Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria

Coming of age for Microbiome gene breeding in plants

The plant microbiota can complement host functioning, leading to improved growth and health under unfavorable conditions. Microbiome engineering could therefore become a transformative technique for crop production. Microbiome genes, abbreviated as M genes, provide valuable targets for shaping plant-associated microbial communities.

Impact of IPM practices on microbial population and disease development in transplanted and direct-seeded rice

Integrated pest management (IPM) is a comprehensive approach to managing diseases, focusing on combining various strategies to reduce pathogen populations effectively and in an environmentally conscious way. We investigated the effects of IPM on beneficial microbial populations and its relationship with pathogen populations in both direct-seeded rice (DSR) and transplanted rice (TR) systems. This study demonstrates that IPM practices have significantly higher populations of beneficial microbes, such as Trichoderma harzianum and Pseudomonas fluorescens, and lower level of the pathogen Fusarium verticillioides compared to non-IPM (farmer practices). The average mean population of T. harzianum was 6.38 × 103 CFU/g in IPM compared to 3.22 × 103 CFU/g in non-IPM during 2019 in TR at Bambawad. P. fluorescens mean population in 2019 was significantly higher in IPM (4.67 × 103 CFU/g) than in non-IPM (3.82 × 103 CFU/g) at the Karnal location in DSR. The F. verticillioides populations were significantly lower in IPM fields (9.46 × 103 CFU/g) compared to non-IPM fields (11.48 × 103 CFU/g) during 2017 at Haridwar in TR. Over three years, a significant increase in the populations of beneficial microbes in IPM plots was observed in all three locations of both TR and DSR, highlighting the sustainable impact of IPM practices. Disease dynamics analysis revealed that IPM effectively managed key diseases in both DSR and TR systems, with significant correlations between microbial density and disease severity. A significant positive correlation was recorded between F. verticillioides population and bakanae incidence at all three locations. Sheath blight incidence was negatively correlated with P. fluorescens population in both TR and DSR. In DSR, bacterial blight and brown spot diseases are reduced with the increased population of T. harzianum. Bioagents T. harzianum and P. fluorescens reduced disease incidence, underscoring the role of beneficial microbes in disease suppression and their importance for sustainable production using IPM practices.

Molecular insights into PGPR fluorescent Pseudomonads complex mediated intercellular and interkingdom signal transduction mechanisms in promoting plant's immunity

The growth-promoting and immune modulatory properties of different strains of plant growth promoting rhizobacteria (PGPR) fluorescent Pseudomonads complex (PFPC) can be explored to combat food security challenges. These PFPC prime plants through induced systemic resistance, fortify plants to overcome future pathogen-mediated vulnerability by eliciting robust systemic acquired resistance through regulation by nonexpressor of pathogenesis-related genes 1. Moreover, outer membrane vesicles released from Pseudomonas fluorescens also elicit a broad spectrum of immune responses, presenting a rapid viable alternative to whole cells. Thus, PFPC can help the host to maintain an equilibrium between growth and immunity, ultimately leads to increased crop yield.

Customized plant microbiome engineering for food security

Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.

Engineering agricultural soil microbiomes and predicting plant phenotypes

Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.

Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities

Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.

Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain

By improving plant nutrition and alleviating abiotic and biotic stresses, plant growth-promoting bacteria (PGPB) can help to develop eco-friendly and sustainable agricultural practices. Besides climatic conditions, soil conditions, and microbe-microbe interactions, the host genotype influences the effectiveness of PGPB. Yet, most GWAS conducted to characterize the genetic architecture of response to PGPB are based on non-native interactions between a host plant and PGPB strains isolated from the belowground compartment of other plants. In this study, a GWAS was set up under in vitro conditions to describe the genetic architecture of the response of Arabidopsis thaliana to the PGPB Pseudomonas siliginis, by inoculating seeds of 162 natural accessions from the southwest of France with one strain isolated from the leaf compartment in the same geographical region. Strong genetic variation of plant growth response to this native PGPB was observed at a regional scale, with the strain having a positive effect on the vegetative growth of small plants and a negative effect on the vegetative growth of large plants. The polygenic genetic architecture underlying this negative trade-off showed suggestive signatures of local adaptation. The main eco-evolutionary relevant candidate genes are involved in seed and root development.

Arabidopsis thaliana Early Foliar Proteome Response to Root Exposure to the Rhizobacterium Pseudomonas simiae WCS417

Pseudomonas simiae WCS417 is a plant growth-promoting rhizobacterium that improves plant health and development. In this study, we investigate the early leaf responses of Arabidopsis thaliana to WCS417 exposure and the possible involvement of formate dehydrogenase (FDH) in such responses. In vitro-grown A. thaliana seedlings expressing an FDH::GUS reporter show a significant increase in FDH promoter activity in their roots and shoots after 7 days of indirect exposure (without contact) to WCS417. After root exposure to WCS417, the leaves of FDH::GUS plants grown in the soil also show an increased FDH promoter activity in hydathodes. To elucidate early foliar responses to WCS417 as well as FDH involvement, the roots of A. thaliana wild-type Col and atfdh1-5 knock-out mutant plants grown in soil were exposed to WCS417, and proteins from rosette leaves were subjected to proteomic analysis. The results reveal that chloroplasts, in particular several components of the photosystems PSI and PSII, as well as members of the glutathione S-transferase family, are among the early targets of the metabolic changes induced by WCS417. Taken together, the alterations in the foliar proteome, as observed in the atfdh1-5 mutant, especially after exposure to WCS417 and involving stress-responsive genes, suggest that FDH is a node in the early events triggered by the interactions between A. thaliana and the rhizobacterium WCS417. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR

Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.

Metabarcoding reveals response of rice rhizosphere bacterial community to rice bacterial leaf blight

Rice bacterial leaf blight (BLB) is a major disease affecting cultivated rice and caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It is well established that rhizosphere microorganisms could help improve the adaptability of plants to biotic stresses. However, it is still unclear about the response mechanism of rice rhizosphere microbial community to BLB infection. Here, we used 16S rRNA gene amplicon sequencing to explore the effect of BLB on the rice rhizosphere microbial community. The results show that the alpha diversity index of the rice rhizosphere microbial community decreased significantly at the onset of BLB and then gradually recovered to normal levels. Beta diversity analysis indicated that BLB significantly affected community composition. In addition, there were significant differences in the taxonomic composition between healthy and diseased groups. For example, ceretain genera were more abundant in diseased rhizospheres, namely Streptomyces, Sphingomonas, and Flavobacterium, among others. In addition, the size and complexity of the rhizosphere co-occurrence network increased after disease onset compared to healthy groups. Also, hub microbe Rhizobiaceae and Gemmatimonadaceae were identified in the diseased rhizosphere co-occurrence network, and these hub microbes played an important role in maintaining network stability. In conclusion, our results provide important insights into the rhizosphere microbial community response to BLB and also provide important data and ideas in using rhizosphere microbes to control BLB.

Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T

Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant-bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4^T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4^T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome.

High killing rate of nematode and promotion of rice growth by synthetic volatiles from Bacillus strains due to enhanced oxidative stress response

The plant parasitic nematode Aphelenchoides besseyi is a major pest that poses serious threats to different vegetables and crop plants. In the present study, volatiles isolated from Bacillus spp. were utilized as green biocontrol agents to overcome nematodes. In in vitro experiment, Bacillus spp. GBSC56, SYST2, and FZB42 showed the strongest nematicidal activity with killing rates of 80.78%, 75.69%, and 60.45%, respectively, as compared with control. The selected synthetic volatile organic compounds (VOCs), namely albuterol, benzaldehyde (BDH), 1,2-benzisothiazol-3(2H)-one (1,2-HIT), dimethyl disulfide (DMDS), 2-undecanone (2-UD), and 1,3-propanediole (1,3-PD), exhibited strong nematicidal activity, with A. besseyi killing rate of 85.58%, 82.65%, 81.75%, 80.36%, 84.45%, and 82.36%, respectively, at 400 μg/mL. Microscopic analysis proved that the rapid mortality was due to the production of reactive oxygen species (ROS). Molecular docking attributed this ROS production to the nematicidal effect of synthetic VOCs on NADH DEHYDROGENASE SUBUNIT 2, which is known to play a critical role in the suppression of ROS in nematode models. In a greenhouse experiment, the Bacillus strains GBSC56, SYST2, and FZB42 and their synthetic VOCs significantly improved the physiological parameters in terms of growth promotion traits. In addition, selected genes related to growth promotion and defense genes showed a significant upregulation of their expression in rice seedlings treated with those synthetic VOCs. Overall, these findings revealed that the selected Bacillus strains and their synthetic VOCs possess high potential against A. besseyi. Moreover, this study also sheds new light on the mechanisms by which specific Bacillus nematicidal VOCs influence important genes involved in rice plant growth promotion and could effectively be used to suppress plant parasitic nematodes.

Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition

Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.

Non-volatile signals and redox mechanisms are required for the responses of Arabidopsis roots to Pseudomonas oryzihabitans

Soil bacteria promote plant growth and protect against environmental stresses, but the mechanisms involved remain poorly characterized, particularly when there is no direct contact between the roots and bacteria. Here, we explored the effects of Pseudomonas oryzihabitans PGP01 on the root system architecture (RSA) in Arabidopsis thaliana seedlings. Significant increases in lateral root (LR) density were observed when seedlings were grown in the presence of P. oryzihabitans, as well as an increased abundance of transcripts associated with altered nutrient transport and phytohormone responses. However, no bacterial transcripts were detected on the root samples by RNAseq analysis, demonstrating that the bacteria do not colonize the roots. Separating the agar containing bacteria from the seedlings prevented the bacteria-induced changes in RSA. Bacteria-induced changes in RSA were absent from mutants defective in ethylene response factor (ERF109), glutathione synthesis (pad2-1, cad2-1, and rax1-1) and in strigolactone synthesis (max3-9 and max4-1) or signalling (max2-3). However, the P. oryzihabitans-induced changes in RSA were similar in the low ascorbate mutants (vtc2-1and vtc2-2) to the wild-type controls. Taken together, these results demonstrate the importance of non-volatile signals and redox mechanisms in the root architecture regulation that occurs following long-distance perception of P. oryzihabitans.

Breeding toward improved ecological plant-microbiome interactions

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions

Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.

Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering

The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.

Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development

Two regions located at chromosome A05 and D04 were found to be significantly associated with 0-0.5 mm and 0.5-2 mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0-0.5 mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24 Mb). For SNPs associated with root surface area, root volume and 0.5-2 mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70 Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT-PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties.

Friend or foe: Hybrid proline-rich proteins determine how plants respond to beneficial and pathogenic microbes

Plant plastids generate signals, including some derived from lipids, that need to be mobilized to effect signaling. We used informatics to discover potential plastid membrane proteins involved in microbial responses in Arabidopsis (Arabidopsis thaliana). Among these are proteins co-regulated with the systemic immunity component AZELAIC ACID INDUCED 1, a hybrid proline-rich protein (HyPRP), and HyPRP superfamily members. HyPRPs have a transmembrane domain, a proline-rich region (PRR), and a lipid transfer protein domain. The precise subcellular location(s) and function(s) are unknown for most HyPRP family members. As predicted by informatics, a subset of HyPRPs has a pool of proteins that target plastid outer envelope membranes via a mechanism that requires the PRR. Additionally, two HyPRPs may be associated with thylakoid membranes. Most of the plastid- and nonplastid-localized family members also have pools that localize to the endoplasmic reticulum, plasma membrane, or plasmodesmata. HyPRPs with plastid pools regulate, positively or negatively, systemic immunity against the pathogen Pseudomonas syringae. HyPRPs also regulate the interaction with the plant growth-promoting rhizobacteria Pseudomonas simiae WCS417 in the roots to influence colonization, root system architecture, and/or biomass. Thus, HyPRPs have broad and distinct roles in immunity, development, and growth responses to microbes and reside at sites that may facilitate signal molecule transport.

Genotype-Specific Plastic Responses to Seed Bacteria under Drought Stress in Lactuca serriola

Recent studies have demonstrated that seed-borne bacteria can enhance the performance of invasive plants in novel introduced habitats with environmental stresses. The effect of this plant-bacteria interaction may vary with plant species or even genotype; however, the genotype-dependent effects of seed bacteria have rarely been assessed. In this study, we examined the effects of bacterial strains isolated from seeds on the genotypes of an invasive xerophytic plant, Lactuca serriola. Plant genotypes were grown under drought conditions, and their plastic responses to bacterial infections were evaluated. Some genotypes produced more biomass, whereas others produced less biomass in response to infection with the same bacterial strain. Notably, the quantity of root-adhering soil depended on the bacterial treatment and plant genotypes and was positively correlated with the plastic responses of plant performance. Because tested bacteria could colonize the plant rhizosphere, bacterial infection appears to induce the differential formation of soil rhizosheaths among plant genotypes, consequently affecting the maintenance of soil water content under drought conditions. Given that drought tolerance is a critical attribute for the invasive success of L. serriola, these results imply that bacterial symbionts can facilitate the establishment of alien plant species, but their effects are likely genotype-specific.

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence.

NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana

Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.

Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition

Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.

Antagonistic and plant growth promotion effects of Mucor moelleri, a potential biocontrol agent

With the increasing demand for high quality and environmentally safe or green food, Biological Control Agents (BCAs) are playing critical roles in green agriculture, which in turn has paved the way for the requirement of effective, appropriate microbial antagonists. In this study, Mucor moelleri AA1 was isolated and investigated for its growth promotion and antagonism against Athelia rolfsii and Colletotrichum gloeosporiodes. The results showed a high antagonistic activity of M. moelleri against A. rolfsii and C. gloeosporiodes with percentage inhibitions of 73 % and 86 % respectively using the dual plate method, and the same antagonistic activity was also observed in liquid cocultures. A pot study analysis showed significant suppression of the diseases as well as growth promotion on tomato. Scanning electron microscopy (SEM) indicated that M. moelleri inhibited the growth of mycelium and the production of web-like materials. Based on headspace-solid phase microextraction (HS-SPME) analysis, microbial volatile compounds were determined, which were mainly aromatic compounds and alkaloids. Also, several antagonistic enzymes, such as β-1, 3- glucanase, proteases, catalase and ACC deaminase as well as the phytohormone IAA, were found to be produced by M. moelleri. Overall, these results combine to make M. moelleri a good prospective candidate for biological control and as a plant growth-promoting agent. The present study appears to be the first report identifying M. moelleri as a biological control agent.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.

Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives

In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.

On the genetic architecture in a public tropical maize panel of the symbiosis between corn and plant growth-promoting bacteria aiming to improve plant resilience

Exploring the symbiosis between plants and plant growth-promoting bacteria (PGPB) is a new challenge for sustainable agriculture. Even though many works have reported the beneficial effects of PGPB in increasing plant resilience for several stresses, its potential is not yet widely explored. One of the many reasons is the differential symbiosis performance depending on the host genotype. This opens doors to plant breeding programs to explore the genetic variability and develop new cultivars with higher responses to PGPB interaction and, therefore, have higher resilience to stress. Hence, we aimed to study the genetic architecture of the symbiosis between PGPB and tropical maize germplasm, using a public association panel and its impact on plant resilience. Our findings reveal that the synthetic PGPB population can modulate and impact root architecture traits and improve resilience to nitrogen stress, and 37 regions were significant for controlling the symbiosis between PGPB and tropical maize. In addition, we found two overlapping SNPs in the GWAS analysis indicating strong candidates for further investigations. Furthermore, genomic prediction analysis with genomic relationship matrix computed using only significant SNPs obtained from GWAS analysis substantially increased the predictive ability for several traits endorsing the importance of these genomic regions for the response of PGPB. Finally, the public tropical panel reveals a significant genetic variability to the symbiosis with the PGPB and can be a source of alleles to improve plant resilience.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01257-6.

Multi-Trait Wheat Rhizobacteria from Calcareous Soil with Biocontrol Activity Promote Plant Growth and Mitigate Salinity Stress

Plant growth promoting rhizobacteria (PGPR) can be functional microbial fertilizers and/or biological control agents, contributing to an eco-spirit and safe solution for chemical replacement. Therefore, we have isolated rhizospheric arylsulfatase (ARS)-producing bacteria, belonging to Pseudomonas and Bacillus genus, from durum wheat crop grown on calcareous soil. These isolates harbouring plant growth promoting (PGP) traits were further evaluated in vitro for additional PGP traits, including indole compounds production and biocontrol activity against phytopathogens, limiting the group of multi-trait strains to eight. The selected bacterial strains were further evaluated for PGP attributes associated with biofilm formation, compatibility, salt tolerance ability and effect on plant growth. In vitro studies demonstrated that the multi-trait isolates, Bacillus (1.SG.7, 5.SG.3) and Pseudomonas (2.SG.20, 2.C.19) strains, enhanced the lateral roots abundance and shoots biomass, mitigated salinity stress, suggesting the utility of beneficial ARS-producing bacteria as potential microbial fertilizers. Furthermore, in vitro studies demonstrated that compatible combinations of multi-trait isolates, Bacillus sp. 1.SG.7 in a mixture coupled with 5.SG.3, and 2.C.19 with 5.SG.3 belonging to Bacillus and Pseudomonas, respectively, may enhance plant growth as compared to single inoculants.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Nematicidal Volatiles from Bacillus atrophaeus GBSC56 Promote Growth and Stimulate Induced Systemic Resistance in Tomato against Meloidogyne incognita

Bacillus volatiles to control plant nematodes is a topic of great interest among researchers due to its safe and environmentally friendly nature. Bacillus strain GBSC56 isolated from the Tibet region of China showed high nematicidal activity against M. incognita, with 90% mortality as compared with control in a partition plate experiment. Pure volatiles produced by GBSC56 were identified through gas chromatography and mass spectrometry (GC-MS). Among 10 volatile organic compounds (VOCs), 3 volatiles, i.e., dimethyl disulfide (DMDS), methyl isovalerate (MIV), and 2-undecanone (2-UD) showed strong nematicidal activity with a mortality rate of 87%, 83%, and 80%, respectively, against M. incognita. The VOCs induced severe oxidative stress in nematodes, which caused rapid death. Moreover, in the presence of volatiles, the activity of antioxidant enzymes, i.e., SOD, CAT, POD, and APX, was observed to be enhanced in M. incognita-infested roots, which might reduce the adverse effect of oxidative stress-induced after infection. Moreover, genes responsible for plant growth promotion SlCKX1, SlIAA1, and Exp18 showed an upsurge in expression, while AC01 was downregulated in infested plants. Furthermore, the defense-related genes (PR1, PR5, and SlLOX1) in infested tomato plants were upregulated after treatment with MIV and 2-UD. These findings suggest that GBSC56 possesses excellent biocontrol potential against M. incognita. Furthermore, the study provides new insight into the mechanism by which GBSC56 nematicidal volatiles regulate antioxidant enzymes, the key genes involved in plant growth promotion, and the defense mechanism M. incognita-infested tomato plants use to efficiently manage root-knot disease.

Pinpointing regulatory protein phosphatase 2A subunits involved in beneficial symbiosis between plants and microbes

BACKGROUND

PROTEIN PHOSPHATASE 2A (PP2A) expression is crucial for the symbiotic association between plants and various microbes, and knowledge on these symbiotic processes is important for sustainable agriculture. Here we tested the hypothesis that PP2A regulatory subunits, especially B'φ and B'θ, are involved in signalling between plants and mycorrhizal fungi or plant-growth promoting bacteria.

RESULTS

Treatment of tomato plants (Solanum lycopersicum) with the plant growth-promoting rhizobacteria (PGPR) Azospirillum brasilense and Pseudomonas simiae indicated a role for the PP2A B'θ subunit in responses to PGPR. Arbuscular mycorrhizal fungi influenced B'θ transcript levels in soil-grown plants with canonical arbuscular mycorrhizae. In plant roots, transcripts of B'φ were scarce under all conditions tested and at a lower level than all other PP2A subunit transcripts. In transformed tomato plants with 10-fold enhanced B'φ expression, mycorrhization frequency was decreased in vermiculite-grown plants. Furthermore, the high B'φ expression was related to abscisic acid and gibberellic acid responses known to be involved in plant growth and mycorrhization. B'φ overexpressor plants showed less vigorous growth, and although fruits were normal size, the number of seeds per fruit was reduced by 60% compared to the original cultivar.

CONCLUSIONS

Expression of the B'θ gene in tomato roots is strongly influenced by beneficial microbes. Analysis of B'φ overexpressor tomato plants and established tomato cultivars substantiated a function of B'φ in growth and development in addition to a role in mycorrhization.

Microbial Derived Compounds, a Step Toward Enhancing Microbial Inoculants Technology for Sustainable Agriculture

Sustainable agriculture remains a focus for many researchers, in an effort to minimize environmental degradation and climate change. The use of plant growth promoting microorganisms (PGPM) is a hopeful approach for enhancing plant growth and yield. However, the technology faces a number of challenges, especially inconsistencies in the field. The discovery, that microbial derived compounds can independently enhance plant growth, could be a step toward minimizing shortfalls related to PGPM technology. This has led many researchers to engage in research activities involving such compounds. So far, the findings are promising as compounds have been reported to enhance plant growth under stressed and non-stressed conditions in a wide range of plant species. This review compiles current knowledge on microbial derived compounds, taking a reader through a summarized protocol of their isolation and identification, their relevance in present agricultural trends, current use and limitations, with a view to giving the reader a picture of where the technology has come from, and an insight into where it could head, with some suggestions regarding the probable best ways forward.

Emerging strategies for precision microbiome management in diverse agroecosystems

Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.

Burying Beetle Parents Adaptively Manipulate Information Broadcast from a Microbial Community

AbstractMicrobial volatiles provide essential information for animals, which compete to detect, respond to, and perhaps control this information. Burying beetle parents have the opportunity to influence microbially derived semiochemicals, because they monopolize a small carcass for their family, repairing feeding holes and applying exudates that alter the microbial community. To study adaptive manipulation of microbial cues, we integrated mechanistic and functional approaches. We contrasted gas chromatography-mass spectrometry (GC-MS) volatile profiles from carcasses that were or were not prepared by a resident pair of Nicrophorus orbicollis. Methyl thiocyanate (MeSCN), the primary attractant for burying beetles seeking a fresh carcass, was reduced 20-fold by carcass preparation, while dimethyl trisulfide (DMTS), which deters breeding beetles, was increased 20-fold. These results suggest that parental care serves to make previously public information more private (crypsis, MeSCN) and to disinform rivals with a deterrent (DMTS). Functional tests in the field demonstrated that carcass preparation reduced discovery and use by congeners (threefold) as well as by dipteran rivals. Because microbes and their chemicals influence nearly every aspect of animal ecology, animal manipulation of microbial cues may be as widespread as manipulation of their own signals.

Pinpointing secondary metabolites that shape the composition and function of the plant microbiome

One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.

Beneficial rhizobacteria Pseudomonas simiae WCS417 induce major transcriptional changes in plant sugar transport

Plants live in close relationships with complex populations of microorganisms, including rhizobacterial species commonly referred to as plant growth-promoting rhizobacteria (PGPR). PGPR are able to improve plant productivity, but the molecular mechanisms involved in this process remain largely unknown. Using an in vitro experimental system, the model plant Arabidopsis thaliana, and the well-characterized PGPR strain Pseudomonas simiae WCS417r (PsWCS417r), we carried out a comprehensive set of phenotypic and gene expression analyses. Our results show that PsWCS417r induces major transcriptional changes in sugar transport and in other key biological processes linked to plant growth, development, and defense. Notably, we identified a set of 13 genes of the SWEET and ERD6-like sugar transporter gene families whose expression is up- or down-regulated in response to seedling root inoculation with the PGPR or exposure to their volatile compounds. Using a reverse genetic approach, we demonstrate that SWEET11 and SWEET12 are functionally involved in the interaction and its plant growth-promoting effects, possibly by controlling the amount of sugar transported from the shoot to the root and to the PGPR. Altogether, our study reveals that PGPR-induced beneficial effects on plant growth and development are associated with changes in plant sugar transport.

Specific PP2A Catalytic Subunits Are a Prerequisite for Positive Growth Effects in Arabidopsis Co-Cultivated with Azospirillum brasilense and Pseudomonas simiae

Plant growth-promoting rhizobacteria (PGPR) stimulate plant growth, but the underlying mechanism is poorly understood. In this study, we asked whether PROTEIN PHOSPHATASE 2A (PP2A), a regulatory molecular component of stress, growth, and developmental signaling networks in plants, contributes to the plant growth responses induced by the PGPR Azospirillum brasilense (wild type strain Sp245 and auxin deficient strain FAJ0009) and Pseudomonas simiae (WCS417r). The PGPR were co-cultivated with Arabidopsis wild type (WT) and PP2A (related) mutants. These plants had mutations in the PP2A catalytic subunits (C), and the PP2A activity-modulating genes LEUCINE CARBOXYL METHYL TRANSFERASE 1 (LCMT1) and PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR (PTPA). When exposed to the three PGPR, WT and all mutant Arabidopsis revealed the typical phenotype of PGPR-treated plants with shortened primary root and increased lateral root density. Fresh weight of plants generally increased when the seedlings were exposed to the bacteria strains, with the exception of catalytic subunit double mutant c2c5. The positive effect on root and shoot fresh weight was especially pronounced in Arabidopsis mutants with low PP2A activity. Comparison of different mutants indicated a significant role of the PP2A catalytic subunits C2 and C5 for a positive response to PGPR.

Potential of Salt Tolerant PGPR in Growth and Yield Augmentation of Wheat (Triticum aestivum L.) Under Saline Conditions

Soil salinity has emerged as a major obstacle to meet world food demands. Halo-tolerant plant growth promoting rhizobacteria (PGPR) are potential bioinoculants to enhance crop productivity in saline agriculture. Current work was aimed at studying individual or synergetic impact of salt tolerant PGPR on wheat growth and yield under saline conditions. A pot experiment was conducted on two wheat genotypes (Aas-11; salt tolerant and Galaxy-13; salt sensitive) inoculated with Pseudomonas fluorescence, Bacillus pumilus, and Exiguobacterium aurantiacum alone and in consortium. The salt tolerant variety (Aas-11) exhibited maximum root fresh (665.2%) and dry biomass (865%), free proline (138.12%) and total soluble proteins (155.9%) contents, CAT (41.7%) activity and shoot potassium uptake (81.08%) upon inoculation with B. pumilus, while improved shoot dry weight (70.39%), water (23.49%) and osmotic (29.65%) potential, POD (60.51%) activity, enhanced root potassium (286.36%) and shoot calcium (400%) were manifested by E. aurantiacum. Highest shoot length (14.38%), fresh weight (72.73%), potassium (29.7%) and calcium (400%) acquisition as well as glycinebetaine (270.31%) content were found in plants treated with PGPR consortium. On the other hand, in the salt sensitive variety (Galaxy-13), P. fluorescens treated plants showed significantly improved leaf-water relations, glycinebetaine (10.78%) content, shoot potassium (23.07%), root calcium (50%) uptake, and yield parameters, respectively. Plant root length (71.72%) and potassium content (113.39%), root and shoot fresh and dry biomass, turgor potential (231.02%) and free proline (317.2%) content were maximum upon PGPR inoculation in consortium. Overall, Aas-11 (salt tolerant variety) showed significantly better performance than Galaxy-13 (salt sensitive variety). This study recommends B. pumilus and E. aurantiacum for the salt tolerant (Aas-11) and P. fluorescens for the salt sensitive (Galaxy-13) varieties, as potential bioinoculants to augment their growth and yield through modulation of morpho-physiological and biochemical attributes under saline conditions.

Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience

Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications.

Bacillus subtilis strain L1 promotes nitrate reductase activity in Arabidopsis and elicits enhanced growth performance in Arabidopsis, lettuce, and wheat

Plant growth promoting rhizobacteria (PGPR) are a group of bacteria that promote plants growth in the rhizosphere. PGPRs are involved in various mechanisms that reinforce plant development. In this study, we screened for PGPRs that were effective in early growth of Arabidopsis thaliana when added to the media and one Bacillus subtilis strain L1 (Bs L1) was selected for further study. When Bs L1 was placed near the roots, seedlings showed notably stronger growth than that in the control, particularly in biomass and root hair. Quantitative reverse transcription polymerase chain reaction analysis revealed a high level of expression of the high affinity nitrate transporter gene, NRT2.1 in A. thaliana treated with Bs L1. After considering how Bs L1 could promote plant growth, we focused on nitrate, which is essential to plant growth. The nitrate content was lower in A. thaliana treated with Bs L1. However, examination of the activity of nitrate reductase revealed higher activity in plants treated with PGPR than in the control. Bs L1 had pronounced effects in representative crops (wheat and lettuce). These results suggest that Bs L1 promotes the assimilation and use of nitrate and plant growth.

Role of Jasmonates in Beneficial Microbe-Root Interactions

The phytohormone jasmonate (JA) modulates various defense and developmental responses of plants, and is implied in the integration of multiple environmental signals. Given its centrality in regulating plant physiology according to external stimuli, JA influences the establishment of interactions between plant roots and beneficial bacteria or fungi. In many cases, moderate JA signaling promotes the onset of mutualism, while massive JA signaling inhibits it. The output also depends on the compatibility between microbe and host plant and on nutritional or environmental cues. Also, JA biosynthesis and perception participate in the systemic regulation of mutualistic interactions and in microbe-induced resistance to biotic and abiotic stress. Here, we review our current knowledge of the role of JA biosynthesis, signaling, and responses during mutualistic root-microbe interactions.

Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense

Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.

Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains

Plants in their natural ecosystems interact with numerous microorganisms, but how they influence their microbiota is still elusive. We observed that sulfatase activity in soil, which can be used as a measure of rhizosphere microbial activity, is differently affected by Arabidopsis accessions. Following a genome-wide association analysis of the variation in sulfatase activity we identified a candidate gene encoding an uncharacterized cytochrome P450, CYP71A27 Loss of this gene resulted in 2 different and independent microbiota-specific phenotypes: A lower sulfatase activity in the rhizosphere and a loss of plant growth-promoting effect by Pseudomonas sp. CH267. On the other hand, tolerance to leaf pathogens was not affected, which agreed with prevalent expression of CYP71A27 in the root vasculature. The phenotypes of cyp71A27 mutant were similar to those of cyp71A12 and cyp71A13, known mutants in synthesis of camalexin, a sulfur-containing indolic defense compound. Indeed, the cyp71A27 mutant accumulated less camalexin in the roots upon elicitation with silver nitrate or flagellin. Importantly, addition of camalexin complemented both the sulfatase activity and the loss of plant growth promotion by Pseudomonas sp. CH267. Two alleles of CYP71A27 were identified among Arabidopsis accessions, differing by a substitution of Glu373 by Gln, which correlated with the ability to induce camalexin synthesis and to gain fresh weight in response to Pseudomonas sp. CH267. Thus, CYP71A27 is an additional component in the camalexin synthesis pathway, contributing specifically to the control of plant microbe interactions in the root.

Maize responsiveness to Azospirillum brasilense: Insights into genetic control, heterosis and genomic prediction

Several studies have shown differences in the abilities of maize genotypes to facilitate or impede Azospirillum brasilense colonization and to receive benefits from this association. Hence, our aim was to study the genetic control, heterosis effect and the prediction accuracy of the shoot and root traits of maize in response to A. brasilense. For that, we evaluated 118 hybrids under two contrasting scenarios: i) N stress (control) and ii) N stress plus A. brasilense inoculation. The diallel analyses were performed using mixed model equations, and the genomic prediction models accounted for the general and specific combining ability (GCA and SCA, respectively) and the presence or not of G×E effects. In addition, the genomic models were fitted considering parametric (G-BLUP) and semi-parametric (RKHS) kernels. The genotypes showed significant inoculation effect for five root traits, and the GCA and SCA were significant for both. The GCA in the inoculated treatment presented a greater magnitude than the control, whereas the opposite was observed for SCA. Heterosis was weakly influenced by the inoculation, and the heterozygosity and N status in the plant can have a role in the benefits that can be obtained from this Plant Growth-Promoting Bacteria (PGPB). Prediction accuracies for N stress plus A. brasilense ranged from 0.42 to 0.78, depending on the scenario and trait, and were higher, in most cases, than the non-inoculated treatment. Finally, our findings provide an understanding of the quantitative variation of maize responsiveness to A. brasilense and important insights to be applied in maize breeding aiming the development of superior hybrids for this association.

Community Composition and Metabolic Potential of Endophytic Actinobacteria From Coastal Salt Marsh Plants in Jiangsu, China

The diversity and functional roles of the plant associated endophytic actinobacteria in unique habitats remain poorly understood. In this paper, we examined the phylogenetic diversity and community composition of endophytic actinobacteria associated with native coastal salt marsh plants in Jiangsu, China using a combination of cultivation and 16S rRNA gene-based high-throughput sequencing (HTS) methods. Further, we evaluated the antifungal, fibrinolytic activities and the secondary metabolite biosynthesis potential of isolates via gene screening. A total of 278 actinobacterial isolates were isolated from 19 plant samples. 16S rRNA gene sequencing revealed that the isolates were highly diverse and belonged to 23 genera within the Actinomycetales order, with Streptomyces, Saccharopolyspora, and Pseudonocardia comprising the most abundant genera. In addition, more than 10 of the isolates were novel actinobacterial taxa distributed across eight genera. HTS analyses of seven representative plant root samples revealed that Actinobacteria phylum constituted 0.04–28.66% of root endophytic bacterial communities. A total of four actinobacterial classes, 14 orders, 35 families, and 63 known genera were detected via HTS, and these communities were found to be dominated by the members of the order Actinomycetales including the genera Streptomyces, Mycobacterium, Arthrobacter, Nocardioides, and Micromonospora. In addition, 30.4% of the representative isolates exhibited antifungal activities, 40.5% of them showed fibrinolytic activities, while 43.0% of the strains harbored secondary metabolite biosynthesis genes. These results demonstrated that coastal salt marsh plants in the Jiangsu Province represented an underexplored new reservoir of diverse and novel endophytic actinobacteria that may be of potential interest in the discovery of bioactive compounds with potential as biocontrol agents and for fibrinolytic enzyme production.

Rhizobacterial Community Assembly Patterns Vary Between Crop Species

Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.

A new regulator of seed size control in Arabidopsis identified by a genome-wide association study

Organ size in plants is controlled by the interaction between genotype and the environment. Seed size, an important agronomic trait, largely determines yield and is an important focus of research. However, the genetic components underpinning natural variation of seed size in undomesticated species remain largely unidentified. Here we report a genome-wide association study (GWAS) of seed size in Arabidopsis thaliana, which identified 38 significantly associated loci, including one locus associated with CYCB1;4. Natural variations in CYCB1;4, which encodes a cyclin protein involved in the cell cycle, significantly influence seed size in A. thaliana. Transgenic plants with enhanced CYCB1;4 expression show normal development, exhibit increased seed size as a result of an accelerated cell cycle progression, and tend to produce higher yields. By contrast, cycb1;4 mutants have smaller seeds, and the effect is especially pronounced in a large-seed accession. The temporal and spatial expression pattern of CYCB1;4 suggests that this gene may function in both maternal tissues and zygotic tissues to coordinate the final size of seeds. Taken together, our results provide genetic insights into natural variation in seed size in Arabidopsis. Moreover, CYCB1;4 homologs in other crops could have great potential as targets for efforts aimed at yield improvement.