Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.^[2] This relationship is often mediated by secondary metabolites produced by microorganisms. These secondary metabolites are known as specialized metabolites and are mostly volatile or non volatile compounds.^[3][4] These metabolites include terpenoids, sulfur compounds, indole compound and many more.^[3]

The study of microorganisms and their interactions with the environment was pioneered by some scientists such as Sergei Winogradsky, Louis Pasteur, Martinus Beijerinck, Robert Koch, Lorenz Hiltner and many more.^[5][6]

Microorganisms are ubiquitous, and play various roles that impact the entire biosphere and any environment they found themselves both positively and negatively. Microbial life plays a primary role in regulating biogeochemical systems in virtually all environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of the deepest oceans, and some of the most familiar, such as the human small intestine, nose, and mouth.^[7][8][9] Microorganisms (soil microbes) are involved in biogeochemical cycles in the soil which helps in fixing nutrients, such as nitrogen, phosphorus and sulphur in the soil (environment).^[10] As a consequence of the quantitative magnitude of microbial life (calculated as 5.0×10³⁰ cells,^[11][12]) microbes, by virtue of their biomass alone, constitute a significant carbon sink.^[13] Microbial interactions with their environment have industrial application such as wastewater treatment and bioremediation^[14][15]

Microorganisms also form several symbiotic relationships with other organisms in their environment where one or both of the partners involved benefit or one partner benefits while the other partner is harmed.^[16] Some symbiotic relationships include mutualism and commensalism.^[17][18]

Certain substances in the environment can kill microorganisms, thus preventing them from interacting with their environment. These substances are called antimicrobial substances. These can be antibiotic, antifungal, or even antiviral.^[19]

While microbes have been studied since the seventeenth century, this research was primarily on physiological perspective rather than an ecological one.^[20] For instance, Louis Pasteur and his disciples were interested in the problem of microbial distribution both on land and in the ocean.^[21] Louis Pasteur was the scientist who invented the pasteurization process. Martinus Beijerinck invented the enrichment culture, a fundamental method of studying microbes from the environment. He is often incorrectly credited with framing the microbial biogeographic idea that "everything is everywhere, but, the environment selects", which was stated by Lourens Baas Becking.^[22] Sergei Winogradsky was one of the first researchers to attempt to understand microorganisms outside of the medical context—making him among the first students of microbial ecology and environmental microbiology—discovering chemosynthesis, and developing the Winogradsky column in the process.^[23]: 644

Beijerinck and Windogradsky, however, were focused on the physiology of microorganisms, not the microbial habitat or their ecological interactions.^[20] Modern microbial ecology was launched by Robert Hungate and coworkers, who investigated the rumen ecosystem. The study of the rumen required Hungate to develop techniques for culturing anaerobic microbes, and he also pioneered a quantitative approach to the study of microbes and their ecological activities that differentiated the relative contributions of species and catabolic pathways.^[20]

Progress in microbial ecology has been tied to the development of new technologies. The measurement of biogeochemical process rates in nature was driven by the availability of radioisotopes beginning in the 1950s. For example, ¹⁴CO₂ allowed analysis of rates of photosynthesis in the ocean (ref). Another significant breakthrough came in the 1980s, when microelectrodes sensitive to chemical species like O2 were developed.^[24] These electrodes have a spatial resolution of 50–100 μm, and have allowed analysis of spatial and temporal biogeochemical dynamics in microbial mats and sediments.^{[citation needed]}

Although measuring biogeochemical process rates could analyse what processes were occurring, they were incomplete because they provided no information on which specific microbes were responsible. It was long known that 'classical' cultivation techniques recovered fewer than 1% of the microbes from a natural habitat. However, beginning in the 1990s, a set of cultivation-independent techniques have evolved to determine the relative abundance of microbes in a habitat. Carl Woese first demonstrated that the sequence of the 16S ribosomal RNA molecule could be used to analyse phylogenetic relationships.^[25] Norm Pace took this seminal idea and applied it to analysfe 'who's there' in natural environments. The procedure involves (a) isolation of nucleic acids directly from a natural environment, (b) PCR amplification of small subunit rRNA gene sequences, (c) sequencing the amplicons, and (d) comparison of those sequences to a database of sequences from pure cultures and environmental DNA.^[26] This has provided tremendous insights into the diversity present within microbial habitats. However, it does not resolve how to link specific microbes to their biogeochemical role. Metagenomics, the sequencing of total DNA recovered from an environment, can provide insights into biogeochemical potential,^[27] whereas metatranscriptomics and metaproteomics can measure actual expression of genetic potential but remains more technically difficult.^[28]

Microorganisms are the backbone of all ecosystems, but even more so in areas where photosynthesis cannot take places due to lack of light. In such zones, chemosynthetic microbes provide energy, and carbon to the other organisms. Chemosynthetic microorganisms gain energy by oxidizing inorganic compounds such as hydrogen, nitrite, ammonia, elemental sulfur and iron(II). These organisms can be found in both aerobic and anaerobic environment.^[29] Chemosynthetic microorganisms are primary producer in extreme environment such as high temperature geothermal environments.^[30] These chemotrophic organisms can also function in anoxic environments by using other electron acceptors for their respiration.^{[citation needed]}

Other microbes are decomposers, with the ability to recycle nutrients from other organisms' waste products. These microbes play a critical role in biogeochemical cycles.^[31] The nitrogen cycle, the phosphorus cycle, the sulphur cycle, and the carbon cycle all depend on microorganisms in one way or another. Each cycle works together to regulate the microorganisms in certain processes.^[32] For example, the nitrogen gas which makes up 78% of the Earth's atmosphere is unavailable to most organisms, until it is converted to a biologically available form by the microbial process of nitrogen fixation.^[33] Through these biogeochemical cycles, microorganisms are able to make nutrients such as nitrogen, phosphorus and potassium available in the soil.^[34] Differing from the nitrogen and carbon cycles, stable gaseous species are not created in the phosphorus cycle in the environment. Microorganisms play a role in solubilizing phosphate, improving soil health, and plant growth.^[35]

Again, microbial interaction are involved in bioremediation. Bioremediation is a technology that is employed to remove heavy metal contaminants from soil^[36] and wastewater^[37] using microorganisms. Microorganisms such as bacteria and fungi removes organic and inorganic pollutants by oxidizing or reducing them.^[38][39] Example of microorganisms that play role in bioremediation of heavy metals include Pseudomonas, Bacillus, Arthrobacter, Corynebacterium, Methosinus, Rhodococcus, Stereum hirsutum, Methanogens, Aspergilus niger, Pleurotus ostreatus, Rhizopus arrhizus, Azotobacter, Alcaligenes, Phormidium valderium, and Ganoderma applantus.^[40]

Symbiosis is a close, long term relationship between organisms of different species. Symbiosis can be ectosymbiosis (one organism lives on the surface of other organism) or endosymbiosis (one organism lives inside other organism).^[41] Symbiotic relationship can also exist between microorganism that live closely together in a given environment.^[16] Symbiotic relationship is found at every level within the ecosystem and has contributed in shaping life.^[42] Microorganism produce, change, and utilize nutrient and natural products in numerous ways and this enable them to be ubiquitous.^[43] Microbes, especially bacteria, often engage in symbiotic relationships (either positive or negative) with other microorganisms or larger organisms.^[44] Plants and animals happen to be the habitat of microorganism that are involved in mutualistic relationship.^[45] While such relationships are vital for the development of the microbes, these microbes can provide protection to their host against unfavorable changes in the environment or against predators. They do this by producing bioactive compounds.^[44] Although physically small, symbiotic relationships amongst microbes are significant in eukaryotic processes and their evolution.^[46][47] The types of symbiotic relationship that microbes participate in include mutualism, commensalism, parasitism,^[48] and amensalism^[49] which affect the ecosystem in many ways.

Mutualism is a close relationship between two different species in which each has a positive affect on the other . In mutualism, one partner provides service to the other partner and also receives service from the other partner as well.^[50] Mutualism in microbial ecology is a relationship between microbial species and other species (example humans) that allows for both sides to benefit.^[51] Microorganisms form mutualistic relationship with other microorganism, plants or animals. One example of microbe-microbe interaction would be syntrophy, also known as cross-feeding,^[49] of which Methanobacterium omelianskii is a classical example.^[52][53] This consortium is formed by an ethanol fermenting organism and a methanogen. The ethanol-fermenting organism provides the archaeal partner with the H₂, which this methanogen needs in order to grow and produce methane.^[46][53] Syntrophy has been hypothesized to play a significant role in energy and nutrient-limited environments, such as deep subsurface, where it can help the microbial community with diverse functional properties to survive, grow and produce maximum amount of energy.^[54][55] Anaerobic oxidation of methane (AOM) is carried out by mutualistic consortium of a sulfate-reducing bacterium and an anaerobic methane-oxidizing archaeon.^[56][57] The reaction used by the bacterial partner for the production of H₂ is endergonic (and so thermodynamically unfavored) however, when coupled to the reaction used by archaeal partner, the overall reaction becomes exergonic.^[46] Thus the two organisms are in a mutualistic relationship which allows them to grow and thrive in an environment, deadly for either species alone. Lichen is an example of a symbiotic organism.^[53]

Microorganisms also engage in mutualistic relationship with plants and a typical example of such relationship is arbuscular mycorrhizal (AM) relationship, a symbiotic relationship between plants and fungi.^[17] This relationship begins when chemical signals are exchange between the plant and the fungi leading to the metabolic stimulation of the fungus.^[58][59] The fungus then attacks the epidermis of the plant’s root and penetrates its highly branched hyphae into the cortical cells of the plant.^[17] In this relationship, the fungi gives the plant phosphate and nitrogen obtained from the soil with the plant in return providing the fungi with carbohydrate and lipids obtained from photosynthesis.^[60] Also, microorganisms are involve in mutualistic relationship with mammals such as humans. As the host provides shelter and nutrient to the microorganisms, the microorganisms also provide benefits such as helping in the growth of the gastrointestinal tract of the host and protecting host from other detrimental microorganisms.^[61]

Commensalism is very common in microbial world, literally meaning "eating from the same table".^[62] It is a relationship between two species where one species benefits with no harm or benefit for the other species.^[18] Metabolic products of one microbial population are used by another microbial population without either gain or harm for the first population. There are many "pairs "of microbial species that perform either oxidation or reduction reaction to the same chemical equation. For example, methanogens produce methane by reducing CO₂ to CH₄, while methanotrophs oxidise methane back to CO₂.^[63]

Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected.^[51] One example of such a relationship that takes place in microbial ecology is between the microbial species Lactobacillus casei and Pseudomonas taetrolens.^[64] When co-existing in an environment, Pseudomonas taetrolens shows inhibited growth and decreased production of lactobionic acid (its main product) most likely due to the byproducts created by Lactobacillus casei during its production of lactic acid.^[65] However, Lactobacillus casei shows no difference in its behaviour.^{[citation needed]}

Biotechnology may be used alongside microbial ecology to address a number of environmental and economic challenges. For example, molecular techniques such as community fingerprinting or metagenomics can be used to track changes in microbial communities over time or assess their biodiversity. Managing the carbon cycle to sequester carbon dioxide and prevent excess methanogenesis is important in mitigating global warming, and the prospects of bioenergy are being expanded by the development of microbial fuel cells. Microbial resource management advocates a more progressive attitude towards disease, whereby biological control agents are favoured over attempts at eradication. Fluxes in microbial communities has to be better characterized for this field's potential to be realised.^[66] In addition, there are also clinical implications, as marine microbial symbioses are a valuable source of existing and novel antimicrobial agents, and thus offer another line of inquiry in the evolutionary arms race of antibiotic resistance, a pressing concern for researchers.^[67]

Microbes exist in all areas, including homes, offices, commercial centers, and hospitals. In 2016, the journal Microbiome published a collection of various works studying the microbial ecology of the built environment.^[68]

A 2006 study of pathogenic bacteria in hospitals found that their ability to survive varied by the type, with some surviving for only a few days while others survived for months.^[69]

The lifespan of microbes in the home varies similarly. Generally bacteria and viruses require a wet environment with a humidity of over 10 percent.^[70] E. coli can survive for a few hours to a day.^[70] Bacteria which form spores can survive longer, with Staphylococcus aureus surviving potentially for weeks or, in the case of Bacillus anthracis, years.^[70]

In the home, pets can be carriers of bacteria; for example, reptiles are commonly carriers of salmonella.^[71]

S. aureus is particularly common, and asymptomatically colonizes about 30% of the human population;^[72] attempts to decolonize carriers have met with limited success^[73] and generally involve mupirocin nasally and chlorhexidine washing, potentially along with vancomycin and cotrimoxazole to address intestinal and urinary tract infections.^[74]

Antimicrobials are substances that are capable of killing microorganism. Antimicrobial can be antibacterial or antibiotic, antifungal or antiviral substance and most of these substance are natural products or may have been obtain from natural products.^[19] Natural products are therefore vital in the discovery of pharmaceutical agents.^[75][76] Most of the naturally obtained antibiotics are produced by organism under the phylum Actinobacteria. The genus Streptomyces are responsible for most of the antibiotic substances produced by Actinobacteria.^[77][78] These natural products with antimicrobial properties belong to the terpenoids, spirotetronate, tetracenedione, lactam, and other groups of compounds. Examples include napyradiomycin, nomimicin, formicamycin, and isoikarugamycin,^{[79][80][81][82]} Some metals, particularly copper, silver, and gold also have antimicrobial properties. Using antimicrobial copper-alloy touch surfaces is a technique that has begun to be used in the 21st century to prevent the transmission of bacteria.^[83][84] Silver nanoparticles have also begun to be incorporated into building surfaces and fabrics, although concerns have been raised about the potential side-effects of the tiny particles on human health.^[85] Due to the antimicrobial properties certain metals possess, products such as medical devices are made using those metals.^[84]

Due to the high level of horizontal gene transfer among microbial communities,^[86] microbial ecology is also of importance to studies of evolution.^[87] Microbial ecology contributes to the evolution in many different parts of the world. For example, different microbial species evolved CRISPR dynamics and functions, allowing a better understanding of human health.^[88]

• Microbial biogeography
• Microbial loop
• Outline of ecology
• International Society for Microbial Ecology
• The ISME Journal