Microbial ecologyMicrobial 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. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine, nose, and mouth.
Community (ecology)In ecology, a community is a group or association of populations of two or more different species occupying the same geographical area at the same time, also known as a biocoenosis, biotic community, biological community, ecological community, or life assemblage. The term community has a variety of uses. In its simplest form it refers to groups of organisms in a specific place or time, for example, "the fish community of Lake Ontario before industrialization".
BenthosBenthos (), also known as benthon, is the community of organisms that live on, in, or near the bottom of a sea, river, lake, or stream, also known as the benthic zone. This community lives in or near marine or freshwater sedimentary environments, from tidal pools along the foreshore, out to the continental shelf, and then down to the abyssal depths. Many organisms adapted to deep-water pressure cannot survive in the upper parts of the water column. The pressure difference can be very significant (approximately one atmosphere for every 10 metres of water depth).
EctosymbiosisEctosymbiosis is a form of symbiotic behavior in which an organism lives on the body surface of another organism (the host), including internal surfaces such as the lining of the digestive tube and the ducts of glands. The ectosymbiotic species, or ectosymbiont, is generally an immobile (or sessile) organism existing off of biotic substrate through mutualism, commensalism, or parasitism. Ectosymbiosis is found throughout a diverse array of environments and in many different species.
BiodiversityBiodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (genetic variability), species (species diversity), and ecosystem (ecosystem diversity) level. Biodiversity is not distributed evenly on Earth; it is usually greater in the tropics as a result of the warm climate and high primary productivity in the region near the equator. Tropical forest ecosystems cover less than 10% of earth's surface and contain about 90% of the world's species.
Beta diversityIn ecology, beta diversity (β-diversity or true beta diversity) is the ratio between regional and local species diversity. The term was introduced by R. H. Whittaker together with the terms alpha diversity (α-diversity) and gamma diversity (γ-diversity). The idea was that the total species diversity in a landscape (γ) is determined by two different things: the mean species diversity at the local level (α) and the differentiation among local sites (β).
BiogeographyBiogeography is the study of the distribution of species and ecosystems in geographic space and through geological time. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, isolation and habitat area. Phytogeography is the branch of biogeography that studies the distribution of plants. Zoogeography is the branch that studies distribution of animals. Mycogeography is the branch that studies distribution of fungi, such as mushrooms.
Microbial loopThe microbial loop describes a trophic pathway where, in aquatic systems, dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. In soil systems, the microbial loop refers to soil carbon. The term microbial loop was coined by Farooq Azam, Tom Fenchel et al. in 1983 to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.
Viral sheddingViral shedding is the expulsion and release of virus progeny following successful reproduction during a host cell infection. Once replication has been completed and the host cell is exhausted of all resources in making viral progeny, the viruses may begin to leave the cell by several methods. The term is variously used to refer to viral particles shedding from a single cell, from one part of the body into another, and from a body into the environment, where the virus may infect another.
Extracellular polymeric substanceExtracellular polymeric substances (EPSs) are natural polymers of high molecular weight secreted by microorganisms into their environment. EPSs establish the functional and structural integrity of biofilms, and are considered the fundamental component that determines the physicochemical properties of a biofilm. EPS in the matrix of biofilms provides compositional support and protection of microbial communities from the harsh environments. Components of EPS can be of different classes of polysaccharides, lipids, nucleic acids, proteins, lipopolysaccharides, and minerals.
SymbiosisSymbiosis (from Greek συμβίωσις, symbíōsis, "living together", from σύν, sýn, "together", and βίωσις, bíōsis, "living") is any type of a close and long-term biological interaction between two biological organisms of different species, termed symbionts, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as "the living together of unlike organisms". The term is sometimes used in the more restricted sense of a mutually beneficial interaction in which both symbionts contribute to each other's support.
Pan-genomeIn the fields of molecular biology and genetics, a pan-genome (pangenome or supragenome) is the entire set of genes from all strains within a clade. More generally, it is the union of all the genomes of a clade. The pan-genome can be broken down into a "core pangenome" that contains genes present in all individuals, a "shell pangenome" that contains genes present in two or more strains, and a "cloud pangenome" that contains genes only found in a single strain.
