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Plant microbiome
Plant microbiome
Plant microbiome
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The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years.[1][2] 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".[3][4]

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.[5] "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."[6]

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.[7] The health status of a plant has been reported in some studies to be reflected by or linked to its microbiome.[8][1][9][2]

Overview

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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).[10]

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.[11] It is thought AM fungi helped in the domestication of plants.[5]

In this animation a root tuber is being colonized by an arbuscular mycorrhizal fungus (AMF)
Microbes are represented by small coloured shapes. Diversity and number of microbes is variable between soils, distance from plant roots, crop species, and plant tissue.[12]

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.[5] 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.[8][13][1] 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.[13][5]

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.[14] The composition of these microbiomes is dynamic and can be modulated by the environment and by climatic conditions.[15] 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.[16][2]

Plant microbiota

[edit]
See also: microbiota

Cyanobacteria are an example of a microorganism which widely interacts in a symbiotic manner with land plants.[17][18][19][20] Cyanobacteria can enter the plant through the stomata and colonise the intercellular space, forming loops and intracellular coils.[21] Anabaena spp. colonize the roots of wheat and cotton plants.[22][23][24] Calothrix sp. has also been found on the root system of wheat.[23][24] Monocots, such as wheat and rice, have been colonised by Nostoc spp.,[25][26][27][28] 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.[25][29]

Microbial colonization of the phyllosphere and rhizosphere [30]
Microbial colonisation occurs both in the above-ground part of the plant (phyllosphere), 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).[30]
Diverse microbial communities of characteristic microbiota are part of plant microbiomes, and are found on the outside surfaces and in the internal tissues of the host plant, as well as in the surrounding soil.[5]
Symbiosis of cyanobacteria with land plants [29]
(1) Cyanobacteria enter the leaf tissue through the stomata 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.[29]

Rhizosphere microbiome

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See also: Root microbiome and Rhizosphere

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.[31] A diverse array of organisms specialize in living in the rhizosphere, including bacteria, fungi, oomycetes, nematodes, algae, protozoa, viruses, and archaea.[32]

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.[33] 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.[34] Recent studies of arbuscular mycorrhizal fungi using sequencing technologies show greater between-species and within-species diversity than previously known.[35][5]

Microbial consortia naturally formed
on the roots of Arabidopsis thaliana
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 (primary root) with numerous root hairs. b) 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.[36]
Associations in the rhizosphere between plant roots,
microbes, and root exudates [37]

"Experimental evidence underlines the importance of the root microbiome in plant health and it is becoming increasingly clear that the plant is able to control the composition of its microbiome. It stands to reason that those plants that manage their microbiome in a way that is beneficial to their reproductive success will be favored during evolutionary selection. It appears that such selective pressure has brought about many specific interactions between plants and microbes, and evidence is accumulating that plants call for microbial help in time of need."

– Berendsen et al, 2012 [8]

The most frequently studied beneficial rhizosphere organisms are mycorrhizae, rhizobium bacteria, plant-growth promoting rhizobacteria (PGPR), and biocontrol microbes. It has been projected that one gram of soil could contain more than one million distinct bacterial genomes,[38] and over 50,000 OTUs (operational taxonomic units) have been found within the potato rhizosphere.[39] Among the prokaryotes in the rhizosphere, the most frequent bacteria are within the Acidobacteriota, Pseudomonadota, Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota.[40][41] 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.[42][43] Certain bacterial groups (e.g. Actinomycetota, Xanthomonadaceae) are less abundant in the rhizosphere than in nearby bulk soil .[40][5] Beyond facilitating access to nutrients and to provide protection to biotic and abiotic stresses, certain PGPR modify root architecture.[44]

Endosphere microbiome

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Main article: Endosphere

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.[45] 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.[40][46][47] 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.[43] The identity and diversity of the endophytic microbiome of above-and below-ground tissues may also differ within the plant.[48][45][5]

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.[49] 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."[50]

Phyllosphere microbiome

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Main article: Phyllosphere
A leaf from a healthy Arabidopsis plant (left) and a leaf from a dysbiosis mutant plant (right)[51]

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.[5] Rain and wind also cause temporal variation to the phyllosphere microbiome.[52]

Interactions between plants and their associated microorganisms in many of these microbiomes can play pivotal roles in host plant health, function, and evolution.[53] The leaf surface, or phyllosphere, harbours a microbiome comprising diverse communities of bacteria, fungi, algae, archaea, and viruses.[54][55] Interactions between the host plant and phyllosphere bacteria have the potential to drive various aspects of host plant physiology.[56][57][58] 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.[59][60]

Overall, there remains high species richness in phyllosphere communities. Fungal communities are highly variable in the phyllosphere of temperate regions and are more diverse than in tropical regions.[61] 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.[62] The population size of the fungal phyllosphere is likely to be smaller.[63]

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.[61] Pseudomonadota seems to be the dominant colonizers, with Bacteroidota and Actinomycetota also predominant in phyllospheres.[64] 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).[45][5]

The assembly of the phyllosphere microbiome, which can be strictly defined as epiphytic bacterial communities on the leaf surface, can be shaped by the microbial communities present in the surrounding environment (i.e., stochastic colonisation) and the host plant (i.e., biotic selection).[54][62][60] However, although the leaf surface is generally considered a discrete microbial habitat,[65][66] 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.[66][45][67][60]

Conversely, microbiomes of the surrounding environment have also been reported to be the primary determinant of phyllosphere community composition.[65][68][61][69] 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.[56][70][71][72][60]

The search for a core microbiome in host-associated microbial communities is a useful first step in trying to understand the interactions that may be occurring between a host and its microbiome.[73][74] 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.[73][75][42][60]

Divergent definitions of "core microbiome" have arisen across scientific literature with researchers variably identifying "core taxa" as those persistent across distinct host microhabitats [76][77] and even different species.[67][70] Given the functional divergence of microorganisms across different host species [67] and microhabitats,[78] 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.[79][60] Tissue- and species-specific core microbiomes across host populations separated by broad geographical distances have not been widely reported for the phyllosphere using the stringent definition established by Ruinen.[57][60]

Example: The mānuka phyllosphere

[edit]

The flowering tea tree commonly known as mānuka is indigenous to New Zealand.[80] Mānuka honey, produced from the nectar of mānuka flowers, is known for its non-peroxide antibacterial properties.[81][82] Microorganisms have been studied in the mānuka rhizosphere and endosphere.[83][84][85] 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.[86][60]

{A} The heatmap 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.[60]

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.[60]

Relative abundance of core phyllosphere taxa in mānuka
Mānuka is a flowering scrub. The chart shows an abundance-occupancy distribution identifying core phyllosphere taxa in non-rarefied (green) and rarefied (purple) datasets. Each point represents a taxon plotted by its mean logarithmic relative abundance and occupancy. Taxa (pink) with an occupancy of 1 (i.e., detected in all 89 phyllosphere samples) were considered members of the core microbiome.[60]

Seed microbiome

[edit]
Main article: Spermosphere

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."[87]

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.[87][88] Rice seeds were found to entail high microbial diversity, with the greatest diversity inhabiting the embryo rather than the pericarp.[89] Fungi of genus Fusarium transmitted via seeds were found to be dominant members of the microbiome within the stems of maize.[87] This facet of the plant microbiome came to be known as the seed microbiome.[90]

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.[48][91] 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.[48] In contrast, the roots (the rhizosphere) acquire only a small fraction of their mutualists from the seed. Most arrive via the surrounding soil, and this includes their vital associations with arbuscular mycorrhizal fungi.[88]

Microbial species consistently found in plant seeds are known as the "core microbiome."[87][92] Benefits to the host plant include their ability to assist in the production of antimicrobial compounds, detoxification, nutrient uptake, and growth-promoting activities.[48] Discerning the functions of symbiotic microbes in seeds is shifting the agricultural paradigm away from seed breeding and preparation that traditionally sought to minimize the presence of fungal and bacterial propagules. The likelihood that a microbe found within a seed is mutualistic is now a routine presumption. Such partners may contribute to "seed dormancy and germination, environmental adaptation, resistance and tolerance against diseases, and growth promotion."[92]

Application of the new understanding of beneficial microbes inhabiting seeds has been suggested for use beyond agriculture and for biodiversity conservation.[88] A citizen group advocating for northward assisted migration of an endangered tree in the USA has pointed to the seed microbiome paradigm shift as a reason for the official institutions to lift their ban on seed transfer beyond the ex situ conservation plantings in northern Georgia.[93]

Plant holobiont

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Main article: Plant holobiont

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.[36]

See also

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References

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Reference books

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Plant microbiome

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The plant microbiome encompasses the collective community of microorganisms—primarily bacteria, fungi, archaea, protists, and viruses—that colonize the external surfaces and internal tissues of plants, including the (soil surrounding roots), phyllosphere (aerial parts like leaves), and endosphere (within plant tissues). These microbes form dynamic associations with their host plants, influencing growth, nutrient acquisition, and resilience to biotic and abiotic stresses through symbiotic, commensal, or pathogenic interactions. The concept of the plant microbiome has evolved from early 19th-century observations of root-associated microbes to modern understandings enabled by high-throughput sequencing since the 2010s. The composition of the plant microbiome is shaped by plant genotype, environmental factors, and ecological processes such as dispersal, recruitment via root exudates, and community assembly. Core microbiomes, consisting of keystone taxa consistently present across individuals of a species, provide essential functions like and solubilization, while satellite members vary by and contribute to functional redundancy. In the , for instance, plant growth-promoting (PGPR) such as and species dominate, whereas the hosts more stress-tolerant epiphytes adapted to UV radiation and . Recent metagenomic studies have revealed that these communities harbor vast , with bacterial taxa like Proteobacteria and Actinobacteria often comprising over 50% of the microbiome in many crops. Functionally, the plant microbiome enhances host fitness by facilitating nutrient cycling, producing phytohormones (e.g., auxins and ), and modulating plant immune responses through mechanisms like induced systemic resistance (ISR) and volatile compound signaling. Beneficial microbes suppress pathogens via direct antagonism—such as production or for resources—and indirect priming of plant defenses, reducing disease incidence in crops like and in field trials. Under global change factors like and elevated temperatures, microbiomes shift toward stress-resilient taxa, aiding plant ; for example, increased abundance of drought-tolerant fungi in has been linked to improved water-use in . The study of plant microbiomes has transformative implications for , enabling the development of microbial inoculants as biofertilizers and biopesticides to reduce chemical inputs and boost yields amid challenges. Advances in high-throughput sequencing and synthetic design have identified consortia that enhance crop resilience, such as multi-strain formulations improving yields while suppressing soil-borne diseases. As integrates ecological, evolutionary, and reductionist approaches, the plant microbiome emerges as a key frontier for engineering resilient agroecosystems.

Introduction

Definition and Scope

The plant microbiome refers to the diverse assemblage of microorganisms, including , fungi, , viruses, and protists, that inhabit the surfaces, tissues, and internal compartments of , along with their collective genetic material and functional interactions with the host. These microbial communities form dynamic associations that span the entire plant life cycle, from to , influencing host development and environmental adaptation. The scope of the plant microbiome encompasses a of relationships, ranging from symbiotic (mutualistic exchanges, such as provisioning), commensal (neutral coexistence), to pathogenic ( causation), which collectively modulate , including acquisition, stress tolerance, and immune responses. Unlike free-living microbiomes, which represent bulk environmental microbial diversity, the plant microbiome is selectively recruited and shaped by host-specific factors like root exudates and immune signaling, resulting in enriched, plant-tailored communities distinct from surrounding s. This host-associated focus highlights the microbiome's integral role in plant health across developmental stages, such as vegetative growth and . The plant microbiome contributes significantly to plant fitness by enhancing resilience to biotic and abiotic stresses, while also providing broader ecosystem services, including through microbial mediation of stabilization. In , microbiome-mediated processes, such as biofertilization and biocontrol, can increase crop yields by 20-30% and reduce reliance on chemical inputs, supporting sustainable production. Key terminology includes the , which describes the plant and its microbiome as a unified ecological unit with extended genomic capabilities, and distinctions between core microbiome members (consistently present taxa essential for host function) and transient members (variable, environmentally acquired microbes).

Historical Development

The study of plant microbiomes began in the late 19th century with foundational observations on symbiotic relationships between plants and microbes. In 1888, Hermann Hellriegel and Herman Wilfarth demonstrated through experiments that leguminous plants could assimilate atmospheric nitrogen via root nodules, attributing this process to microbial activity rather than direct plant uptake. This discovery highlighted the role of root-associated bacteria in nutrient acquisition, laying the groundwork for understanding plant-microbe symbioses. Concurrently, Martinus Beijerinck isolated the nitrogen-fixing bacterium Rhizobium from legume root nodules in the same year, confirming its symbiotic function and enabling pure culture studies that advanced microbiological techniques. Throughout the , research progressed through culture-based methods that allowed isolation and characterization of plant-associated microbes. From the to the 1950s, refinements in selective media and enrichment techniques, building on earlier work by soil microbiologists like Sergei Winogradsky, facilitated the study of diverse bacterial communities in plant roots and soils, though limited by the inability to culture most microbes. A significant expansion occurred in the mid-20th century with the recognition of above-ground microbial habitats; in 1956, Jacoba Ruinen described the "" as the leaf surface ecosystem supporting nitrogen-fixing such as Beijerinckia, emphasizing its ecological importance beyond roots. The genomic era transformed plant microbiome research starting in the 1990s, with the adoption of 16S rRNA gene sequencing enabling culture-independent profiling of bacterial diversity. This molecular approach revealed previously unculturable taxa, accelerating discoveries in the post-2000s boom, which was inspired by initiatives like the Human Microbiome Project (launched in 2007) that modeled comprehensive microbial community analyses. Early plant microbiome studies in the applied these tools to map root and leaf communities, such as the 2012 characterization of thaliana's microbiome. Key reviews in 2014 helped popularize "plant microbiome" as a unifying term, synthesizing ecological and functional insights from bacterial assemblages. In the 2020s, research has shifted toward multi-omics integration, combining , transcriptomics, and to elucidate dynamic plant-microbe interactions at molecular levels. This approach has uncovered regulatory networks influencing plant health, such as those mediating stress responses, building on prior genomic foundations to address complex community functions.

Microbial Habitats

Rhizosphere Microbiome

The refers to the narrow zone of , approximately 1-2 mm thick, immediately surrounding plant , where root activities profoundly influence properties and microbial communities. This zone is characterized by elevated concentrations of root-derived compounds, known as exudates, which can account for up to 40% of a plant's photosynthetically fixed carbon and include low-molecular-weight sugars, , organic acids, and secondary metabolites. As a result, microbial in the is markedly higher than in bulk , often reaching densities of 10^8 to 10^9 bacterial cells per gram of , fostering a hotspot of biological activity compared to the surrounding unimpacted . Recruitment of microbes to the is primarily driven by these exudates, which act as selective signals and nutrient sources to attract compatible from the pool. Sugars and in exudates provide readily available carbon, promoting the proliferation and chemotactic movement of beneficial taxa toward the , while specific compounds like can trigger or symbiotic signaling in targeted microbes. This selective enrichment favors plant-growth-promoting , such as of Pseudomonas and Bacillus, which efficiently utilize these exudates to establish dense populations in close proximity to the surface. In terms of composition, the microbiome is typically dominated by Proteobacteria and Actinobacteria, which together can comprise a significant portion of the bacterial community in various plant systems, such as . These phyla include key functional groups; for example, certain strains within Proteobacteria solubilize insoluble phosphates through the secretion of organic acids like gluconic and , thereby increasing bioavailability in the nutrient-limited environment. Similarly, Actinobacteria such as streptomycetes contribute to community stability via analogous mechanisms. The dynamics of community assembly are governed by microscale environmental gradients induced by activity, including shifts from exudate acidification, fluctuating oxygen levels due to respiration and , and ephemeral hotspots from localized exudate release. These factors create heterogeneous niches that drive deterministic selection and dispersal processes, ultimately structuring a resilient adapted to the root-soil interface.

Phyllosphere Microbiome

The encompasses the microbial communities inhabiting the aerial surfaces of plants, primarily leaves, but extending to stems, flowers, and other above-ground parts, forming one of the largest microbial habitats on . These communities, known as epiphytes, face a challenging environment characterized by intense (UV) , fluctuating temperatures, periodic , and scarce nutrients leached from plant tissues, resulting in relatively low microbial of approximately 10^6 to 10^7 bacterial cells per gram of fresh leaf weight. Colonization of the occurs primarily through aerial dispersal mechanisms, such as wind, rain, and insects, allowing microbes to settle on surfaces where they form microcolonies or biofilms, often concentrated around protective structures like stomata, trichomes, and depressions that offer shelter from desiccation and UV exposure. Dominant bacterial genera include wind-dispersed taxa such as and , which are adapted to utilize and other volatile compounds exuded by plants, enabling them to establish persistent populations despite the hostile conditions. Fungal colonization follows similar dispersal patterns, with spores landing and germinating under favorable moisture levels to form hyphal networks on surfaces. In certain plant species, fungi exhibit dominance within the microbiome, with phylum comprising a significant proportion of the community, often exceeding 50% relative abundance and contributing to epiphytic growth through spore production and nutrient scavenging. A notable case study is the native mānuka (Leptospermum scoparium), where phyllosphere communities on flowers display unique bacterial-fungal interactions, featuring high abundances of Pseudomonas bacteria and Cladosporium fungi that correlate with the plant's renowned antimicrobial properties, such as elevated levels in derived . These interactions highlight how phyllosphere microbes can influence host , potentially enhancing plant defense against pathogens. Environmental factors profoundly shape community structure, with rainfall and humidity promoting epiphytic growth by alleviating and facilitating microbial dispersal via and wash-in effects, leading to temporary increases in bacterial and fungal diversity. Conversely, rising temperatures associated with , as demonstrated in 2025 analyses, induce heat stress that reduces overall microbial diversity in the , particularly diminishing fungal taxa and altering community composition to favor heat-tolerant bacteria.

Endosphere Microbiome

The endosphere microbiome encompasses the microbial communities residing in the intracellular and intercellular spaces of plant tissues, including , stems, and leaves. These endophytes represent a subset of the plant microbiome that has successfully navigated host selective pressures, such as immune responses and nutrient limitations, leading to significantly lower diversity than in external habitats like the . Bacterial densities in the endosphere typically range from 10^4 to 10^6 cells per gram of fresh weight, with harboring higher abundances (up to 10^5–10^7 cultivable cells per gram) compared to aerial tissues like leaves and stems (10^3–10^4 cells per gram). Endophytes primarily gain access to the endosphere through passive translocation from the , entering via cracks at emergence sites or wounds, and subsequently spreading systemically through the vessels. Once inside, they persist by evading or modulating host defenses, often colonizing specific niches like vascular tissues or apoplastic spaces. For instance, bacteria of the genus , such as B. phytofirmans and B. vietnamiensis, are prominent root endophytes isolated from diverse plants including onions, potatoes, and , where they establish stable intracellular populations. Notable examples include fungal endophytes like Serendipita indica (formerly Piriformospora indica), which colonizes root cortical cells in crops such as , , and . In woody plants, endophytes exhibit from parent to offspring, often through reproductive structures, maintaining specific microbial lineages across generations. Some endophytes overlap with the seed microbiome through this pathway. Core endophyte communities demonstrate remarkable stability, with conserved taxa persisting across plant generations and even phylogenetic distances within species like (Zea mays). This conservation underscores the role of host genetics in shaping a stable endosphere . Advances in 2025, particularly in host DNA depletion techniques such as and computational decontamination tools like Kraken2, have improved metagenomic sequencing accuracy for these low-biomass communities by reducing host DNA interference from over 90% to below 10% in root samples.

Seed and Other Microbiomes

The seed microbiome encompasses microbial communities residing on the surface and within the internal tissues of seeds, serving as a critical vector for intergenerational transmission of beneficial microbes. These communities are dominated by bacteria from the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, with common genera including Pantoea, , and . Fungi such as Ascomycetes are also prevalent, alongside emerging evidence of viral components that may influence seed health and dynamics. Recent metagenomic analyses have identified over 200 bacterial genera across diverse species, underscoring the seed's role as a selective microbial reservoir. Vertical transmission from the maternal parent plant is the primary assembly pathway for the seed microbiome, enabling the inheritance of endophytes that colonize reproductive tissues during seed development. This maternal inheritance ensures continuity of adaptive traits, with studies demonstrating that seed microbes migrate from maternal endosphere compartments to offspring seeds. Horizontal acquisition from the environment, such as soil or air during maturation, supplements this process but is often filtered by plant selective mechanisms. Surface sterilization techniques, commonly used in experiments, can disrupt these communities by removing epiphytic microbes, potentially reducing seedling viability if key endophytes are lost; however, some protocols paradoxically enhance internal diversity and promote growth by alleviating competitive pressures. Seed-associated microbes significantly contribute to seedling establishment and early plant development, with seed-transmitted bacteria and fungi comprising the majority of juvenile microbiomes by abundance in crops like wheat and maize. For instance, in maize (Zea mays), endophytic bacteria isolated from seeds, such as Enterobacter and Pseudomonas species, confer drought tolerance by modulating physiological responses, including improved water use efficiency and reduced oxidative stress. These vertically transmitted microbes establish a foundational inoculum that persists into the adult endosphere, linking reproductive and vegetative phases. Emerging 2025 research on seed viromes has revealed diverse RNA and DNA viruses in crops like common bean (Phaseolus vulgaris), potentially transmitted maternally and impacting germination rates. In addition to seeds, floral microbiomes represent transient yet ecologically vital communities shaped by pollinator-mediated dispersal. These assemblages feature nectar-adapted yeasts (e.g., Metschnikowia spp.) and bacteria (e.g., Acinetobacter and Rosenberiella), introduced via insect vectors, which colonize petals, anthers, and stigmas to influence nectar chemistry and pollinator behavior. Fruit microbiomes, particularly in berries like blueberries and grapes, are enriched with lactic acid bacteria such as Lactiplantibacillus and Leuconostoc species, which drive fermentation-like processes during ripening, enhancing flavor volatiles and softening tissues while mitigating spoilage. Transmission in these sites balances maternal provisioning with environmental inputs, such as pollinator contact for flowers and post-flowering exposure for fruits, highlighting niche-specific adaptations distinct from vegetative habitats.

Composition and Diversity

Key Microbial Taxa

The plant microbiome is dominated by , which constitute the majority of microbial taxa across various plant compartments. Proteobacteria represent one of the most prevalent phyla, often comprising 40-60% of bacterial communities in the and endosphere, with genera such as known for their symbiotic associations with . Actinobacteria, accounting for 5-20% of bacterial diversity in soil-associated microbiomes, include antibiotic-producing genera like that contribute to microbial community structure. Firmicutes, typically 10-15% of the bacterial fraction, feature spore-forming genera such as , which exhibit resilience in diverse environments. Other notable bacterial groups include Bacteroidetes and Acidobacteria, which together with Proteobacteria and Actinobacteria form over 70% of prokaryotic communities in many plant . Fungi form a significant eukaryotic component of the plant microbiome, with and being the most abundant phyla, often exceeding 50% of fungal diversity in and habitats. includes saprophytic and endophytic taxa that colonize plant surfaces and tissues, while encompasses wood-decaying species and ectomycorrhizal associates. Glomeromycota, though less diverse, plays a pivotal role through arbuscular mycorrhizal fungi (AMF), such as those in the Rhizophagus, which form symbiotic networks with over 80% of terrestrial and are enriched in root endospheres. These fungal groups exhibit varying prevalence, with dominating global fungal communities through 83 dominant phylotypes. Archaea constitute a minor fraction of the plant microbiome, typically less than 1-5% of total microbial diversity, but are present in specific niches like rhizospheres where methanogenic taxa such as thrive under anaerobic conditions. Viruses, primarily bacteriophages, are integral regulators of bacterial populations within plant microbiomes, with recent metagenomic surveys revealing high diversity, including over 9,700 viral genomes with more than 1,500 previously unreported genus-level clusters in root-associated communities. Protists, including like , represent another underrepresented group, comprising 1-10% of eukaryotic diversity and showing compartment-specific structuring, such as higher specialization in root endospheres compared to foliar areas. The plant microbiome features a distinction between core and accessory taxa, where core members are universally present across host species and environments. For instance, Pseudomonas species are frequently part of the conserved core in rhizosphere samples from diverse crops, providing a stable bacterial backbone. Accessory taxa, in contrast, vary by host and habitat, such as host-specific Rhizobium strains in legumes. Metagenomic analyses from 2024 highlight the vast viral accessory diversity, with soil and root viromes uncovering thousands of previously unknown phages that modulate bacterial dynamics without universal conservation. This core-accessory dichotomy underscores the balance between stable, foundational microbes and variable contributors shaped by plant-specific interactions. Recent 2025 studies have further expanded the catalog of crop root viromes, revealing 9,736 non-redundant viral genomes that enhance understanding of viral modulation in microbiomes.

Factors Influencing Diversity

The diversity of plant-associated microbiomes is profoundly shaped by host factors, particularly plant and developmental . Plant influences microbial community structure and composition across compartments, with distinct cultivars selectively recruiting specific taxa through root exudates and immune responses. For instance, in , genotypic variations drive consistent differences in bacterial and viral communities, explaining up to 20% of the observed variation in diversity. Similarly, in , effects are more pronounced in than shoots, highlighting compartment-specific . Developmental further modulates diversity, with juvenile often exhibiting higher alpha-diversity due to broader of beneficial microbes before specialization in mature stages. Studies on and other model show that microbiome assembly shifts dynamically with , with early stages supporting more transient and diverse assemblages compared to reproductive phases. Abiotic environmental factors, including , moisture, and , act as primary drivers of variation across plant compartments. is a dominant regulator, with neutral to slightly acidic conditions favoring higher bacterial diversity, while extremes reduce richness; for example, Beta-Proteobacteria abundance increases with decreasing in soils. Moisture levels influence community assembly by altering nutrient availability and oxygen , with optimal hydration promoting diverse oligotrophic taxa, whereas waterlogging selects for anaerobes. Temperature gradients similarly impact diversity, as elevated heat stresses microbial populations; a seven-year grassland warming experiment demonstrated a 9.6% reduction in bacterial richness and 14.5% in fungal richness under moderate warming. exacerbates these effects, with drought conditions selectively enriching resilient taxa such as and Leifsonia, which enhance host tolerance, while reducing overall community evenness by favoring dormancy in sensitive groups. Biotic interactions within the plant microbiome contribute to diversity patterns through competitive dynamics and cross-kingdom synergies. Competition with pathogens structures communities by excluding deleterious microbes and promoting protective consortia, as seen in rhizosphere suppression of fungal wilt pathogens via bacterial antagonists. Cross-kingdom effects, particularly fungal-bacterial antagonism, further modulate composition; for example, bacterial metabolites inhibit fungal overgrowth, maintaining balanced diversity in the phyllosphere and endosphere. Anthropogenic influences, such as application and cropping practices, significantly alter ratios and diversity. Excess fertilization shifts communities toward copiotrophs, including Proteobacteria and Bacteroidetes, by enhancing resource availability and suppressing oligotrophs, as observed in long-term agricultural trials. systems induce through repetitive host selection pressures, leading to reduced fungal diversity and enrichment of pathogen-associated taxa; a 2024 analysis of continuous cropping revealed progressive shifts toward less resilient communities, with implications for decline.

Functions and Interactions

Nutrient Acquisition and Cycling

The plant microbiome significantly enhances nutrient acquisition by transforming otherwise inaccessible forms of essential elements into bioavailable compounds, thereby supporting growth and maintaining soil nutrient pools. Microbes, particularly in the , perform biogeochemical processes that mobilize macronutrients like and , as well as micronutrients such as iron and , through enzymatic activities and production. These interactions not only improve plant uptake but also contribute to broader nutrient cycling, influencing over time. Nitrogen fixation represents a cornerstone of microbiome-mediated nutrient acquisition, where diazotrophic bacteria convert atmospheric dinitrogen into ammonia via the nitrogenase enzyme complex. In symbiotic relationships, genera like Rhizobium and Bradyrhizobium form nodules on legume roots, fixing nitrogen through the reaction \ceN2+8H++8e−−>2NH3+H2\ce{N2 + 8H+ + 8e- -> 2NH3 + H2}, which supplies ammonium directly to the host plant. This process can provide 50-70% of the nitrogen requirements for plants in legume-dominated ecosystems, reducing reliance on synthetic fertilizers. Free-living diazotrophs, such as Azospirillum and Azotobacter in the rhizosphere, also contribute to non-symbiotic fixation, albeit at lower rates, by assimilating N2 under aerobic or microaerobic conditions. Phosphorus solubilization by the plant microbiome addresses the low bioavailability of soil phosphorus, which is often bound in insoluble mineral forms. Phosphate-solubilizing bacteria and fungi produce extracellular phosphatases that hydrolyze organic phosphorus compounds into inorganic orthophosphate, while secreting low-molecular-weight organic acids—such as gluconic, citric, and lactic acids—that chelate cations and lower rhizosphere pH to release bound phosphorus. For instance, Pseudomonas and Bacillus species generate gluconic acid via glucose oxidation, enhancing phosphorus availability by up to several-fold in acidic soils. These mechanisms are particularly vital in phosphorus-limited environments, where microbial activity can increase plant phosphorus uptake by 20-50%. Beyond macronutrients, the microbiome facilitates micronutrient cycling, notably through siderophore production for iron acquisition. Bacteria like Pseudomonas fluorescens synthesize siderophores—high-affinity iron-chelating compounds such as pyoverdine—that solubilize ferric iron (Fe³⁺) from soil oxides, making it accessible to plants via direct uptake or microbial re-release as ferrous iron (Fe²⁺). Similar siderophore-mediated strategies support zinc mobilization, with rhizobacteria enhancing zinc solubility through acidification and ligand exchange, thereby improving biofortification in crops like wheat and rice. These processes collectively boost soil fertility by recycling nutrients and preventing depletion, though they also influence gaseous emissions; for example, microbiome-driven denitrification in agricultural soils contributes to nitrous oxide (N₂O) fluxes, with nitrogen fertilization significantly elevating N₂O emissions, as indicated by 2024 meta-analyses showing increases of up to 150% in intensive cropping systems due to enhanced denitrification processes.

Growth Promotion and Stress Resistance

Plant-associated microbes, particularly plant growth-promoting rhizobacteria (PGPR), enhance plant vigor through the modulation of phytohormones such as (IAA), which stimulates development and overall accumulation. For instance, species produce IAA that can increase length by 20-30% in crops like and , leading to improved uptake and plant establishment. Similarly, microbial synthesis of promotes stem elongation and expansion, contributing to taller plants with greater photosynthetic capacity, as observed in and inoculated with gibberellin-producing bacteria. These hormonal effects often synergize with to bolster growth, though the primary impact stems from direct signaling rather than elemental supply. Microbes also confer resistance to abiotic stresses, enabling plants to maintain productivity under challenging conditions. In drought scenarios, endophytic bacteria such as Pseudomonas and Bacillus species produce osmoprotectants like trehalose, which stabilizes cellular structures and reduces water loss, thereby enhancing survival rates in crops like maize by up to 40%. For salinity stress, rhizosphere microbes facilitate ion exclusion by regulating sodium transporters and maintaining potassium homeostasis, as demonstrated in salt-tolerant tomato varieties associated with Halomonas and Arthrobacter strains that lower sodium accumulation in leaves. A notable example is Bacillus subtilis, which induces systemic growth promotion and stress tolerance through volatile organic compounds that upregulate plant defense genes, resulting in 15-25% higher yields under combined drought and heat in soybean. Recent studies highlight the role of microbiomes in mitigating heat stress via production. A 2025 review on development highlights the role of microbiomes, including like Methylobacterium on , in enhancing tolerance to heat stress through defenses and metabolic adjustments that mitigate oxidative damage. These protective effects are mediated by microbial mechanisms such as , where autoinducers like N-acyl homoserine lactones coordinate community behaviors to optimize hormone release and stress responses in the plant . Additionally, formation by root-associated microbes ensures persistence in harsh environments, encapsulating cells in a protective matrix that withstands and promotes long-term colonization. Additionally, and plant viruses can influence microbiome functions; for example, certain archaeal methanogens aid in cycling under flooded conditions, while viruses regulate bacterial populations to enhance overall to stresses.

Pathogen Defense and Dysbiosis

The plant microbiome plays a crucial role in defense through mechanisms such as induced systemic resistance (ISR), where beneficial microbes prime the plant's without direct antagonism of the . For instance, volatile organic compounds (VOCs) emitted by rhizobacteria like trigger ISR by activating (JA) and signaling pathways, enhancing resistance to a broad spectrum of . A seminal study demonstrated that the VOC 2,3-butanediol produced by Bacillus species induces systemic resistance in against the bacterial Pseudomonas syringae, mediated by JA-dependent defenses that upregulate pathogenesis-related genes. This priming effect allows plants to respond more rapidly to subsequent infections, reducing disease severity without compromising growth. Antagonistic interactions within the further bolster defense by direct competition and production. Beneficial bacteria such as species produce secondary metabolites like phenazines, which inhibit fungal pathogens through and disruption of their cell membranes. For example, phenazine-1-carboxylic acid from Pseudomonas chlororaphis suppresses take-all disease caused by Gaeumannomyces graminis in by interfering with respiration and promoting iron in the . Additionally, niche competition occurs as core microbiome members occupy space and resources, limiting colonization; studies show that stable core bacterial communities in the act as a barrier, preventing invasion by pathogens like through resource exclusion and formation. These mechanisms highlight the 's role as the plant's first line of biotic defense. Dysbiosis, or microbial community imbalance, disrupts these protective functions, increasing susceptibility to diseases such as . Overuse of antibiotics or chemical treatments in reduces microbial diversity, favoring pathogen proliferation; for instance, application of to the induces by depleting beneficial taxa, leading to aboveground symptoms and heightened vulnerability to necrotrophic pathogens. Recent 2024 research has advanced understanding of microbiome-mediated resistance to necrotrophs, revealing that resilient communities restore JA-ethylene pathways to counter tissue-necrotizing fungi like . Furthermore, core microbiomes in suppressive soils prevent invasion by maintaining functional diversity, as disruptions correlate with disease outbreaks. Emerging 2025 studies on the soil-plant-human axis underscore how soil contributes to crop health declines, with reduced bacterial alpha-diversity linked to impaired nutrient cycling and increased pathogen loads, ultimately affecting through microbiome transmission.

The Plant Holobiont

Conceptual Framework

The holobiont concept defines the plant and its associated microbiome as an integrated ecological unit that functions collectively, rather than as isolated entities. This framework posits the holobiont as a dynamic system where the host plant and its microbial partners interact to influence fitness, adaptation, and survival. Central to this model is the hologenome theory, proposed by Zilber-Rosenberg and Rosenberg in 2008, which asserts that the combined genetic material of the plant host and its microbiota—termed the hologenome—serves as a unit of inheritance and evolution, enabling rapid responses to environmental pressures through microbial community shifts. The hologenome theory, while influential, remains debated among scientists, with criticisms focusing on the partial heritability of microbiomes and the extent to which holobionts function as units of selection. Key components of the plant include the extended , encompassing the plant's nuclear, , and mitochondrial genes alongside the collective microbial , which can vastly expand functional capabilities. This extended contributes to an extended , where microbial activities enable traits beyond the host's inherent capacities, such as enhanced salt tolerance in colonized by halotolerant fungal endophytes that modulate and osmotic balance. These interactions highlight how the augments the plant's adaptive toolkit, allowing for emergent properties at the level. Empirical evidence supports the model's heritability, with studies demonstrating rates of microbial taxa ranging from 8% to 56% across host generations, indicating partial inheritance of the that influences offspring phenotypes. Recent reviews emphasize the 's role in resilience to , where microbial communities buffer against stressors like drought and temperature extremes by altering metabolic pathways and resource allocation. For instance, engineered have shown improved yield stability under abiotic pressures, underscoring the model's practical implications for adaptive . Unlike traditional symbiosis, which typically describes pairwise host-microbe relationships (e.g., a single plant-pathogen interaction), the framework encompasses community-level effects across diverse microbial taxa, including emergent dynamics from interspecies , , and environmental filtering within the entire assemblage. This broader scope accounts for how collective variations drive holobiont-level outcomes, such as ecosystem-level stability, without reducing to isolated mutualisms.

Host-Microbe Co-Evolution

Host-microbe co-evolution within the plant holobiont encompasses the reciprocal genetic adaptations that have shaped enduring symbioses between plants and their microbial partners over geological timescales. Key mechanisms driving this process include (HGT), which facilitates the rapid dissemination of symbiotic traits among microbial lineages. For instance, the nif genes responsible for in have been horizontally transferred between bacterial , enabling the evolution of nitrogen-fixing symbioses in diverse hosts. Complementing HGT, plants enforce partner fidelity through host sanctions, such as the abortion of root nodules in containing non-cooperative that fail to fix , thereby reducing the fitness of cheating microbes and stabilizing mutualistic interactions. Phylogenetic evidence underscores the ancient origins of these co-evolutionary dynamics, with striking congruence observed between and microbial lineages. Arbuscular mycorrhizal fungi, for example, share a common ancestry with land dating back over 400 million years, as evidenced by fossil records of vesicular-arbuscular mycorrhizae in Early Devonian and conserved symbiotic genes in modern angiosperms. This deep-time alignment suggests that mycorrhizal associations co-evolved alongside the colonization of terrestrial environments by , providing mutual benefits like enhanced uptake that influenced plant diversification. Recent genomic studies have illuminated how co-evolutionary processes manifest in contemporary plant variation, identifying microbiome-interactive traits that influence microbial recruitment. In cultivars, distinct profiles and characteristics act as cultivar-specific attractors for beneficial microbes, enhancing growth and resilience in a manner tied to host . These findings highlight implications for breeding holobionts—integrated plant-microbe units—where selecting for such traits could propagate co-evolved symbioses to improve agricultural outcomes. Despite these advances, challenges persist in delineating co-evolution from ecological sorting, where microbial communities assemble based on abiotic filters and host physiology rather than shared evolutionary . Distinguishing these processes requires integrating phylogenetic, genomic, and ecological data to avoid conflating transient adaptations with long-term genetic reciprocity. Furthermore, microbiomes contribute to by modulating hybrid fitness, as disrupted microbial associations in plant hybrids can lead to inviability or reduced viability through altered symbiotic support.

Research Methods and Advances

Sampling and Analytical Techniques

Sampling plant microbiomes requires compartment-specific protocols to distinguish microbial communities associated with different plant parts, such as the , rhizoplane, and endosphere, while minimizing . For the —the soil layer closely adhering to —samples are typically collected by gently shaking to remove bulk soil, followed by vortexing or in a phosphate buffer to detach loosely attached microbes, yielding the microbial fraction for analysis. In contrast, the endosphere, comprising internal tissues, necessitates surface sterilization to eliminate epiphytic contaminants; a common protocol involves sequential immersion in 70% for 1-5 minutes, followed by 1-5% (NaClO) with 0.01-0.05% Tween 20 for 3-10 minutes, and rinsing in sterile water, with efficacy verified by plating rinsates on nutrient media to confirm absence of surface growth. Throughout these processes, sterile tools, hoods, and negative controls (e.g., sterile water blanks) are essential to prevent cross-, as highlighted in consensus guidelines emphasizing rigorous procedural standardization. Traditional culture-based methods, which isolate microbes on selective media, recover only a small fraction—typically 1-5%—of the total plant-associated microbial diversity due to the unculturable nature of many taxa under laboratory conditions, limiting insights into community structure. This has driven a shift to molecular approaches, beginning with DNA or RNA extraction from homogenized samples using kits optimized for plant tissues (e.g., bead-beating to disrupt cells), enabling culture-independent profiling of total microbial communities. Molecular analysis primarily relies on sequencing techniques tailored to microbial domains. For bacteria, amplification and sequencing of the 16S rRNA hypervariable regions (e.g., V3-V4) via amplicon methods provide taxonomic resolution at the genus level, while for fungi, the (ITS) region is targeted to capture eukaryotic diversity. Shotgun metagenomics, by contrast, sequences all DNA fragments without targeted amplification, offering broader taxonomic coverage, strain-level resolution, and access to functional for inference, though at higher cost and computational demand. Quantification of microbial abundance and viability complements taxonomic profiling. Quantitative PCR (qPCR) targeting 16S rRNA or ITS genes estimates copy numbers per gram of sample, providing absolute abundance data when calibrated with standards, while flow cytometry enables rapid, single-cell enumeration of viable cells using fluorescent stains (e.g., SYBR Green for total DNA or propidium iodide for membrane integrity). Recent 2024 standards for multi-omics integration advocate harmonized protocols combining these with transcriptomics and metabolomics, using shared extraction methods and bioinformatics pipelines to correlate microbial composition with host function. These techniques yield diversity metrics such as alpha diversity (e.g., Shannon index) that reflect community richness and evenness derived from sequencing outputs.

Emerging Technologies and Challenges

Recent advances in host DNA depletion have significantly improved the resolution of microbial sequencing in plant microbiome studies by minimizing interference from abundant plant genetic material. For instance, protocols utilizing enzymatic treatments and selective lysis can reduce host DNA, enabling deeper metagenomic profiling of root-associated bacteria and fungi. Similarly, single-cell sequencing technologies have emerged as powerful tools for characterizing unculturable microbes, which constitute the majority of plant microbiome diversity. Techniques like microbial single-cell genomics and high-throughput platforms isolate and sequence individual cells from rhizosphere samples, revealing novel taxa and their functional genes in crops such as rice, where traditional culturing fails to capture over 99% of the community. Multi-omics approaches are integrating metabolomics with metagenomics to elucidate how plant root exudates drive microbial community assembly and shifts. Studies using liquid chromatography-mass spectrometry (LC-MS) on exudates from model plants like Arabidopsis have identified key metabolites, such as flavonoids and organic acids, that correlate with recruitment of beneficial nitrogen-fixing bacteria, leading to observable community restructuring under varying soil conditions. Complementing this, AI-driven predictive modeling employs machine learning algorithms, including random forests and neural networks, to detect dysbiosis patterns from multi-omics datasets. For example, supervised learning models trained on rhizosphere sequencing data can forecast microbial imbalances associated with pathogen outbreaks, aiding in early intervention strategies. Despite these innovations, several challenges persist in plant microbiome research, particularly regarding across studies. Batch effects in high-throughput sequencing, arising from variations in library preparation and instrumentation, can introduce artifacts that obscure true biological signals, with analyses showing up to 30% variance attributable to technical sources rather than environmental factors. Ethical concerns also surround microbiome editing techniques, such as CRISPR-based microbial engineering for plant inoculation, which raise issues of unintended ecological release, , and equitable access to modified strains in . Furthermore, research remains biased toward model plants like and major crops, leaving non-model species—such as wild perennials and underrepresented staples in developing regions—undersampled, which limits generalizable insights into diverse ecosystems. Looking ahead, spatial metagenomics promises to map in situ plant-microbe interactions at micron scales, with tools like NanoSIMS (nanoscale secondary ion mass spectrometry) combined with (FISH) enabling visualization of nutrient exchange between roots and symbionts, such as carbon transfer in mycorrhizal associations. Additionally, expansions in viral metagenomics as of 2025 are uncovering the overlooked virome component of plant microbiomes, with high-throughput sequencing of crop revealing thousands of novel viral genomes that modulate bacterial communities and influence host resilience. These developments, building on established sampling prerequisites, are poised to address current limitations and enhance holistic understanding of the plant .

Applications

Agricultural Engineering

In agricultural engineering, the manipulation of plant microbiomes through inoculants represents a key strategy for enhancing productivity. Commercial plant growth-promoting (PGPR) products, such as strains used for crops, have been widely adopted to facilitate and improve yields. For instance, with in soils with average fertility can increase yields by 15-25% by enhancing symbiotic and reducing reliance on synthetic fertilizers. These inoculants are typically applied as coatings or soil amendments, with established commercial formulations like those containing Rhizobium leguminosarum bv. viciae for peas and beans demonstrating consistent field performance in diverse agroecosystems. Microbial , comprising multiple PGPR strains, often outperform single-strain inoculants by providing synergistic benefits, such as combined solubilization, production, and suppression. Studies show that consortium inoculations can boost plant growth by up to 48%, compared to 29% for single strains, due to enhanced community stability and functional diversity in the . This advantage is particularly evident in , where co-inoculation of with other PGPR like or species has led to yield increases of 19-34% in crops such as chickpeas and common beans, attributed to improved uptake and stress tolerance. However, the efficacy of consortia depends on strain compatibility and environmental matching to avoid competitive exclusion. Breeding strategies increasingly incorporate microbiome-friendly traits to engineer plants that recruit beneficial microbes more effectively. (MAS) targets genetic loci associated with root exudate profiles, which influence microbiome assembly by releasing specific sugars, , and secondary metabolites that attract growth-promoting . For example, MAS has been used to select cultivars with distinct root exudate patterns that enhance microbiome diversity, leading to improved nutrient cycling and plant vigor. Recent advances include microbiome-assisted breeding approaches that integrate host with microbial community profiling to identify heritable traits fostering beneficial associations. Engineered endophytes offer targeted solutions for pest resistance, with enabling the introduction of genes for antimicrobial compound production. Research has developed bacterial endophytes modified to express insecticidal metabolites, such as those mimicking , which colonized crop roots and reduced pest damage by inducing systemic resistance without yield penalties. These engineered strains, often derived from native endophytes like or , demonstrate potential for integration into breeding programs to create pest-resistant varieties while maintaining balance. Field trials have validated microbiome inoculations for improving nitrogen-use efficiency (NUE) in cereals like . In multi-year studies, seed inoculation with beneficial increased NUE by optimizing root-associated and mineralization, resulting in higher yields under reduced inputs. For instance, inoculating with consortia of diazotrophic enhanced N assimilation, contributing to gains in fertilized fields. Despite these successes, challenges persist, including poor microbial survival in heterogeneous soils due to abiotic stresses like and competition from resident communities, which can reduce establishment rates in some trials. Strategies such as protective formulations and repeated applications are being explored to improve persistence. Regulatory frameworks ensure the of genetically modified (GM) microbes in , focusing on environmental and . In the United States, the USDA's Animal and Plant Health Inspection Service (APHIS) oversees permits for GM microorganisms under 7 CFR Part 340, evaluating potential , pathogenicity, and ecological impacts before field release. Reforms, including the 2022 Executive Order on the Bioeconomy, aim to streamline approvals for low-risk GM microbes while maintaining rigorous standards to prevent unintended . Sustainable farming initiatives have explored applications to boost resilience and reduce chemical inputs. These efforts align with global goals for eco-friendly , emphasizing verifiable safety and efficacy.

Climate Resilience and Sustainability

The plant microbiome plays a in mediating plant responses to , particularly through shifts in community composition under elevated temperatures and . Rising temperatures alter the and function of microbial communities associated with , often favoring opportunistic pathogens while diminishing beneficial taxa that support provisioning and stress tolerance. For instance, experimental and modeling studies indicate that under projected warming scenarios, beneficial plant involved in biocontrol and stress resistance could decline by approximately 0.6% across 80% of global regions by mid-century, potentially exacerbating vulnerability in ecosystems. Similarly, conditions select for resilient microbial consortia in the , such as drought-tolerant and fungi that enhance water uptake and osmotic adjustment, thereby stabilizing plant performance in water-limited environments. Microbiome modulation offers promising avenues for engineering climate-smart crops that maintain yield stability amid abiotic stresses. Recent advancements demonstrate that targeted inoculation with synthetic microbial communities or beneficial isolates, such as arbuscular mycorrhizal fungi and , can improve and tolerance in crops like and under stress conditions. This approach integrates genotype and root exudates to recruit protective microbes, fostering resilience without relying on genetic modification alone. Furthermore, the soil--human gut axis underscores broader implications for , as soil-derived microbes enhance in crops, which in turn supports human gut health and nutritional outcomes in stress-affected agricultural systems. In terms of sustainability, plant microbiomes enable reductions in chemical inputs by leveraging biofertilizers that fix and solubilize , potentially replacing 25-30% of synthetic nitrogen fertilizers while maintaining or boosting . Mycorrhizal associations further contribute to , with global estimates suggesting that allocate over 13 Gt CO₂ equivalents annually to mycorrhizal fungi, much of which stabilizes organic carbon pools and mitigates feedbacks. Globally, microbiome applications hold particular promise for developing regions, such as , where crops like benefit from microbial inoculants that enhance and nutrient efficiency in marginal soils. Future directions include designing synthetic microbial communities tailored to specific climates, which could predictably assemble resilient consortia to address emerging threats like compound stresses.

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