plant microbiome plant microbiome the plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. the microbiome has been defined as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. the term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". part of a series onmicrobiomes plant microbiomes endosphere phyllosphere rhizosphere laimosphere root microbiome soil microbiome spermosphere marine microbiomes seagrass coral cetacean marine microbial symbiosis human microbiomes human milk fecal transplant gut–brain axis placental salivary uterine necrobiome other microbiomes mycobiome phycosphere built environment drosophila gut microbiota plant endophyte epiphyte rhizobacteria human gut lung oral skin vaginal marine microbial community initial acquisition accessible carbohydrates flora (microbiology) holobionts plant holobiont marine holobiont coral crab seagrass sponge rhodolith hologenomics hologenome evolution viromes bat human mangrove viriome virosphere related biomass partitioning dysbiosis gnotobiosis phytobiome quorum sensing biological dark matter microbial population biology microbial cooperation metagenomics viral metatranscriptomics metabolomics pan-genome superorganism symbiogenesis projects human microbiome project earth microbiome project category plants live in association with diverse microbial consortia. these microbes, referred to as the plant's microbiota, live both inside (the endosphere) and outside (the episphere) of plant tissues, and play important roles in the ecology and physiology of plants. "the core plant microbiome is thought to comprise keystone microbial taxa that are important for plant fitness and established through evolutionary mechanisms of selection and enrichment of microbial taxa containing essential functions genes for the fitness of the plant holobiont." plant microbiomes are shaped by both factors related to the plant itself, such as genotype, organ, species and health status, as well as factors related to the plant's environment, such as management, land use and climate. the health status of a plant has been reported in some studies to be reflected by or linked to its microbiome. overview microbiome in plant ecosystem schematic plant and plant-associated microbiota colonizing different niches on and inside the plant tissue. all the above-ground plant parts together, called the phyllosphere, are a continuously evolving habitat due to ultraviolet (uv) radiation and altering climatic conditions. it is primarily composed of leaves. below-ground plant parts, mainly roots, are generally influenced by soil properties. harmful interactions affect the plant growth through pathogenic activities of some microbiota members (left side). on the other hand, beneficial microbial interactions promote plant growth (right side). the study of the association of plants with microorganisms precedes that of the animal and human microbiomes, notably the roles of microbes in nitrogen and phosphorus uptake. the most notable examples are plant root-arbuscular mycorrhizal (am) and legume-rhizobial symbioses, both of which greatly influence the ability of roots to uptake various nutrients from the soil. some of these microbes cannot survive in the absence of the plant host (obligate symbionts include viruses and some bacteria and fungi), which provides space, oxygen, proteins, and carbohydrates to the microorganisms. the association of am fungi with plants has been known since 1842, and over 80% of land plants are found associated with them. it is thought am fungi helped in the domestication of plants. in this animation a root tuber is being colonized by an arbuscular mycorrhizal fungus (amf) traditionally, plant-microbe interaction studies have been confined to culturable microbes. the numerous microbes that couldn't be cultured have remained uninvestigated, so knowledge of their roles is largely unknown. the possibilities of unraveling the types and outcomes of these plant-microbe interactions has generated considerable interest among ecologists, evolutionary biologists, plant biologists, and agronomists. recent developments in multiomics and the establishment of large collections of microorganisms have dramatically increased knowledge of the plant microbiome composition and diversity. the sequencing of marker genes of entire microbial communities, referred to as metagenomics, sheds light on the phylogenetic diversity of the microbiomes of plants. it also adds to the knowledge of the major biotic and abiotic factors responsible for shaping plant microbiome community assemblages. the composition of microbial communities associated with different plant species is correlated with the phylogenetic distance between the plant species, that is, closely related plant species tend to have more alike microbial communities than distant species. the focus of plant microbiome studies has been directed at model plants, such as arabidopsis thaliana, as well as important economic crop species including barley (hordeum vulgare), corn (zea mays), rice (oryza sativa), soybean (glycine max), wheat (triticum aestivum), whereas less attention has been given to fruit crops and tree species. plant microbiota