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".
Plants live in association with diverse microbial consortia. These microbes, referred to as the plant's microbiota, live both inside and outside 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
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 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, 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.Traditionally, plant-microbe interaction studies have been confined to culturable microbes. The numerous microbes that could not 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 composition of these microbiomes is dynamic and can be modulated by the environment and by climatic conditions. 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, corn, rice, soybean, wheat, whereas less attention has been given to fruit crops and tree species.
Plant microbiota
are an example of a microorganism which widely interacts in a symbiotic manner with land plants. Cyanobacteria can enter the plant through the stomata and colonise the intercellular space, forming loops and intracellular coils. Anabaena spp. colonize the roots of wheat and cotton plants. Calothrix sp. has also been found on the root system of wheat. Monocots, such as wheat and rice, have been colonised by Nostoc spp., In 1991, Ganther and others isolated diverse heterocystous nitrogen-fixing cyanobacteria, including Nostoc, Anabaena and Cylindrospermum, from plant root and soil. Assessment of wheat seedling roots revealed two types of association patterns: loose colonization of root hair by Anabaena and tight colonization of the root surface within a restricted zone by Nostoc.File:Microbial colonization of the phyllosphere and rhizosphere.jpg|thumb|upright=2|left| Microbial colonisation occurs both in the above-ground part of the plant, as well as the below-ground part. The microbial colonisation on the leaf takes place on the leaf surface from air-borne and soil-borne inocula and the inner leaf part. Microbial colonisation can lead to exogenous intraspecies biofilm formation on the leaf surface. Microbe–microbe interactions occur between interspecies and interkingdoms, referred to as quorum sensing. Quorum-sensing molecules impacting microbial recognition and biofilm formation on leaves. Pathogenic microbes colonize host plants by means of their virulence. The genetic make-up of both the host and pathogen contributes to disease progression. However, other microbes in the host phyllosphere can influence this plant–pathogen interaction by either facilitation or antagonism. Plant immune responses are of specific interest as host–microbe interactions shaping the phyllosphere microbiome. Non-host-adapted pathogens are involved in PAMP-triggered immunity and recognised via pattern recognition receptors. Host-adapted microbes are recognised via nucleotide-binding leucine-rich repeat receptors, summarised in effector-triggered immunity.
File:Leaf and root colonization by cyanobacteria.jpg|thumb|upright=2|left| Cyanobacteria enter the leaf tissue through the stomata and colonize the intercellular space, forming a cyanobacterial loop.
On the root surface, cyanobacteria exhibit two types of colonization pattern; in the root hair, filaments of Anabaena and Nostoc species form loose colonies, and in the restricted zone on the root surface, specific Nostoc species form cyanobacterial colonies.
Co-inoculation with 2,4-D and Nostoc spp. increases para-nodule formation and nitrogen fixation. A large number of Nostoc spp. isolates colonize the root endosphere and form para-nodules.
Rhizosphere microbiome
The rhizosphere comprises the 1–10 mm zone of soil immediately surrounding the roots that is under the influence of the plant through its deposition of root exudates, mucilage and dead plant cells. A diverse array of organisms specialize in living in the rhizosphere, including bacteria, fungi, oomycetes, nematodes, algae, protozoa, viruses, and archaea.Mycorrhizal fungi are abundant members of the rhizosphere community, and have been found in over 200,000 plant species, and are estimated to associate with over 80% of all plants. Mycorrhizae–root associations play profound roles in land ecosystems by regulating nutrient and carbon cycles. Mycorrhizae are integral to plant health because they provide up to 80% of the nitrogen and phosphorus requirements. In return, the fungi obtain carbohydrates and lipids from host plants. Recent studies of arbuscular mycorrhizal fungi using sequencing technologies show greater between-species and within-species diversity than previously known.
File:Microbial consortia naturally formed on the roots of Arabidopsis thaliana.webp|thumb|upright=1.7|left| Scanning electron microscopy pictures of root surfaces from natural A. thaliana populations showing the complex microbial networks formed on roots.
a) Overview of an A. thaliana root Biofilm-forming bacteria. c) Fungal or oomycete hyphae surrounding the root surface. d) Primary root densely covered by spores and protists. e, f) Protists, most likely belonging to the Bacillariophyceae class. g) Bacteria and bacterial filaments. h, i) Different bacterial individuals showing great varieties of shapes and morphological features.
The most frequently studied beneficial rhizosphere organisms are mycorrhizae, rhizobium bacteria, plant-growth promoting rhizobacteria, and biocontrol microbes. It has been projected that one gram of soil could contain more than one million distinct bacterial genomes, and over 50,000 OTUs have been found within the potato rhizosphere. Among the prokaryotes in the rhizosphere, the most frequent bacteria are within the Acidobacteriota, Pseudomonadota, Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota. In some studies, no significant differences were reported in the microbial community composition between the bulk soil and rhizosphere soil. Certain bacterial groups are less abundant in the rhizosphere than in nearby bulk soil. Beyond facilitating access to nutrients and to provide protection to biotic and abiotic stresses, certain PGPR modify root architecture.
Endosphere microbiome
Some microorganisms, such as endophytes, penetrate and occupy the plant internal tissues, forming the endospheric microbiome. The arbuscular mycorrhizal and other endophytic fungi are the dominant colonizers of the endosphere. Bacteria, and to some degree archaea, are important members of endosphere communities. Some of these endophytic microbes interact with their host and provide obvious benefits to plants. Unlike the rhizosphere and the rhizoplane, the endospheres harbor highly specific microbial communities. The root endophytic community can be very distinct from that of the adjacent soil community. In general, diversity of the endophytic community is lower than the diversity of the microbial community outside the plant. The identity and diversity of the endophytic microbiome of above-and below-ground tissues may also differ within the plant.In 2025, the "tree microbiome" was presented in an article in the journal Nature. The focus was microbial symbionts regularly found in the wood of trees with even very large trunk diameters. Distinctly different microbes were found not only in diverse tree species but also as they varied between the sapwood and the deep heartwood. As reported in the New York Times, "Sapwood is dominated by microbes that require oxygen, whereas heartwood is dominated by microbes that don't. Much of the methane produced by a tree originates from the heartwood, the study found."