Түбір маңы топырақ микробиом аймағы

Region of soil or substrate comprising the root microbiome

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. Soil pores in the rhizosphere can contain 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 plant soil feedback loop and other physical factors occurring at the plant root soil interface are important selective pressures in communities and growth in the rhizosphere and rhizoplane.

The term "rhizosphere" was used first in 1904 by the German plant physiologist Lorenz Hiltner to describe how plant roots interface with the surrounding soil. Plant root exudates, such as organic acids, change the chemical structure and the biological communities of the rhizosphere in comparison with the bulk soil or parent soil. Concentrations of organic acids and saccharides affect the ability of the biological communities to shuttle phosphorus, nitrogen, potassium, and water to the root cap, The ability of the plant's root and its associated soil microorganisms to provide specific transport proteins affects the availability of iron and other minerals for it and its neighbors. This can affect the composition of the community and its fitness. Root exudates come in the form of chemicals released into the rhizosphere by cells in the roots and cell waste referred to as "rhizodeposition." This rhizodeposition comes in various forms of organic carbon and nitrogen that provide for the communities around plant roots and dramatically affect the chemistry surrounding the roots. Exopolysaccharides, such as polyglycolide (PGA), affect the ability of roots to uptake water by maintaining the physical stability of the soil carbon sponge and controlling the flow of water. For example, a tomato field study showed that exopolysaccharides extracted from the rhizosphere were different (total sugar amounts and mean infrared measurements) depending on the tomato varieties grown, and that under water deficit conditions (limited irrigation), the increase in exopolysaccharide production and microbial activity affected water retention in the soil and field performance of tomato. In potato cultivar root exudates, phenols and lignins comprise the greatest number of ion influencing compounds regardless of growing location; however, the intensity of different compounds was found to be influenced by soils and environmental conditions, resulting in variation amongst nitrogen compounds, lignins, phenols, carbohydrates, and amines.

Although it goes beyond the rhizosphere area, it is notable that some plants secrete allelochemicals from their roots that inhibit the growth of other organisms. For example, garlic mustard produces a chemical that is believed to prevent mutualisms forming between the surrounding trees and mycorrhiza in mesic North American temperate forests where it is an invasive species.

Rhizodeposition allows for the growth of communities of microorganisms directly surrounding and inside plant roots. This leads to complex interactions between species, including mutualism, predation/parasitism, and competition.

Predation is considered to be top down because these interactions decrease the population, but the closeness of the interactions of species directly affects the availability of resources causing the population to also be affected by bottom up controls. Without soil fauna, microbes that directly prey upon competitors of plants and plant mutualists, interactions within the rhizosphere would be antagonistic toward the plants. Soil fauna provide the top down component of the rhizosphere while also allowing for the bottom up increase in nutrients from rhizodeposition and inorganic nitrogen. The complexity of these interactions has also been shown through experiments with common soil fauna, such as nematodes and protists. Predation by bacterial feeding nematodes was shown to influence nitrogen availability and plant growth. There was also an increase in the populations of bacteria to which nematodes were added. Predation upon Pseudomonas by amoeba shows predators are able to upregulate toxins produced by prey without direct interaction using supernatant. The ability of predators to control the expression and production of biocontrol agents in prey without direct contact is related to the evolution of prey species to signals of high predator density and nutrient availability. The food web in the rhizosphere can be considered as three different channels with two different sources of energy: the detritus dependent channels are fungi and bacterial species, and the root energy dependent channel consists of nematodes, symbiotic species, and some arthropods. Geometrical properties are the density of roots, root diameter, and distribution of the roots. Physicochemical properties are exudation rate, decay rate of exudates, and the properties of the environment that affect diffusion. These properties define the rhizosphere of roots and the likelihood that plants can directly compete with neighbors. Plants and soil microflora indirectly compete against one another by tying up limiting resources, such as carbon and nitrogen, into their biomass. This competition can occur at varying rates due to the ratio of carbon to nitrogen in detritus and the ongoing mineralization of nitrogen in the soil. Mycorrhizae and heterotrophic soil microorganisms compete for both carbon and nitrogen, depending upon which is limiting at the time, which itself heavily depends on the species, scavenging abilities, and the environmental conditions affecting nitrogen input. Plants are less successful at the uptake of organic nitrogen, such as amino acids, than the soil microflora that exist in the rhizosphere. This informs other mutualistic relationships formed by plants in relation to nitrogen uptake. Competition over other resources, such as oxygen in limited environments, is directly affected by the spatial and temporal locations of species and the rhizosphere. In methanotrophs, proximity to higher density roots and the surface are important and help to determine where they are dominant over heterotrophs in rice paddies. The weak connection between the various channels of energy is important in the regulation of the populations of both predator and prey and the availability of resources to the biome. Strong connections between resource consumer and consumer consumer create coupled systems of oscillators, which are then determined by the nature of the available resources. These systems can then be considered cyclical, quasi periodic, or chaotic.

Plants secrete many compounds through their roots to serve symbiotic functions in the rhizosphere. Strigolactones, secreted and detected by mycorrhizal fungi, stimulate the germination of spores and initiate changes in the mycorrhiza that allow it to colonize the root. The parasitic plant, Striga also detects the presence of strigolactones and will germinate when it detects them; they will then move into the root, feeding off the nutrients present. Symbiotic nitrogen fixing bacteria, such as Rhizobium species, detect compounds like flavonoids secreted by the roots of leguminous plants and then produce nod factors that signal to the plant that they are present and will lead to the formation of root nodules. Bacteria are housed in symbiosomes in these nodules, where they are sustained by nutrients from the plant and convert nitrogen gas to a form that can be used by the plant. Non symbiotic (or "free living") nitrogen fixing bacteria may reside in the rhizosphere just outside the roots of certain plants (including many grasses) and similarly "fix" nitrogen gas in the nutrient rich plant rhizosphere. Even though these organisms are thought to be only loosely associated with the plants they inhabit, they may respond very strongly to the status of the plants. For example, nitrogen fixing bacteria in the rhizosphere of the rice plant exhibit diurnal cycles that mimic plant behavior and tend to supply more fixed nitrogen during growth stages when the plant exhibits a high demand for nitrogen. In exchange for the resources and shelter that plants and roots provide, fungi and bacteria control pathogenic microbes. which plays into the bigger cycles of nutrients that impact the ecosystem, such as biogeochemical pathways. This description has been used to explain the complex interactions that plants, their fungal mutualists, and the bacterial species that live in the rhizosphere have entered into over the course of their evolution. Certain species like Trichoderma are interesting because of their ability to select for species in this complex web. Trichoderma is a biological control agent because of evidence that it can reduce plant pathogens in the rhizosphere. Plants themselves also affect which bacterial species in the rhizosphere are selected against because of the introduction of exudates and the relationships that they maintain. The control of which species are in these small diversity hotspots can drastically affect the capacity of these spaces and future conditions for future ecologies.

Communication is often the basis of biotic interactions. Frequently, more than two organisms can take part in the communication, resulting in a complex network of crosstalking. Recent advances in plant microbe interactions research have shown that communication, both inter kingdom and intra kingdom, is shaped by a broad spectrum of factors. In this context, the rhizosphere (i. e., the soil close to the root surface) provides a specific microhabitat where complex interactions occur. The complex environment that makes up the rhizosphere can select for certain microbial populations, which are adapted to this unique niche. Among them, rhizobia have emerged as an important component of the rhizospheric microbiome. Rhizospheric crosstalk is found in rhizobium legume interactions. This symbiosis is a complex process that involves signalling that can be shaped by plant rhizospheric exudates and microbiome composition. The relationship established by rhizobia with other rhizospheric organisms, together with the influence of environmental factors, results in their beneficial role on host plant health. biological signals and the exchange of information are part of the definition of communication, while the signals themselves are considered as "every structure able to shape the behavior of the organisms". Consequently, the signals can evolve and persist thanks to the interaction between signal producers and receivers. Then, cooperation and fitness improvement are the basis of biological communication. A large number of signals can be exchanged involving the plant itself, insects, fungi, and microbes. This all takes place in a high density environmental niche. Usually, communication is the result of chemical responses of cells to signatory molecules coming from other cells. These signals affect both the metabolism and transcription of genes activating several regulatory mechanisms. Nevertheless, a large number of nutrients issued by the plant can be of interest to pathogenic organisms, which can take advantage of plant products for their survival in the rhizosphere. Indeed, because of the chemical signals conveyed by nutrient rich exudates released by the plant roots, a large variety of microbes can first colonize the rhizosphere and then gradually penetrate the root and the overall plant tissue (endophytes). Otherwise, they can colonize the host plant establishing a lasting and beneficial symbiotic relationship. To date, numerous investigations on root exudates composition have been performed. However, the knowledge about the earlier steps of rhizosphere colonization, namely the opening line at the root surface, remains poorly characterized. Nonetheless, increasing data have shown the importance of intraspecies and multispecies communications among rhizospheric biotic components for the improvement of rhizobia–legumes interaction. In addition, it has been shown that rhizobia are part of the rhizosphere of a wide variety of non legume plants where they can play a role as plant growth promoting components, recovering a central role in plant core microbiome. Pyrolysis–field ionization mass spectrometry allows for spectrometry of agricultural fields to find fulvic and humic acids and the extraction residues (humins) in certain studies and expanded to general organic compounds in other recent work. A = amoeba consuming bacteria; BL = energy limited bacteria; BU = non energy limited bacteria; RC = root derived carbon; SR = sloughed root hair cells; F = fungal hyphae; N = nematode worm.]]