Root microbiome

The root microbiome (also called rhizosphere 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. The root microbiome (also called rhizosphere 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. Different microorganisms, both beneficial and harmful affect development and physiology of plants. Beneficial microorganisms include bacteria that fix nitrogen, promote plant growth, mycorrhizal fungi, mycoparasitic fungi, protozoa and certain biocontrol microorganisms. Pathogenic microorganisms also span certain bacteria, pathogenic fungi and certain nematodes that can colonize the rhizosphere. Pathogens are able to compete with protective microbes and break through innate plant defense mechanisms. Apart from microbes that cause plant diseases, certain bacteria that are pathogenic and can be carried over to humans, such as Salmonella, enterohaemorhagic Escherichia coli, Burkholedria (ceno)cepacia, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia can also be detected in root associated microbiome and in plant tissues. Root microbiota affect plant host fitness and productivity in a variety of ways. Members of the root microbiome benefit from plant sugars or other carbon rich molecules. Individual members of the root microbiome may behave differently in association with different plant hosts, or may change the nature of their interaction (along the mutualist-parasite continuum) within a single host as environmental conditions or host health change. Despite the potential importance of the root microbiome for plants and ecosystems, our understanding of how root microbial communities are assembled is in its infancy. This is in part because until recent advances in sequencing technologies, root microbes were difficult to study due to high species diversity, the large number of cryptic species, and the fact that most species have yet to be retrieved in culture. Evidence suggests both biotic (such as host identity and plant neighbor) and abiotic (such as soil structure and nutrient availability) factors affect community composition. Root associated microbes include fungi, bacteria, and archaea. In addition, other organisms such as viruses, algae, protozoa, nematodes and arthropods are part of root microbiota. Symbionts associated with plant roots subsist off of photosynthetic products (carbon rich molecules) from the plant host and can exist anywhere on the mutualist/parasite continuum. Root symbionts may improve their host's access to nutrients, produce plant-growth regulators, improve environmental stress tolerance of their host, induce host defenses and systemic resistance against pests or pathogens, or be pathogenic. Parasites consume carbon from the plant without providing any benefit, or providing too little benefit relative to what they cost in carbon, thereby compromising host fitness. Symbionts may be biotrophic (subsisting off of living tissue) or necrotrophic (subsisting off of dead tissue). While some microbes may be purely mutualistic or parasitic, many may behave one way or the other depending on the host species with which it is associated, environmental conditions, and host health. A host’s immune response controls symbiont infection and growth rates. If a host’s immune response is not able to control a particular microbial species, or if host immunity is compromised, the microbe-plant relationship will likely reside somewhere nearer the parasitic side of the mutualist-parasite continuum. Similarly, high nutrients can push some microbes into parasitic behavior, encouraging unchecked growth at a time when symbionts are no longer needed to aid with nutrient acquisition. Roots are colonized by fungi, bacteria and archaea. Because they are multicellular, fungi can extend hyphae from nutrient exchange organs within host cells into the surrounding rhizosphere and bulk soil. Fungi that extend beyond the root surface and engage in nutrient-carbon exchange with the plant host are commonly considered to be mycorrhizal, but external hyphae can also include other endophytic fungi. Mycorrhizal fungi can extend a great distance into bulk soil, thereby increasing the root system’s reach and surface area, enabling mycorrhizal fungi to acquire a large percentage of its host plant’s nutrients. In some ecosystems, up to 80% of plant nitrogen and 90% of plant phosphorus is acquired by mycorrhizal fungi. In return, plants may allocate ~20-40% of their carbon to mycorrhizae. Mycorrhizal (from greek) literally means “fungus roots” and defines symbiotic interaction between plants and fungus. Fungi are important to decompose and recycle organic material, however the boundaries between pathogenic and symbiotic lifestyles of fungi are not always clear-cut. Most of the time the association is symbiotic with fungus improving acquisition of nutrients and water from soil or increasing stress tolerance and fungus benefiting from carbohydrates produced by plant. Mycorrhizae include a broad variety of root-fungi interactions characterized by mode of colonization. Essentially all plants form mycorrhizal associations, and there is evidence that some mycorrhizae transport carbon and other nutrients not just from soil to plant, but also between different plants in a landscape. The main groups include ectomycorrhizae, arbuscular mycorhizae, ericoid mycorrhizae, orchid mycorrhizae, and monotropoid mycorrhizae. Monotropoid mycorrhizae are associated with plants in the monotropaceae, which lack chlorophyll. Many Orchids are also achlorophyllous for at least part of their life cycle. Thus these mycorrhizal-plant relationships are unique because the fungus provides the host with carbon as well as other nutrients, often by parasitizing other plants. Achlorophyllous plants forming these types of mycorrhizal associations are called mycoheterotrophs.