Plant microbiome

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. is being colonized by an arbuscular mycorrhizal fungus (AMF) 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. 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 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 (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==

Cyanobacteria 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. 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. ), as well as the below-ground part (rhizosphere). (A) The microbial colonisation on the leaf takes place on the leaf surface (epiphytes) from air-borne and soil-borne inocula and the inner leaf part (endophytes). Microbial colonisation can lead to exogenous intraspecies biofilm formation on the leaf surface. (B) Microbe–microbe interactions occur between interspecies and interkingdoms, referred to as quorum sensing. Quorum-sensing molecules impacting microbial recognition and biofilm formation on leaves. (C) 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. (D) 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 (PTI) and recognised via pattern recognition receptors (PRRs). Host-adapted microbes are recognised via nucleotide-binding leucine-rich repeat receptors (NLRs), summarised in effector-triggered immunity (ETI). and colonize the intercellular space, forming a cyanobacterial loop. (2) 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. (3) 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. and over 50,000 OTUs (operational taxonomic units) 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 (soil not attached to the plant root) and rhizosphere soil. Certain bacterial groups (e.g. Actinomycetota, Xanthomonadaceae) are less abundant in the rhizosphere than in nearby bulk soil . ==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. 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." ==Phyllosphere microbiome==

'' plant (left) and a leaf from a dysbiosis mutant plant (right) The aerial surface of a plant (stem, leaf, flower, fruit) is called the phyllosphere and is considered comparatively nutrient poor when compared to the rhizosphere and endosphere. The environment in the phyllosphere is more dynamic than the rhizosphere and endosphere environments. Microbial colonizers are subjected to diurnal and seasonal fluctuations of heat, moisture, and radiation. In addition, these environmental elements affect plant physiology (such as photosynthesis, respiration, water uptake etc.) and indirectly influence microbiome composition. Interactions between plants and their associated microorganisms in many of these microbiomes can play pivotal roles in host plant health, function, and evolution. The leaf surface, or phyllosphere, harbours a microbiome comprising diverse communities of bacteria, fungi, algae, archaea, and viruses. Interactions between the host plant and phyllosphere bacteria have the potential to drive various aspects of host plant physiology. However, as of 2020 knowledge of these bacterial associations in the phyllosphere remains relatively modest, and there is a need to advance fundamental knowledge of phyllosphere microbiome dynamics. There can be up to 107 microbes per square centimetre present on the leaf surfaces of plants, and the bacterial population of the phyllosphere on a global scale is estimated to be 1026 cells. The population size of the fungal phyllosphere is likely to be smaller. Phyllosphere microbes from different plants appear to be somewhat similar at high levels of taxa, but at the lower levels taxa there remain significant differences. This indicates microorganisms may need finely tuned metabolic adjustment to survive in phyllosphere environment. Although there are similarities between the rhizosphere and soil microbial communities, very little similarity has been found between phyllosphere communities and microorganisms floating in open air (aeroplankton). there is no consensus on the dominant driver of community assembly across phyllosphere microbiomes. For example, host-specific bacterial communities have been reported in the phyllosphere of co-occurring plant species, suggesting a dominant role of host selection. As a result, the processes that drive phyllosphere community assembly are not well understood but unlikely to be universal across plant species. However, the existing evidence does indicate that phyllosphere microbiomes exhibiting host-specific associations are more likely to interact with the host than those primarily recruited from the surrounding environment. The prevailing core microbiome concept is built on the notion that the persistence of a taxon across the spatiotemporal boundaries of an ecological niche is directly reflective of its functional importance within the niche it occupies; it therefore provides a framework for identifying functionally critical microorganisms that consistently associate with a host species. and even different species. defining core taxa sensu stricto as those persistent across broad geographic distances within tissue- and species-specific host microbiomes, represents the most biologically and ecologically appropriate application of this conceptual framework. Mānuka honey, produced from the nectar of mānuka flowers, is known for its non-peroxide antibacterial properties. Microorganisms have been studied in the mānuka rhizosphere and endosphere. Earlier studies primarily focussed on fungi, and a 2016 study provided the first investigation of endophytic bacterial communities from three geographically and environmentally distinct mānuka populations using fingerprinting techniques and revealed tissue-specific core endomicrobiomes. on the left illustrates how the composition of OTUs in the mānuka phyllosphere and associated soil communities differed significantly. No core soil microbiome was detected.(B) The chart on the right shows how OTUs in phyllosphere and associated soil communities differed in relative abundances. A 2020 study identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. The results demonstrated the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka. == Seed microbiome ==

Plant seeds can serve as natural vectors for vertical transmission of their beneficial endophytes, such as those that confer disease resistance. A 2021 research paper explained, "It makes sense that their most important symbionts would be vertically transmitted through seed rather than gambling that all of the correct soil-dwelling microbes might be available at the germination site." The new paradigm regarding mutualistic fungi and bacterial transmission via the seeds of host plants has been fostered largely by research pertaining to plants of agricultural value. Rice seeds were found to entail high microbial diversity, with the greatest diversity inhabiting the embryo rather than the pericarp. Fungi of genus Fusarium transmitted via seeds were found to be dominant members of the microbiome within the stems of maize. Forestry researchers have also begun to identify members of the seed microbiome pertaining to valuable tree species. Vertical transmission of fungal and bacterial mutualists was confirmed in 2021 for the acorns of oak trees. If the research on oaks turns out to apply to other tree species, it will be understood that the above-soil portions of a plant (the phyllosphere) obtain nearly all of their beneficial fungi from those carried in the seed. Application of the new understanding of beneficial microbes inhabiting seeds has been suggested for use beyond agriculture and for biodiversity conservation. ==Putting it together==

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a holobiont. Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. ==See also==

• Saleem M (2015) Microbiome Community Ecology: Fundamentals and Applications Springer. . • Kumar V, Prasad R, Kumar M and Choudhary DK (2019) Microbiome in Plant Health and Disease: Challenges and Opportunities Springer. . • • • • • • • • • • • • • • •