Industrial microbiology may be defined as the study of the large-scale and profit motivated production of microorganisms or their products for direct use, or as inputs in the manufacture of other goods. Thus yeasts may be produced for direct consumption asfood for humans or as animal feed, or for use in bread-making; their product, ethanol,may also be consumed in the form of alcoholic beverages, or used in the manufacture of perfumes, pharmaceuticals, etc. Industrial microbiology is clearly a branch of biotechnology and includes the traditional and nucleic acid aspects.

Aero-Microbiology is the study of living animate microbes that are quiescent in the air. These microbes are attributed to as bio-aerosols .There are significantly less atmosphericmicroorganisms than in oceans and soils; there is still a large bounteous number that they can affect the atmosphere . Once attributed in the air column, these microbes have the scope to travel long distances with the help of air and precipitation, increasing the occurrence of widespread disease by these microbes. These aerosols are ecologically suggestive because they can be identify with disease in humans, animals and plants. Typically microbes will be dependent in clouds.where they are able to execute processes that alter the chemical composition of the cloud, and may even induce condensation. 

Applied Microbiology is about the composition and physiology of microbial communities in the environment. The environment in this case includes soil, water, air, sediments, animals and plants. It also includes artificial environments like Bioreactors. Molecular biology has revolutionized the study of microorganisms in the environment and improved our understanding of the composition, phylogeny, and physiology of microbial communities. The present molecular technologies include DNA-based technologies and new methods for RNA and protein studies from environment samples. Currently there is a major emphasis on the application of "omics" approaches to determine the identities and functions of microbes inhabiting different environments. Microbial life is amazingly diverse and microorganisms literally cover the planet. 

This  Forest micorbiology is  on sympathetic the activities of living organisms in the forest, like trees and mushrooms, from the organic and inorganic biochemical point of view  these actions can be used to magnify human life, such as by depressed down and detoxifying environmental pollutants, and searching for physiologically active substances obtainable from trees. It plays the role of a natural protective that prevents timber from decaying easily. Although ordinary micro-organisms like bacteria and fungi cannot decompose lignin, there is one oddball micro-organism in forests that does break lignin down. This microbes  is called white rot fungus because it makes timber turn white and disintegration.

Subsurface microbiology is a rising field in geomicrobiology, environmental microbiology and microbial ecology that focuses on the molecular detection and quantification, cultivation, biogeographic examination, and distribution of bacteria, archaea, and eukarya that permeate the subsurface biosphere. The deep biosphere includes a variety of subsurface habitats, such as terrestrial deep aquifer systems or mines, deeply buried hydrocarbon reservoirs, marine sediments and the basaltic ocean crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and at best incompletely understood microbial populations. So far, microbial cells and DNA remain detectable at sediment depths of more than 1 km and life appears limited mostly by heat in the deep subsurface. 

The diversity of a microbial consortium can vary and change with environmental factors (operating parameters) like for example temperature, ammonium concentration and CO2 concentration. Different types of microbes can sometimes perform different functions and sometimes complement each other. Bacteria are the most diverse and abundant group of organisms on Earth. Attempts to describe bacterial diversity and abundance often yield impressive numbers. For example, there are reports that there is one billion times more individual bacteria on earth than stars in the universe, that the number of prokaryotic species exceeds that of all other species, that prokaryotic cells comprise the majority of all biomass, and that even the most hostile habitats are inhabited by bacteria.

Plant pathology or phytopathology is the scientific study of diseases in plants caused by pathogens (infectious organisms) and environmental conditions (physiological factors). Organisms that cause infectious disease include fungi, oomycetes, bacteria, viruses,viroids, virus-like organisms, phytoplasmas, protozoa, nematodes and parasitic plants. Not included are ectoparasites like insects, mites,vertebrate, or other pests that affect plant health by consumption of plant tissues. Plant pathology also involves the study of pathogen identification, disease etiology, disease cycles, economic impact, plant disease epidemiology, plant disease resistance, how plant diseases affect humans and animals, pathosystem genetics, and management of plant diseases.Microbiology  methods in  mycology, bacteriology, virology, nematology, applied microbiology etc.

Water microbiology is concerned with the microorganisms that live in water, or transferred from one habitat to another by water. Another group of microbes of concern in water microbiology are protozoa. The two protozoa of the most concern are Giardia and Cryptosporidium. They live normally in the intestinal tract of animals such as beaver and deer. Giardia and Cryptosporidium form dormant and hardy forms called cysts during their life cycles. The cyst forms are resistant to chlorine, which is the most popular form of drinking water disinfection, and can pass through the filters used in many water treatment plants. If ingested in drinking water they can cause debilitating and prolonged diarrhea in humans, and can be life threatening to those people with impaired immune.

Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.

The oceans represent the largest ecosystem on Earth and 90% of its biomass is microbial. The diversity of microbial life in the oceans is extremely high and spans all known groups of Bacteria, Archaea and microbial Eukarya. However, this diversity is highly under sampled and a thorough understanding of the identity and physiology of marine microbes and their interactions is a major field of research where progress urgently demanded.

Cyanobacteria were responsible for the oxygenation of the atmosphere 2.2 billion years ago but this group of organisms may be as old as 3.5 billion years. Almost all life in the oceans is directly or indirectly dependent on photosynthesis. Nitrogen is after carbon the most important component of organisms, but only a few specialized bacteria – especially cyanobacteria – are capable of utilizing the omnipresent atmospheric nitrogen (N2). 

Environmental Toxicology is a scientific principles of toxicology and it focuses primarily upon the biology, chemistry, and mechanisms by which xenobiotics and natural toxins interact with the biosphere, including humans. Studies on mechanisms of toxicity complement research directed towards understanding the movement of toxics through soil, water, and air and for the development of procedures to reduce pollution and clean up contaminated sites.

Fossil fuels like coal and oil have played a critical role in humanity’s recent history, providing a vast energy source which has fueled much of society’s development and industrialization. These fuels are still the primary source of energy for the world’s developed nations, and yet it is agreed that these traditional sources of energy cannot continue to power humanity’s growth into the future. The demand for oil production is at an all-time high, and will only increase as developing nations continue to grow. Furthermore, many experts predict that the rate of world oil production has already peaked, and that it will only decrease from now onwards as fewer and fewer oil reserves are discovered. 

Microbiologically-Influenced Corrosion (MIC), also known as microbial corrosion or biological corrosion, is the deterioration of metals as a result of the metabolic activity of microorganisms. There are about a dozen of bacteria known to cause microbiologically influenced corrosion of carbon steels, stainless steels, aluminium alloys and copper alloys in waters and soils with pH 4~9.These bacteria can be broadly classified as aerobic (requires oxygen to become active) or anaerobic (oxygen is toxic to the bacteria). Sulphate reducing bacteria (SRB) is anaerobic and is responsible for most instances of accelerated corrosion damages to ships and offshore steel structures. Iron and manganese oxidizing bacteria are aerobic and are frequently associated with accelerated pitting attacks on stainless steels at welds.

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm.

Cellular microbiology attempts to use pathogenic microbes as tools for cell-biology research, and to employ cell-biology methods to understand the pathogenicity of microbes. Toxins and virulence factors from microbes have been used for decades to influence processes in eukaryotic cells and to study them. It has increasingly appeared that applying a purified toxin on a cell does not always provide the complete picture, and that understanding the role of the toxin in pathogenicity, the way the toxin promotes the microbe, the way the toxin is produced and the co-evolution of the toxin and its host-cellcounterparts, is crucial.

Bioremediation is a waste management technique that involves the use of organisms to remove or neutralize pollutants from a contaminated site. According to the EPA, bioremediation is a “treatment that uses naturally occurring organisms to break down hazardous substances into less toxic or non toxic substances”. 

Coastal upwelling regimes associated with eastern boundary currents are the most biologically productive ecosystems in the ocean. As a result, they play a disproportionately important role in the microbially mediated cycling of marine nutrients. These systems are characterized by strong natural variations in carbon dioxide concentrations, pH, nutrient levels and sea surface temperatures on both seasonal and interannual timescales. Despite this natural variability, changes resulting from human activities are starting to emerge. Carbon dioxide derived from fossil fuel combustion is adding to the acidity of upwelled low-pH waters. Low-oxygen waters associated with coastal upwelling systems are growing in their extent and intensity as a result of a rise in upper ocean temperatures and productivity. 

Mycology is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, medicine, food, and entheogens, as well as their dangers, such as poisoning or infection. Fungi are fundamental for life on earth in their roles as symbionts, e.g. in the form of mycorrhizae, insect symbionts, and lichens. Many fungi are able to break down complex organic biomolecules such as lignin, the more durable component of wood, and pollutants such as xenobiotics, petroleum, and polycyclic aromatic hydrocarbons. By decomposing these molecules, fungi play a critical role in the global carbon cycle.

 Environmental pollution had been a fact of life for many centuries but it became a real problem since the start of the industrial revolution. Environmental pollution is “the contamination of the physical and biological components of the earth/atmosphere system to such an extent that normal environmental processes are adversely affected. Pollution is the introduction of contaminants into the environment that cause harm or discomfort to humans or other living organisms, or that damage the environment” which can come “in the form of chemical substances, or energy such as noise, heat or light”. “Pollutants can be naturally occurring substances or energies, but are considered contaminants when in excess of natural levels.

The distribution and function of microorganisms are of crucial importance for the flow of matter in the Earth's biogeochemical cycles. Effects of microbial communities on the carbon and nitrogen cycles are particularly important for producing climate gases such as CO2, CH4, or N2O. However, the biogeochemical cycles are reversely impacted by global climate change, for example by increasing temperature, increasing CO2 concentration, or changing soil humidity. However microbes may respond differently, by accelerating or by alleviating, human-caused climate change.

Microbial biodegredation 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.

The 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.

Environmental biotechnology is biotechnology that is applied to and used to study the natural environment. Environmental biotechnology could also imply that one try to harness biological process for commercial uses and exploitation.  Environmental Biotechnology defines environmental biotechnology as "the development, use and regulation of biological systems for remediation of contaminated environments (land, air, water), and for environment-friendly processes (green manufacturing technologies and sustainable .

Microbiology and clinical science are interconnected by the pathological conditions caused by microbial pathogens requiring clinical detection and treatment. Understanding such microbe induced pathological conditions demand the detection of clinical manifestation and prescribing proper therapeutic approaches