The host-pathogen interaction is defined as how microbes or viruses sustain themselves within host organisms on a molecular, cellular, organismal or population level. This term is most commonly used to refer to disease-causing microorganisms although they may not cause illness in all hosts. Because of this, the definition has been expanded to how known pathogens survive within their host, whether they cause disease or not. On the molecular and cellular level, microbes can infect the host and divide rapidly, causing disease by being there and causing a homeostatic imbalance in the body, or by secreting toxins which cause symptoms to appear. Viruses can also infect the host with virulent DNA, which can affect normal cell processes (transcription, translation, etc.), protein folding, or evading the immune response.

Soil-plant-microbe interactions along with organic manure in solving stressed agriculture problems. Beneficial microbes associated with plants are known to stimulate plant growth and enhance plant resistance to biotic (diseases) and abiotic (salinity, drought, pollutions, etc.) stresses. The plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, a key component of soil microbiota, could play vital roles in the maintenance of plant fitness and soil health under stressed environments.

 Microbial ecology is the study of relationship between microbes and their surrounds, biased image of the role of microbes in nature obtained from laboratory studies of pure culture cultures  data leads to inappropriate conclusions about their relevance. Eg. E. coli grows in animals intestinal tracts but merely survive in aquatic environments , E. coli are transients and not residents of aquifers from which they can be isolated.Microbial ecology studies entail the use of conventional microbiological techniques (cultural / enumeration procedures, EM, radioactive tracer methods) and modern molecular techniques (gene analysis, nuclei acid probes, sequencing) .

 The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community.

A microorganism may be a microbe that has the potential to cause sickness. To cause an infection, microbes should enter our bodies. Microbes will enter the body through the four sites listed below: Respiratory tract (mouth and nose) e.g. respiratory  disease virus that causes the contagious disease.     Gastrointestinal tract (mouth oral cavity) e.g. eubacteria epidemic cholera that causes    cholera. Urogenital tract  e.g. Escherichia  that causes    urinary tract infection. Breaks within the skin surface e.g. eubacteria tetani that causes tetanus.

The occurrence of infectious disease is affected by interaction between microorganisms in three ways. The indigenous flora (commensal microorganisms) of some mucous surfaces provide one of the main protective mechanisms against infection by pathogens (disease-producing microbes). The commensal populations interfere with the establishment of pathogens on mucous membranes by evoking anaerobic conditions, by competing for space and nutrients and by producing inhibitors. How, at the beginning of successful infection, pathogens in relatively small numbers overcome this protective activity of the commensal population is unknown.

Soil microbiology is the study of organisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about in Earth's oceans. These bacteria could fix nitrogen, in time multiplied and as a result released oxygen into the atmosphere. This led to more advanced microorganisms. Microorganisms in soil are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.

Environmental Microbiology is devoted to the advancement of our understanding of microbial interactions and microbial processes in the environment; Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganisms that exist in artificial environments such as bioreactors.

 Microorganisms and viruses can also interact with host cells to induce alterations in cellular phenotype and function in order to subvert host cell metabolism to meet their own needs. Some microbes and viruses exert effects on the host immune response in order to evade host immune control. Understanding the interplay between infectious pathogens and their host cells is important in order to identify potential new targets for drug therapy.

 Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons (e.g. oil), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds (such as pyridine or quinoline), pharmaceutical substances, radionuclides and metals. Biological processes play a major role in the removal of contaminants and take advantage of the catabolic versatility of microorganisms to degrade or convert such compounds. Interest in the microbial biodegradation of pollutants has intensified in recent years,and recent major methodological breakthroughs have enabled detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analyses of environmentally relevant microorganisms, providing new insights into biodegradative pathways and the ability of organisms to adapt to changing environmental conditions.