Plant–microbiome interactions: from community assembly to plant health 
Trivedi et al., 2020

Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant- associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant- associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions.

Beneficial effects of the plant-associated microbiome. The plant- associated microbiome can provide benefits to the plant through various direct or indirect mechanisms. These benefits include growth promotion (blue), stress control (green) and defence against pathogens and pests (red). Microbiome- mediated benefits can be initiated in any part of a plant (mostly belowground) and can be transmitted to other parts via plant- mediated transport or signals (shown as blue, green and red dashed arrows, representing mechanisms that contribute to plant growth, stress relief and defence, respectively). Direct effects are mediated through nitrogen fixation, through unlocking of essential nutrients from minerals and through enhancing the capability of plants to take up nutrients from the soil. In addition, other direct effects include the stimulation of plant growth via stress alleviation, through the modulation of aminocyclopropane-1- carboxylate (ACC) deaminase expression and the production of plant hormones, detoxification enzymes and osmoprotectants. Benefits can also be indirect, as the plant- associated microbiome protects the plant against pathogens or pests through antagonism or through inducing systemic resistance in plants. Complex microorganism–microorganism and host–microorganism interactions maintain the balance between different members of the microbial community in favour of beneficial microorganisms that contribute to plant health (yellow). Diazotrophic bacteria can fix atmospheric nitrogen (N 2 ) and might actively transport ammonium (NH 4 + ) and nitrate (NO 3 − ) to the host. Ammonifying bacteria convert organic N 2 present in the soil to NH 4 + , which is further converted to NO 3 − by nitrifying bacteria. Leguminous plants develop root nodule symbiosis with N 2 - fixing bacteria. Arbuscular mycorrhizal fungi convert arginine (Arg) to urea and then to NH 4 + . Microbiomes can unlock essential elements by oxidizing, solubilizing or chelating minerals into plant- available nutrients such as phosphate (Pi), nitrogen (NH 4 + ) and potassium (K + ) through the production of organic acids and siderophores. Furthermore, arbuscular mycorrhizal fungi might enhance nutrient availability by long- distance transport through the mycelium and specialized structures called arbuscules (fungal hyphae ensheathed in a modified form of the cortical cell plasma membrane) that transport elements directly to the host cytoplasm. Microbiomes can stimulate plant growth by metabolizing tryptophan and other small molecules in the plant exudates and producing phytohormones that include auxins, gibberellins, cytokinins and phytohormone mimics. Auxins can also induce transcription of the ACC synthase that catalyses the formation of ACC. ACC, the direct precursor of ethylene, is metabolized by bacteria via the enzyme ACC deaminase, thus ameliorating abiotic stress. Members of plant- associated microbiomes produce a range of enzymes that can detoxify reactive oxygen species, thus minimizing plant- induced stress. The plant- associated microbiome protects the plant against pathogens by the production of antibiotics, lytic enzymes, volatiles and siderophores. Various microbial structures — such as secretion systems, flagella and pili — along with proteins such as effector proteins, indirectly contribute to plant defence by triggering an induced systemic resistance response. Siderophore- mediated nutrient competition between commensals and plant pathogens can reduce pathogen titres. Interkingdom and intrakingdom interactions within the microbiome maintain the microbial balance, thus protecting plants from dysbiosis. Furthermore, hub microorganisms can amplify host signals in order to promote the assembly of a microbiome that provides benefits to the plant. Overall, beneficial plant–microbiome interactions improve the growth performance and/or health of plants

https://go.nature.com/3fXCHBX
.