Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture.

The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.

Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria.

Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.

Nitrogen fertilization modulates beneficial rhizosphere interactions through signaling effect of nitric oxide.

Chemical nitrogen (N) fertilization is customary for increasing N inputs in agroecosystems. The nutritional effects of N fertilization on plants and soil microbes have been well studied. However, the signaling effects of N fertilization on rhizosphere plant-microbe interactions and the following feedback to plant performance remain unknown. Here, we investigated the effect of different N fertilizations on the behavior of the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis SQR9 in the cucumber (Cucumis sativus L.) rhizosphere. Moderate N fertilization promoted higher rhizosphere colonization of strain SQR9 than insufficient or excessive N input. Nitric oxide (NO) produced through the denitrification process under N fertilization was identified as the signaling molecule that dominates the root colonization of PGPR, and this effect could be neutralized by the NO-specific scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxy-3-oxide. Gene expression analysis demonstrated that NO regulated the biofilm formation of strain SQR9 by affecting the synthesis of extracellular matrix γ-polyglutamic acid, consequently impacting its root colonization. Finally, we demonstrated that moderate N fertilization-modulated enhanced PGPR root colonization can significantly promote plant growth and nitrogen use efficiency. This study provides insights into our understanding of the beneficial rhizosphere plant-microbe interactions under N fertilization and suggests that rational fertilization is critical to promote beneficial rhizosphere interactions for sustainable agricultural production.

The volatile cedrene from Trichoderma guizhouense modulates Arabidopsis root development through auxin transport and signalling.

Rhizosphere microorganisms interact with plant roots by producing chemical signals that regulate root development. However, the distinct bioactive compounds and signal transduction pathways remain to be identified. Here, we showed that sesquiterpenes are the main volatile compounds produced by plant-beneficial Trichoderma guizhouense NJAU4742. Inhibition of sesquiterpene biosynthesis eliminated the promoting effect of this strain on root growth, indicating its involvement in plant-fungus cross-kingdom signalling. Sesquiterpene component analysis identified cedrene, a highly abundant sesquiterpene in strain NJAU4742, to stimulate plant growth and root development. Genetic analysis and auxin transport inhibition showed that the TIR1 and AFB2 auxin receptors, IAA14 auxin-responsive protein, and ARF7 and ARF19 transcription factors affected the response of lateral roots to cedrene. Moreover, the AUX1 auxin influx carrier and PIN2 efflux carrier were also found to be indispensable for cedrene-induced lateral root formation. Confocal imaging showed that cedrene affected the expression of pPIN2:PIN2:GFP and pPIN3:PIN3:GFP, which might be related to the effect of cedrene on root morphology. These results suggested that a novel sesquiterpene molecule from plant-beneficial T. guizhouense regulates plant root development through the transport and signalling of auxin.

Overcoming diverse homologous recombinations and single chimeric guide RNA competitive inhibition enhances Cas9-based cyclical multiple genes coediting in filamentous fungi.

Deciphering the complex cellular behaviours and advancing the biotechnology applications of filamentous fungi increase the requirement for genetically manipulating a large number of target genes. The current strategies cannot cyclically coedit multiple genes simultaneously. In this study, we firstly revealed the existence of diverse homologous recombination (HR) types in marker-free editing of filamentous fungi, and then, demonstrated that sgRNA efficiency-mediated competitive inhibition resulted in the low integration of multiple genetic sites during coediting, which are the two major obstacles to limit the efficiency of cyclically coediting of multiple genes. To overcome these obstacles, we developed a biased cutting strategy by Cas9 to greatly enhance the desired HR type and applied a new selection marker labelling strategy for multiple donor DNAs, in which only the donor DNA with the lowest sgRNA efficiency was labelled. Combined with these strategies, we successfully developed a convenient method for cyclically coediting multiple genes in different filamentous fungi. In addition, diverse HRs resulted in a useful and convenient one-step approach for gene functional study combining both gene disruption and complementation. This research provided both a useful one-step approach for gene functional study and an efficient strategy for cyclically coediting multiple genes in filamentous fungi.

Volatile compounds from beneficial rhizobacteria Bacillus spp. promote periodic lateral root development in Arabidopsis.

Lateral root formation is coordinated by both endogenous and external factors. As biotic factors, plant growth-promoting rhizobacteria can affect lateral root formation, while the regulation mechanism is unclear. In this study, by applying various marker lines, we found that volatile compounds (VCs) from Bacillus amyloliquefaciens SQR9 induced higher frequency of DR5 oscillation and prebranch site formation, accelerated the development and emergence of the lateral root primordia and thus promoted lateral root development in Arabidopsis. We demonstrated a critical role of auxin on B. amyloliquefaciens VCs-induced lateral root formation via respective mutants and pharmacological experiments. Our results showed that auxin biosynthesis, polar transport and signalling pathway are involved in B. amyloliquefaciens VCs-induced lateral roots formation. We further showed that acetoin, a major component of B. amyloliquefaciens VCs, is less active in promoting root development compared to VC blends from B. amyloliquefaciens, indicating the presence of yet uncharacterized/unknown VCs might contribute to B. amyloliquefaciens effect on lateral root formation. In summary, our study revealed an auxin-dependent mechanism of B. amyloliquefaciens VCs in regulating lateral root branching in a non-contact manner, and further efforts will explore useful VCs to promote plant root development.

Participating mechanism of a major contributing gene ysnE for auxin biosynthesis in Bacillus amyloliquefaciens SQR9.

The phytohormone indole-3-acetic acid (IAA) has been demonstrated to contribute to the plant growth-promoting effect of rhizobacteria, but the IAA biosynthesis pathway in rhizobacteria remains unclear. The ysnE gene, encoding a putative tryptophan acetyltransferase, has been demonstrated to be involved in and strongly contribute to IAA production in Bacillus, but the mechanism is unknown. In this study, to investigate how ysnE participates in IAA biosynthesis in the plant growth-promoting rhizobacterium Bacillus amyloliquefaciens SQR9, differences in the produced IAA biosynthesis intermediates between wild-type SQR9 and ΔysnE were analyzed and compared, and the effects of different intermediate compounds on the production of IAA and the accumulation of other intermediates were also investigated. The results showed that the mutant ΔysnE produced more indole-3-lactic acid (ILA) and tryptamine (TAM) than the SQR9 wild-type strain (nearly 1.6- and 2.1-fold), while the production of tryptophol (TOL) was significantly decreased by 46%. When indole-3-pyruvic acid (IPA) served as the substrate, the concentration of ILA in the ΔysnE fermentation broth was much higher than that of the wild type, while IAA and TOL were significantly lower, and ΔysnE was lower than SQR9 in IAA and TOL with the addition of TAM. The TOL content in the ΔysnE fermentation broth was much lower than that in the wild-type SQR9 with the addition of ILA. We suggest that ysnE may be involved in the IPA and TAM pathways and play roles in indole acetaldehyde (IAAld) synthesis from IPA and TAM and in the conversion of ILA to TOL.

Bacillus velezensis Wall Teichoic Acids Are Required for Biofilm Formation and Root Colonization.

Rhizosphere colonization by plant growth-promoting rhizobacteria (PGPR) along plant roots facilitates the ability of PGPR to promote plant growth and health. Thus, an understanding of the molecular mechanisms of the root colonization process by plant-beneficial Bacillus strains is essential for the use of these strains in agriculture. Here, we observed that an sfp gene mutant of the plant growth-promoting rhizobacterium Bacillus velezensis SQR9 was unable to form normal biofilm architecture, and differential protein expression was observed by proteomic analysis. A minor wall teichoic acid (WTA) biosynthetic protein, GgaA, was decreased over 4-fold in the Δsfp mutant, and impairment of the ggaA gene postponed biofilm formation and decreased cucumber root colonization capabilities. In addition, we provide evidence that the major WTA biosynthetic enzyme GtaB is involved in both biofilm formation and root colonization. The deficiency in biofilm formation of the ΔgtaB mutant may be due to an absence of UDP-glucose, which is necessary for the synthesis of biofilm matrix exopolysaccharides (EPS). These observations provide insights into the root colonization process by a plant-beneficial Bacillus strain, which will help improve its application as a biofertilizer.IMPORTANCEBacillus velezensis is a Gram-positive plant-beneficial bacterium which is widely used in agriculture. Additionally, Bacillus spp. are some of the model organisms used in the study of biofilms, and as such, the molecular networks and regulation systems of biofilm formation are well characterized. However, the molecular processes involved in root colonization by plant-beneficial Bacillus strains remain largely unknown. Here, we showed that WTAs play important roles in the plant root colonization process. The loss of the gtaB gene affects the ability of B. velezensis SQR9 to sense plant polysaccharides, which are important environmental cues that trigger biofilm formation and colonization in the rhizosphere. This knowledge provides new insights into the Bacillus root colonization process and can help improve our understanding of plant-rhizobacterium interactions.

Haloprofundus marisrubri gen. nov., sp. nov., an extremely halophilic archaeon isolated from a brine-seawater interface.

We isolated a Gram-stain-negative, pink-pigmented, motile, pleomorphic, extremely halophilic archaeon from the brine-seawater interface of Discovery Deep in the Saudi Arabian Red Sea. This strain, designated SB9T, was capable of growth within a wide range of temperatures and salinity, but required MgCl2. Cells lysed in distilled water, but at 7.0 % (w/v) NaCl cell lysis was prevented. The major polar lipids from strain SB9T were phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, an unidentified glycolipid and two unidentified phospholipids. The major respiratory quinones of strain SB9T were menaquinones MK8 (66 %) and MK8 (VIII-H2) (34 %). Analysis of the 16S rRNA gene sequence revealed that strain SB9T was closely related to species in the genera Halogranum and Haloplanus; in particular, it shared highest sequence similarity with the type strain of Halogranum rubrum (93.4 %), making it its closest known relative. The unfinished draft genome of strain SB9Twas 3 931 127 bp in size with a total G+C content of 62.53 mol% and contained 3917 ORFs, 50 tRNAs and eight rRNAs. Based on comparisons with currently available genomes, the highest average nucleotide identity value was 83 % to Halogranum salarium B-1T (GenBank accession no. GCA_000283335.1). These data indicate that this new isolate cannot be classified into any recognized genera of the family Haloferacaceae, and therefore strain SB9T is considered to be a representative of a novel species of a new genus within this family, for which the name Haloprofundus marisrubri gen. nov., sp. nov. is proposed. The type strain of Haloprofundus marisrubri is SB9T (=JCM 19565T=CGMCC 1.14959T).

Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea.

Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae, designated ZGT108T and ZGT118T, were isolated from the brine-seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108T and ZGT118T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108T to its closest relative, Ruegeria conchae JCM 17315T, was 98.9 %, while the 16S rRNA gene of ZGT118T was most closely related to that of Ruegeria intermedia LMG 25539T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108T) and 4 012 109 bp (strain ZGT118T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108T) and 62.94 mol% (ZGT108T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria. This was also confirmed by low DNA-DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeriaprofundi sp. nov. (type strain ZGT108T=JCM 19518T=ACCC 19861T) and Ruegeriamarisrubri sp. nov. (type strain ZGT118T=JCM 19519T=ACCC 19862T).

Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae.

Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol%. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).

Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system.

To study the influence of straw incorporation with and without straw decomposer on bacterial community structure and biological traits, a 3-year field experiments, including four treatments: control without fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer plus 7500 kg ha-1 straw incorporation (NPKS), and chemical fertilizer plus 7500 kg ha-1 straw incorporation and 300 kg ha-1 straw decomposer (NPKSD), were performed in a rice-wheat cropping system in Changshu (CS) and Jintan (JT) city, respectively. Soil samples were taken right after wheat (June) and rice (October) harvest in both sites, respectively. The NPKS and NPKSD treatments consistently increased crop yields, cellulase activity, and bacterial abundance in both sampling times and sites. Moreover, the NPKS and NPKSD treatments altered soil bacterial community structure, particularly in the wheat harvest soils in both sites, separating from the CK and NPK treatments. In the rice harvest soils, both NPKS and NPKSD treatments had no considerable impacts on bacterial communities in CS, whereas the NPKSD treatment significantly shaped bacterial communities compared to the other treatments in JT. These practices also significantly shifted the bacterial composition of unique operational taxonomic units (OTUs) rather than shared OTUs. The relative abundances of copiotrophic bacteria (Proteobacteria, Betaproteobacteria, and Actinobacteria) were positively correlated with soil total N, available N, and available P. Taken together, these results indicate that application of straw incorporation with and without straw decomposer could particularly stimulate the copiotrophic bacteria, enhance the soil biological activity, and thus, contribute to the soil productivity and sustainability in agro-ecosystems.

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China.

Different fertilization managements of red soil, a kind of Ferralic Cambisol, strongly affected the soil properties and associated microbial communities. The association of the soil microbial community and functionality with long-term fertilization management in the unique low-productivity red soil ecosystem is important for both soil microbial ecology and agricultural production. Here, 454 pyrosequencing analysis of 16S recombinant ribonucleic acid genes and GeoChip4-NimbleGen-based functional gene analysis were used to study the soil bacterial community composition and functional genes involved in soil organic carbon degradation. Long-term nitrogen-containing chemical fertilization-induced soil acidification and fertility decline and significantly altered the soil bacterial community, whereas long-term organic fertilization and fallow management improved the soil quality and maintained the bacterial diversity. Short-term quicklime remediation of the acidified soils did not change the bacterial communities. Organic fertilization and fallow management supported eutrophic ecosystems, in which copiotrophic taxa increased in relative abundance and have a higher intensity of labile-C-degrading genes. However, long-term nitrogen-containing chemical fertilization treatments supported oligotrophic ecosystems, in which oligotrophic taxa increased in relative abundance and have a higher intensity of recalcitrant-C-degrading genes but a lower intensity of labile-C-degrading genes. Quicklime application increased the relative abundance of copiotrophic taxa and crop production, although these effects were utterly inadequate. This study provides insights into the interaction of soil bacterial communities, soil functionality and long-term fertilization management in the red soil ecosystem; these insights are important for improving the fertility of unique low-productivity red soil.

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China.

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.

Root colonization by beneficial rhizobacteria.

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling.

Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.

Nonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant "cry for help" response to assemble disease suppressing and growth promoting rhizomicrobiome.

Plants are capable of assembling beneficial rhizomicrobiomes through a "cry for help" mechanism upon pathogen infestation; however, it remains unknown whether we can use nonpathogenic strains to induce plants to assemble a rhizomicrobiome against pathogen invasion. Here, we used a series of derivatives of Pseudomonas syringae pv. tomato DC3000 to elicit different levels of the immune response to Arabidopsis and revealed that two nonpathogenic DC3000 derivatives induced the beneficial soil-borne legacy, demonstrating a similar "cry for help" triggering effect as the wild-type DC3000. In addition, an increase in the abundance of Devosia in the rhizosphere induced by the decreased root exudation of myristic acid was confirmed to be responsible for growth promotion and disease suppression of the soil-borne legacy. Furthermore, the "cry for help" response could be induced by heat-killed DC3000 and flg22 and blocked by an effector triggered immunity (ETI) -eliciting derivative of DC3000. In conclusion, we demonstrate the potential of nonpathogenic bacteria and bacterial elicitors to promote the generation of disease-suppressive soils.

Sustained Inhibition of Maize Seed-Borne Fusarium Using a Bacillus-Dominated Rhizospheric Stable Core Microbiota with Unique Cooperative Patterns.

Seed-borne pathogens can inhabit the rhizosphere and infect the plant after germination. The rhizosphere microbiome plays critical roles in defending against seed-borne pathogens. However, the assembly of a core rhizosphere microbiome to suppress seed-borne pathogens is unknown. Here, the root-associated microbiome is infested with seed-borne Fusarium in sterile environment, while the root-associated microbiome is not infested when it interacts with the native soil microbiome across maize cultivars, suggesting that a core rhizosphere microbiome assembles to suppress seed-borne Fusarium. Two strategies of progressive dilution and rhizodepositional attraction are applied to identify the core rhizobacteria. A synthetic microbiota (SynM) is constructed using the isolates of the core rhizobacteria and optimized according to superior community stability and Fusarium-suppression capability, which surpasses the single strain and randomly formed microbiota. The optimized SynM (OptSynM) presents a distinctive cooperative pattern in which a key strain harbors the Fusarium suppression function by synthesizing the antagonistic substance fengycin, while other members intensify the functional performance by promoting the growth and the expression of the antagonistic and plant-growth-promoting related genes of the key strain. This study demonstrates innovative approaches to construct stable and minimal microbiota for sustainable agriculture and proposes a unique cooperative pattern to sustain community stability and functionality.

Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes.

Harnessing the power of beneficial microbes in the rhizosphere to improve crop performance is a key goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant-rhizomicrobiome relationship. In this review, we discuss the latest research progress on root colonisation by representative beneficial microbes (e.g. Bacillus spp. and Pseudomonas spp.). We also highlight the bidirectional chemical communication between microbes and plant roots for precise functional control of beneficial microbes in the rhizosphere, as well as advances in understanding how beneficial microbes overcome the immune system of plants. Finally, we propose future research objectives that will help us better understand the complex network of plant-microbe interactions.