An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments. Oligotrophs are characterized by slow growth, low rates of metabolism, and generally low population density. Oligotrophic environments are those that offer little to sustain life. These environments include deep oceanic sediments, caves, glacial and polar ice, deep subsurface soil, aquifers, ocean waters, and leached soils.
The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. The rhizosphere involving the soil pores contains many bacteria and other microorganisms that feed on sloughed-off plant cells, termed rhizodeposition, and the proteins and sugars released by roots, termed root exudates. This symbiosis leads to more complex interactions, influencing plant growth and competition for resources. Much of the nutrient cycling and disease suppression by antibiotics required by plants, occurs immediately adjacent to roots due to root exudates and metabolic products of symbiotic and pathogenic communities of microorganisms. The rhizosphere also provides space to produce allelochemicals to control neighbours and relatives.
The 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.
The microbial food web refers to the combined trophic interactions among microbes in aquatic environments. These microbes include viruses, bacteria, algae, heterotrophic protists.
In taxonomy, Roseobacter is a genus of the Rhodobacteraceae. The Roseobacter clade falls within the {alpha}-3 subclass of the class Alphaproteobacteria. The first strain descriptions appeared in 1991 which described members Roseobacterlitoralis and Roseobacterdenitrificans, both pink-pigmented bacteriochlorophyll a-producing strains isolated from marine algae. The role members of the Roseobacter lineage play in marine biogeochemical cycles and climate change cannot be overestimated. Roseobacters make up 25% of coastal marine bacteria and members of this lineage process a significant portion of the total carbon in the marine environment. Roseobacter clade plays an important role in global carbon and sulphur cycles. It can also degrade aromatic compounds, uptake trace metal, and form symbiotic relationship. In term of its application, Roseobacter clade produces bioactive compounds, has been used widely in aquaculture and quorum sensing.
Rhizobacteria are root-associated bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties (mutualism). They are an important group of microorganisms used in biofertilizer. Biofertilization accounts for about 65% of the nitrogen supply to crops worldwide. Rhizobacteria are often referred to as plant growth-promoting rhizobacteria, or PGPRs. The term PGPRs was first used by Joseph W. Kloepper in the late 1970s and has become commonly used in scientific literature. PGPRs have different relationships with different species of host plants. The two major classes of relationships are rhizospheric and endophytic. Rhizospheric relationships consist of the PGPRs that colonize the surface of the root, or superficial intercellular spaces of the host plant, often forming root nodules. The dominant species found in the rhizosphere is a microbe from the genus Azospirillum. Endophytic relationships involve the PGPRs residing and growing within the host plant in the apoplastic space.
In the deep ocean, marine snow is a continuous shower of mostly organic detritus falling from the upper layers of the water column. It is a significant means of exporting energy from the light-rich photic zone to the aphotic zone below, which is referred to as the biological pump. Export production is the amount of organic matter produced in the ocean by primary production that is not recycled (remineralised) before it sinks into the aphotic zone. Because of the role of export production in the ocean's biological pump, it is typically measured in units of carbon. The term was first coined by the explorer William Beebe as he observed it from his bathysphere. As the origin of marine snow lies in activities within the productive photic zone, the prevalence of marine snow changes with seasonal fluctuations in photosynthetic activity and ocean currents. Marine snow can be an important food source for organisms living in the aphotic zone, particularly for organisms which live very deep in the water column.
A biofertilizer is a substance which contains living micro-organisms which, when applied to seeds, plant surfaces, or soil, colonize the rhizosphere or the interior of the plant and promotes growth by increasing the supply or availability of primary nutrients to the host plant. Biofertilizers add nutrients through the natural processes of nitrogen fixation, solubilizing phosphorus, and stimulating plant growth through the synthesis of growth-promoting substances. The micro-organisms in biofertilizers restore the soil's natural nutrient cycle and build soil organic matter. Through the use of biofertilizers, healthy plants can be grown, while enhancing the sustainability and the health of the soil. Biofertilizers can be expected to reduce the use of synthetic fertilizers and pesticides, but they are not yet able to replace their use. Since they play several roles, a preferred scientific term for such beneficial bacteria is "plant-growth promoting rhizobacteria" (PGPR).
A microbial consortium or microbial community, is two or more bacterial or microbial groups living symbiotically. Consortiums can be endosymbiotic or ectosymbiotic, or occasionally may be both. The protist Mixotricha paradoxa, itself an endosymbiont of the Mastotermes darwiniensis termite, is always found as a consortium of at least one endosymbiotic coccus, multiple ectosymbiotic species of flagellate or ciliate bacteria, and at least one species of helical Treponema bacteria that forms the basis of Mixotricha protists' locomotion.
Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism is any microscopic living organism or virus, that is too small to see with the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify biologically active entities such as viruses and viroids as microorganisms, but others consider these as non-living.
Soil microbiology is the study of microorganisms 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 on 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, which 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.
The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.
A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit, though there is controversy over this discreteness. The components of a holobiont are individual species or bionts, while the combined genome of all bionts is the hologenome. The holobiont concept was initially introduced by the German theoretical biologist Adolf Meyer-Abich in 1943, and then apparently independently by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation. The concept has evolved since the original formulations. Holobionts include the host, virome, microbiome, and any other organisms which contribute in some way to the functioning of the whole. Well-studied holobionts include reef-building corals and humans.
Mary Ann Moran is a distinguished research professor of marine sciences at the University of Georgia in Athens. She studies the role of bacteria in Earth's marine nutrient cycles, and is a leader in the fields of marine sciences and biogeochemistry. Her work is focused on how microbes interact with dissolved organic matter and the impact of microbial diversity on the global carbon and sulfur cycles. By defining the roles of diverse bacteria in the carbon and sulfur cycles, she connects the biogeochemical and organismal approaches in marine science.
Dinoroseobacter shibae is a facultative anaerobic anoxygenic photoheterotroph belonging to the family, Rhodobacteraceae. First isolated from washed cultivated dinoflagellates, they have been reported to have mutualistic as well as pathogenic symbioses with dinoflagellates.
Sea Ice Microbial Communities (SIMCO) refer to groups of microorganisms living within and at the interfaces of sea ice at the poles. The ice matrix they inhabit has strong vertical gradients of salinity, light, temperature and nutrients. Sea ice chemistry is most influenced by the salinity of the brine which affects the pH and the concentration of dissolved nutrients and gases. The brine formed during the melting sea ice creates pores and channels in the sea ice in which these microbes can live. As a result of these gradients and dynamic conditions, a higher abundance of microbes are found in the lower layer of the ice, although some are found in the middle and upper layers. Despite this extreme variability in environmental conditions, the taxonomical community composition tends to remain consistent throughout the year, until the ice melts.
The viral shunt is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.
Disease suppressive soils function to prevent the establishment of pathogens in the rhizosphere of plants. These soils develop through the establishment of beneficial microbes, known as plant growth-promoting rhizobacteria (PGPR) in the rhizosphere of plant roots. These mutualistic microbes function to increase plant health by fighting against harmful soil microbes either directly or indirectly. As beneficial bacteria occupy space around plant roots they outcompete harmful pathogens by releasing pathogenic suppressive metabolites.
All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of marine microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment.
The holobiont concept is a renewed paradigm in biology that can help to describe and understand complex systems, like the host-microbe interactions that play crucial roles in marine ecosystems. However, there is still little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them and their ecological consequences. The holobiont concept posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution.
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