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Review: The genetic basis of a plant's strategy of 'calling for help' to the microbiota
https://doi.org/10.1002/imt2.8
2022/3/14
● On March 14, 2022, Song Yi's team from the School of Life Sciences, Southern University of Science and Technology published a review article entitled " Toward understanding the genetic bases underlying plants mediated 'cry for help' to the microbiota " on iMeta online .
● This article systematically reviews the genetic basis of the host's active remodeling of the beneficial microbiome to enhance biotic and abiotic stress tolerance, and summarizes practical research approaches to establish the link between microbiome changes and plant functional traits.
● First author: Wang Zhenghong
● Corresponding author: Song Yi
Summary
Classical stress biology research mainly focuses on the regulation of endogenous genetic pathways related to plant stress response. Plant-mediated remodeling of the microbiota also contributes to enhancing its own tolerance to some specific biotic and abiotic stresses . More and more plant genetic regulators have been found to integrate biotic/abiotic stress signals and participate in active remodeling of plant microbiota, further supporting the hypothesis that plants "call for help" from microorganisms. Although multiple genetic mutations have been reported to affect the composition of plant microbial communities, due to the complexity of microbial community composition, it is desirable to determine the exact relationship between changes in specific microbial communities and plant phenotypic outputs such as improved environmental fitness. Causation remains extremely challenging. This also limits our understanding of plant-mediated changes in microbial community dynamics. This study reviews the genetic basis of host active remodeling of the beneficial microbiome to enhance biotic and abiotic stress tolerance, and summarizes practical research approaches to establish the link between microbiome changes and plant functional traits . Further understanding of the mechanism of how plant key regulators and related signaling pathways actively reshape the assembly of relevant microbial communities to enhance their own stress tolerance will enable future designs that can enrich beneficial microbial flora in a timely manner to alleviate plant tolerance to specific stresses It provides important theoretical and data support for precision breeding and precision agriculture.
Highlights
● Less research has been done on how plants actively remodel beneficial microbiota to enhance fitness
● Reviewed current understanding of the genetic mechanisms underlying plant-mediated remodeling of the microbiota
● Summarized methods to study the effects of microbiota changes on plant phenotypes
Video explanation
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Full text explanation
Introduction
Global climate change has increased the frequency of agricultural production-related stresses, and the accompanying population growth has created enormous challenges for the global food supply. The application of pesticides and chemical fertilizers in modern agriculture has significantly increased crop yields, but has also created a number of environmental problems. Therefore, sustainable agricultural development needs new and environmentally friendly biotechnology to support. Plant (host)-associated microbiota typically carry 10-100-fold more functional genes than the host, which significantly increases the genetic and metabolic potential of the plant-microbe community (host and its associated microbiota). Therefore, designing microbiota that can recruit plants to relieve stress and promote their own growth would be an environmentally friendly way to help them fight against multiple stresses. However, due to the large differences in indigenous microbial communities and soil heterogeneity in different regions, the biological and ecological effects of direct application of single or multiple combinations of beneficial strains in the field are unstable. Exploring the genetic and molecular mechanisms of plant-mediated dynamic regulation of its own microbiota under stress induction will help to design stress-resistant crops that can timely and robustly recruit microbiota that are beneficial to stress mitigation in the future.
In the past few decades, research on plant stress biology has mainly focused on the role of endogenous genetic regulators in abiotic and biotic stress responses, such as related hormones, (plant and animal) membranes or intracellularly localized immune receptors, etc. (Fig. 1) , but the role of plant-associated microorganisms in their stress response is less studied. Plants can secrete about 20-40% of photosynthetically fixed carbon sources into the rhizosphere and selectively form root-associated microbiota (containing rhizosphere, root surface and endothelial components) with high microbial diversity , and it has been reported that, 10 3 -10 4 OTUs (Operating Taxonomic Units) and 10 7 -10 8 CFUs (Colony Forming Units) per gram of rhizosphere soil . The development of high-throughput sequencing technology has revolutionized modern microbial ecology research. For example, amplicon sequencing of variant regions of bacterial 16S rRNA genes or fungal ITS genes can provide taxonomic and relative abundance information on microbial communities. Metagenome sequencing can further provide high-resolution taxonomic and functional information of the microbiome. Currently, plant genetic mutation and microbiome sequencing-related analyses suggest that phytoimmune hormone (especially salicylic acid) signaling can influence the composition of the microbiota, and that specialized triterpenoid metabolites also shape the composition of the Arabidopsis root-specific microbiota . Precise mutant screening experiments have also confirmed the involvement of plant genetic factors (especially immune genes) in the formation of specific microbial communities, but it remains a challenge to determine whether changes in the microbiome lead to corresponding changes in plant fitness. This study reviews known genetic regulators of the microbiota ("call for help") that are involved in active plant remodeling (response to stress or helping plants to relieve stress) and summarizes the genetic regulators that can be used to determine the relationship between microbiota changes and plant-specific Practical means of causality between functional traits.
Figure 1. A new perspective on improving stress tolerance in plants: remodeling the microbiota that mitigates stress
To resist biotic and abiotic stresses in terrestrial ecosystems, such as pathogen infection, insect feeding, nutrient deficiencies (nitrogen, phosphorus, and iron, etc.), drought, low or far-red light conditions (shading), etc., plants evolved complex genetic regulators. The stress response pathways within plants have been extensively studied (black arrows). For example, plants mainly utilize immune hormones (salicylic acid SA, jasmonic acid JA) to defend against pathogen infection, while abscisic acid (ABA) and ethylene (ETH) serve as the main abiotic stress response hormones. Plant membranes (FLS2, BAK1) or cytoplasmically localized immune receptors (NLR, TLR) mediate the recognition of microbe-associated molecular patterns or pathogen effectors, thereby enhancing plant immune responses when infected. In addition, some new studies have shown that a variety of plant genes (such as MYB72, NRT1.1B, FERONIA, PHR1, F6'H1, HY5 , etc.) are involved in the remodeling of the rhizosphere microbiota, which may be a new process in plant evolution. Adversity adaptation strategies.
Plant-mediated microbiota changes under various stresses
● Biological stress enriches rhizosphere Pseudomonas fluorescens and its potential regulators
Since the early 19th century, researchers have discovered that soil microbes have the potential to fight pathogens. For example, pathogen infection and wheat monocropping can create "disease-suppressive soil" and reduce the frequency of disease in the growth of progeny plants. In addition, this disease-suppressive property of soil can be inhibited by sterilization, and this disease-suppressive property can also be transferred by migrating 0.1–10% of the disease-suppressive soil to other soils. This leads to the hypothesis that pathogen infection triggers host signals to recruit beneficial microbes in the rhizosphere (the "cry for help" hypothesis, "Cry for help"). For a long time, it has been found that Pseudomonas is enriched in a variety of pathogen-related disease-suppressing soil systems and inhibits soil diseases through multiple mechanisms. Microbial high-throughput sequencing results broadly confirmed dramatic changes in microbial flora following pathogenic infection and found extensive enrichment of Pseudomonas spp. For example, Fusarium wilt infection affects pepper-associated microbiota composition, function, and symbiotic patterns and leads to enrichment of Pseudomonas, Streptomyces, and Bacillus. Proteobacteria (including Pseudomonas), Firmicutes and Actinobacteria are related to soil disease inhibition after R. beetella infection. The results of metagenomic sequencing showed that Pseudomonas, Chitinophage and Flavobacterium were enriched in roots after R. solani infection. Notably, aboveground insect (whitefly) infestation also caused changes in root-associated microbiota and recruited Pseudomonas fluorescens in the rhizosphere. In addition, studies have pointed out that nematode infection in roots can also lead to Pseudomonas enrichment and the production of disease-suppressing soils. The reason why Pseudomonas enriched in disease-suppressing soil can directly or indirectly endow soil with disease-suppressing characteristics. As strong colonizers of plant roots, they can directly compete with pathogens for colonization and rhizosphere nutrition. In addition, secondary metabolites such as phenazine and 2,4-diacetylchloroglucitol produced by Pseudomonas can also be Antagonize the growth of pathogenic fungi.
Several recent studies have provided new insights into the mechanisms of Pseudomonas colonization in the rhizosphere. The results based on genetic screening show that the receptor kinase FERONIA (FER) with multiple functions negatively regulates Pseudomonas by regulating guanosine triphosphatase (GTPase) ROP2 and maintaining basal reactive oxygen species (ROS) levels in roots. Colonization of bacteria in the rhizosphere. Notably, the ROP pathway is also involved in the regulation of soybean-rhizobia symbiosis, suggesting that the GEF-ROP system plays a key role in plant evolution and interactions with symbiotic microorganisms. The role of ROS in regulating Pseudomonas colonization is supported by multiple studies. For example, a mutant of Pseudomonas deficient in catalase activity ( katB , solubilizing H2O2) also exhibited defects in rhizosphere fitness, and application of catalase to the rhizosphere enhanced the adaptation of some Pseudomonas sex. Interestingly, both the fungal pathogen Furasium and some nematodes secrete analogs of RALF peptides (ligand peptides of FER) to enhance virulence, suggesting that RALF production in pathogens is associated with FER-mediated Pseudomonas colonization There is a link between regulation. These evidences provide a plausible explanation for the origin of disease-suppressive soils, whereby plants sense RALF secreted by pathogens (possibly together with other infection/injury signals) to recruit Pseudomonas. In fact, RALF23 treatment also resulted in the enrichment of Pseudomonas in the rhizosphere of Arabidopsis, but the extent to which this pathway mediates the disease-induced plant "call for help" and the enrichment of Pseudomonas remains to be determined. Further research in field-grown crops.
● Synergistic regulators between nutrient stress and microbiota changes
Soil nutrient content or availability directly limits crop growth, yield, and quality, and studies have identified endogenous signaling regulators that actively reshape the microbiota during plant nutrient starvation. Generally, plant roots mainly absorb inorganic nitrogen (nitrate and ammonium) rather than organic nitrogen, and soil microbial communities can affect the balance between soil organic nitrogen and inorganic nitrogen and thus affect nitrogen availability. Under natural conditions, indica varieties of rice ( Oryza sativa L. ) have higher nitrogen use efficiency than japonica varieties, partly because indica varieties contain more root-associated microbial communities that are rich in nitrogen metabolism-related functions . Further studies showed that NRT1.1B , the main transporter of nitrogen assimilation in rice, was involved in the formation of the microbiome related to the ammonification function of the rice rhizosphere (Fig. 1) . The results of metagenomic sequencing also showed that the nrt1.1b mutant had lower abundance. degree of microbiota associated with ammonification function. These results serve as genetic evidence that during the long-term evolution of rice, NRT1.1B can selectively form a beneficial microbiota that facilitates nitrogen assimilation. Maize root transcriptome and microbiome analysis showed that there was a correlation between the expression of flavonoid biosynthesis-related genes (such as type I2 flavonoid synthase, FNSI2) and the relative abundance of Oxalobacteriaceae. Synthesis of flavonoids to enrich the rhizosphere of Oxobacteriaceae and to promote growth and nitrogen acquisition when plants face nitrogen starvation.
Although iron is abundant in soils, iron is less soluble in both neutral and alkaline soils and therefore less available to plants. Plants have evolved complex iron starvation response pathways, for example, increasing the solubility of ferric iron through rhizosphere acidification, and secreting a series of secondary metabolites, such as coumarins (including scopoletin, fraxetin, and sideretin), to promote iron Assimilate and modulate the microbiome. MYB72 is a major regulator of phytocoumarin biosynthesis induced under iron starvation conditions, and both MYB72 and FERULOYL-COA 6-HYDROXYLASE1 (F6'H1, scopolactone synthase)-deficient mutants were observed in iron-deficient plants Significant changes in rhizosphere microbiota composition ( Table 1 ). This may be because scopolide can selectively inhibit the growth of fungal pathogens, while having little effect on the growth-promoting Pseudomonas. Another study in a controlled plate system demonstrated that the f6'h1 mutant significantly affected the composition of the rhizosphere microbiota under iron-deficiency conditions by using a synthetic microbiota consisting of 22 lines and found that coumarin ROS stress in bacteria can be triggered to exert antibacterial activity. These studies suggest that plants can secrete antibacterial coumarin to reshape the microbiota during iron starvation, but the exact mechanism by which changes in the microbiota alleviate iron stress is unclear . A recent study showed that inoculation of a synthetic flora (115 strains isolated from the Arabidopsis rhizosphere) under iron-deficient conditions increased iron content and fresh weight in wild-type Arabidopsis, but not in coumarin biosynthesis No expression in the deficient mutant. This suggests that coumarin-induced microbial community changes, rather than the original microbial community itself, can effectively alleviate iron starvation stress in plants . Meanwhile, transcriptome analysis showed that SynCom inoculation alleviated iron deficiency responses under low iron conditions, and mutants with iron uptake defects also blocked SynCom-mediated alleviation of iron starvation responses. These evidences further confirm that coumarin-induced microbiota changes mitigate plant iron stress responses by directly increasing iron utilization efficiency, rather than promoting iron assimilation-related pathways in roots.. Collectively, these studies detail the pathways by which plants remodel the microbiota to alleviate iron starvation and provide a paradigm for the systematic study of the relevant "call for help" mechanisms under plant nutrient stress.
There is a lot of total phosphorus in the soil, but plants can only take up orthophosphate. In contrast to the promotion of iron assimilation in plant roots by bacteria, bacteria compete with plants for orthophosphate and reduce the amount of orthophosphate in the soil. PHR1 acts as a master regulator of the phosphate starvation response, coordinating plant-rhizosphere microbiota interactions during phosphate starvation. Studies have shown that mutants deficient in a series of phosphate starvation regulators or phosphate transporters significantly alter the plant rhizosphere microbiota ( Table 1 ), and that the association of plants with symbiotic fungi is also regulated by phosphate starvation signals. For example, only under phosphate starvation conditions Arabidopsis thaliana can establish a beneficial symbiotic relationship with the growth-promoting endophytic fungus Colletotrichum tofieldiae , which assists in the transfer of phosphate into plants. This is because the production of indole glucosinolates associated with phosphate starvation prevents anthracnose overgrowth, which in turn limits anthracnose colonization in the rhizosphere, which is essential for mutualism. Some regulators of phosphate starvation ( PHR1 ) or indole glucosinolate synthesis ( MYB34, MYB51, MYB122 triple mutants) are also involved in maintaining this beneficial symbiosis, and mutants of these regulators were found to prevent anthrax under phosphate starvation conditions Bacteria-mediated plant growth promotion. Recruitment of mycorrhizal fungi is an energy-intensive process for plants and is therefore tightly regulated by the plants themselves. It has been reported that the association with beneficial mycorrhizal fungi in rice is also positively regulated by phosphorus starvation regulators PHRs, which enables rice to actively promote symbiosis during phosphorus deficiency and indirectly absorb phosphorus through mycorrhizal fungi. These studies show that plant-fungal symbiosis is subject to its own tight and timely control and is dependent on phosphate status.
Table 1. Studies on the remodeling of microbial communities in plants in the process of resisting stress
Interaction studies of plants and their associated microbial communities under nutrient stress reveal a pervasive interaction between nutrient homeostasis and root-associated microbial communities. Indeed, mutants that enhanced or disrupted root diffusion barriers (Kjeldahl zone and suberin sediments) affected both the ionome and the root-associated microbiome. At the same time, a large number of isolated root-associated bacteria can induce suberin deposition or Kjeldahl zone formation in roots and affect root ionome composition and adaptation to different mineral nutrient stresses. These studies demonstrate extensive interactions between roots and microbiota members that influence root dispersal barriers, nutrient homeostasis, and ultimately plant fitness.
● Coordinated cooperation with subterranean microbiota to adapt to light stress
As an energy source for photosynthesis, light is also a key signal for plants to coordinate growth, defense, and interactions with the microbiota. Plants have evolved complex photosensitive systems to sense light intensity and quality, including the phytochrome system for red light and the cryptochrome (CRY) system for blue light. A recent study showed that after rhizobia colonized soybean roots, light on the aerial part was required to successfully form nodules. Compared with red light, blue light had a stronger effect on promoting root nodulation. The blue light receptor CRYs in soybean Overexpression in can significantly promote nodulation. This process is regulated by the light-induced translocation of GmSTF3 (an ortholog of HY5, the master transcription factor for photomorphogenesis in Arabidopsis) and GmFT2a from shoot to root. Rhizobia activates the calcium/calmodulin-dependent kinase GmCCaMK to phosphorylate GmSTF3, promote the interaction between GmFT2a and GmSTF3, form a transcriptional activation complex, and further promote the expression of nodulation-related genes. Since rhizobia nodulation and symbiosis is an energy-consuming process that requires sufficient photosynthetic fixation energy, the GmCCaMK-GmSTF3-GmFT2 pathway allows plants to precisely tune root-rhizobia association according to above-ground light availability. Therefore, it would be interesting to further test whether the GmSTF3-GmFT2 pathway broadly affects the entire rhizosphere microbial community composition.
In the natural state, unfavorable light conditions such as shading (low light intensity or long wavelength light) are common light stress in high-density environments, which can easily lead to "shade avoidance syndrome" and inhibit plant growth and immunity. It has been noted that aboveground shading (low light intensity and "twilight-phase far-red light treatment") can reshape growth-promoting microbial communities (eg, Pseudomonas enrichment). After inoculation with artificial SynCom, the growth of plants in the shade and the resistance to pathogenic bacteria were enhanced compared with the plants grown under sterile conditions. Multiple mutants lacking photoreceptors (CRY1CRY2) or regulators such as jasmonic acid, gibberellin, and brassinosteroid signaling significantly affected shade-induced microbiota dynamics, and differences based on distance quantification (PCoA) were also associated with shade. Shade microbiota-mediated growth promotion is relevant. This strongly suggests that the involvement of plant genetic pathways (photoreceptor and hormonal signaling) alters the microbiota composition under shade stress, thereby promoting growth.
● Metabolic changes are associated with drought-induced changes in root microbiota
Drought causes dramatic and conservative changes in microbial community composition. For example, analysis of the microbiome profiles of 18 phylogenetically distant plant species revealed conservative changes in bacterial community composition during drought, such as the enrichment of Actinomycetes, especially Streptomyces strains. Notably, the relative abundance of Streptomyces rhizogenes in different plant species correlated with their drought tolerance. Several studies have found that inoculation with Streptomyces can promote crop growth and yield under drought stress. Studies in semi-sterile systems further confirmed the relationship between drought-induced enrichment of Streptomyces strains and plant growth promotion under drought stress. These evidences suggest that drought-induced changes in the microbiota, especially the enrichment of Streptomyces, can alleviate drought stress in plants. In addition, a beneficial fungus, Piriformospora indica , isolated from the rhizosphere of desert plants, can enhance plant tolerance to various stresses such as drought and salinity. The colonization of P. indianis promoted the biosynthesis of the antimicrobial compound camalexin in plant roots, but the drought-responsive hormone abscisic acid (ABA) inhibited the biosynthesis of camalexin and promoted its colonization. These evidences suggest that drought promotes the colonization of the plant rhizosphere by P. indica to enhance its adaptability to stress.
The effects of drought also depend on the timing and duration of drought stress. For example, drought stress had a greater effect on plant rhizosphere microbial communities before flowering than after flowering, while prolonged drought resulted in persistent 'memory' changes in root endophytic microbial communities enriched for Streptomyces, even after rehydration also cannot be recovered. Multi-omics integrative analysis (holomics) has greatly deepened our understanding of plant-mediated microbiota changes under drought stress in recent years. Studies have shown that the changes of plant root-related microbiota under drought stress are far greater than those of non-rhizosphere soil (Bulk soil) and toothpicks (simulating dead roots) and other related microbiota . Metabolic analysis showed that glycerol-3-phosphate (G3P) was significantly enriched in roots under drought, and transcriptome data showed that carbohydrate, amino acid transport, and metabolism-related genes were highly expressed in root-associated microbiota. A study presents 55 draft metagenomic recombinant genomes (MAGs) associated with roots and soils under drought stress and compares drought-enriched and non-enriched actinomycete-associated MAGs and found that in drought-enriched Iron transport and metabolism-related functional genes were more abundant in the genome. This suggests that the response of plants to iron deficiency is related to the enrichment of actinomycetes under drought. Similarly, in the absence of drought stress, the maize tom1 mutant with siderophore transport deficiency inhibited its own iron uptake and also led to the enrichment of rhizosphere actinomycetes. In addition, the relative abundance of Streptomyces was significantly higher in the rhizosphere of f6'h1 mutants (which prevented iron transfer-related coumarin biosynthesis and reduced plant fitness in iron-starved soils). These studies all confirmed that plant effects (especially iron deficiency response) are associated with drought-induced changes in the microbiota.
Methods for establishing the effects of plant-mediated microbiota changes on plant phenotypes
● Correlation between microbial abundance and plant phenotype
We can first quantify the mathematical correlation between the abundance of a particular taxa (culture-dependent or culture-independent) and the host trait of interest (Fig. 2a). For example, the relative abundance of Streptomyces endophytes after drought was significantly associated with drought tolerance in different plant species. This indicates that the enrichment of Streptomyces helps plants to alleviate drought stress. The number of beneficial Pseudomonas fluorescens in the rhizosphere can be directly quantified by counting fluorescent colonies on King's B medium, a medium used to detect Pseudomonas. This has been used to validate a significant correlation between plant rhizosphere levels of Pseudomonas fluorescens and its growth-promoting effect. Although this method only revealed correlation effects, it provided clues for the next step in the systematic validation of more convincing correlations.
Figure 2. Genus-level microbial composition and hierarchical clustering analysis
(A) For mutants of Pseudomonas or other microorganisms that are easy to isolate and quantify, CFU can be directly quantified in different treatment groups. If the abundance of strains of interest is related to plant traits (fresh weight or other stress response-related indicators), it provides preliminary clues for establishing the link between microbial changes and plant phenotypes. For most strains that are not easy to isolate and identify, the correlation with the trait of interest can be analyzed based on microbiome sequencing results (such as relative abundance) or qPCR results of species-specific marker genes;
(B) Plant-soil feedback (PSF) systems can be used to determine whether dynamic changes in the microbiota lead to plant-specific phenotypes (eg, growth promotion or increased stress tolerance). The green bacteria in the figure refer to the bacteria with growth-promoting effect or other beneficial effects, which are enriched by the primary plants;
(C) SynCom-based microbiota transplantation assays can be used to confirm causal relationships between microbial community changes and specific phenotypes. As shown, dysbiosis in plants can lead to a diseased phenotype in leaves or other tissues. To confirm causality, strains can be isolated from healthy and dysregulated communities, and SynCom transplants performed to determine whether specific microbiota transplants give plants the same phenotype as the original plant containing the dysregulated microbiota. SynCom-based methods are flexible enough to perform single-strain (single-association) screening or to combine modules of strains of interest.
● Plant-soil feedback system
Plants can selectively shape distinct rhizosphere microbiomes compared to non-rhizosphere soils, so that first-generation plants can alter indigenous microbial communities and preserve a lasting microbial "legacy" for future plants. This phenomenon, known as plant-soil feedback (PSF), can be used to detect whether changes in the microbial community lead to certain phenotypes in offspring (Fig. 2b). Previous studies have shown that infection of the first-generation Arabidopsis with the downy mildew pathogen can enrich the rhizosphere with disease-resistant beneficial microorganisms, thereby enhancing the disease resistance of the second-generation plants when grown in the same soil. However, PSF effects may also arise from changes in soil nutrients, therefore, two additional avenues are needed to further confirm the main effects of microbiota changes on PSF: 1) Ensuring adequate nutrient supply in the first and next generation (not applicable to Nutrient stress studies), adequate fertilizer (Hoagland or MS broth) must be used for each generation of plants. 2) If pasteurization or autoclaving attenuates the PSF effect, it indicates that the effect is caused by microorganisms rather than nutrients.
● Using SynCom to link microbiota changes to plant phenotypes
SynCom provides a powerful and controllable system to link microbiota changes to host phenotypes (Fig. 2c). Typically, about 30-200 isolated microorganisms can be used to assemble an artificial SynCom (taxonomic composition similar to natural soil communities). We found that an immunocompromised Arabidopsis mutant had a dysbiosis of leaf endophytic flora and a necrotic phenotype, and a community of 52 isolated bacteria from the mutant leaves was inoculated into wild-type Arabidopsis grown in a sterile environment. Plants exhibited necrosis and stunting-related phenotypes. This demonstrates that plant microbial dysbiosis can lead to plant necrosis, and more importantly, the artificial SynCom gives researchers the flexibility to select strains of interest and perform functional tests. A recent study divided rhizosphere microbial strains into four modules according to their symbiotic patterns under different environmental disturbances, and tested the effect of deconstructed (removing different modules and key strains) SynComs on root growth, and further verified that a single Functional characteristics of bacterial strains such as Variovorax can counteract root growth inhibition induced by different strains. This enhances the convincingness of the simplified artificial SynCom deconstruction in revealing the influence of the microbiota on host traits.
● Mathematical prediction of key strains associated with community function
In carrying out SynCom's transplant trials, it was difficult to engineer the perfect combination of strains and best mimic the function of the original microbiome. At present, some machine learning methods (support vector machines, random forests, logistic regression, etc.) have been effectively applied to predict disease incidence in different soil community backgrounds, and mathematical models based on the composition of key strains to predict the maturity of rice microbiome. This suggests that changes in relevant biological functions of interest in soil can be predicted mathematically, or based on key strains (OTUs). For example, 37 strains identified in a study grouping mutants according to their ability to block microbiota-induced growth promotion in shade were sufficient to predict whether the target phenotypes would develop in different mutants. This result further confirms the role of microbiota changes in promoting growth under shade and provides the basis for the construction of a SynCom that does not contain 37 strains, and also links shade-induced microbiota changes to plant growth-promoting phenotypes .
Summarize
The plant's "cry for help" hypothesis originated from the phenomenon that plant monocultures and diseases induce changes in the microbiome and produce disease-suppressing soils. However, an increasing number of studies have identified relevant genetic factors involved in remodeling the microbiota to overcome abiotic stresses, especially nutrient starvation and adverse light conditions, suggesting that plant "call for help" mechanisms also exist in response to abiotic stresses in the reaction. Plants can reshape microbiota composition both temporally (when stress occurs) and spatially (eg, by coordinating above-ground light stress and below-ground microbiota changes) in response to environmental disturbances. These results highlight the importance of precise regulation of microbial community dynamics in plant environmental adaptation, and that inoculation by "beneficial microorganisms" alone may not be sufficient to help plants resist multiple stresses in complex soils. Therefore, further understanding of the genetic and biochemical mechanisms of the interaction between host plants and microbiota, especially under unfavorable conditions, will pave the way for the precise design of future crops that can recruit specific beneficial microbial communities at the right time.
引文格式：Zhenghong Wang, Yi Song. Toward understanding the genetic bases underlying plant‐mediated “cry for help” to the microbiota. iMeta e8 (2022). https://doi.org/10.1002/imt2.8
About the Author
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Wang Zhenghong , postdoctoral fellow at the Department of Biology, Southern University of Science and Technology; in 2021, he graduated from Kunming Institute of Botany, Chinese Academy of Sciences with a Ph.D.
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He mainly studies the changes of soil microbial ecological characteristics and its response to climate change under land use changes in mountain ecosystems, and has experience in microbial amplicon and metagenome sequencing de novo data analysis. In January 2022, he joined the Department of Biology, Southern University of Science and Technology to carry out postdoctoral research.
First author
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Song Yi, Assistant Professor of Southern University of Science and Technology; graduated from the Department of Biochemistry and Molecular Biology of Fudan University with a Ph.D. Department, Shenzhen Pengcheng Peacock Overseas Talent Project selected.
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He has published many papers in academic journals such as Nature Plants and Molecular Plant , and he has been cited more than 350 times. With a background in plant molecular biology and microbiome, he mainly studies the mechanism of root immune regulation and the mechanism of plants shaping the rhizosphere microbiome. Served as the Young Editorial Board of iMeta, Reviewing Editor of Frontiers in Microbiology and Frontiers in Plant Science .
Corresponding Author
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