels off at the carrying capacity (the maximum number the environment can support), giving an S-shaped (sigmoid) curve. In nature, resources are usually limited, so logistic growth is more realistic.

The main population interactions between two species are: (1) Mutualism - both species benefit (for example, lichens, and pollination of flowers by insects). (2) Competition - both species are harmed as they compete for the same resources. (3) Predation - one species (predator) kills and eats the other (prey), benefiting the predator. (4) Parasitism - one species (parasite) benefits at the expense of the other (host), which is harmed. (5) Commensalism - one species benefits while the other is neither harmed nor benefited (for example, an orchid growing on a tree).

An adaptation is any attribute (morphological, physiological or behavioural) of an organism that enables it to survive and reproduce in its habitat. For example, the desert kangaroo rat is adapted to conserve water: it can meet almost all its water requirement from the internal oxidation of the food it eats (fat) and it produces very concentrated urine, so it loses very little water. Similarly, desert plants have thick cuticles and sunken stomata to reduce water loss (transpiration).