Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean

The transcriptional response to yellow and wilt disease, caused by race 6 of Fusarium oxysporum f. sp. Ciceris in two contrasting chickpea cultivars

BACKGROUND

Chickpea (Cicer arietinum L.) ranks as the third most crucial grain legume worldwide. Fusarium wilt (Fusarium oxysporum f. sp. ciceri (Foc)) is a devastating fungal disease that prevents the maximum potential for chickpea production.

RESULTS

To identify genes and pathways involved in resistance to race 6 of Foc, this study utilized transcriptome sequencing of two chickpea cultivars: resistant (Ana) and susceptible (Hashem) to Foc race 6. Illumina sequencing of the root samples yielded 133.5 million raw reads, with about 90% of the clean reads mapped to the chickpea reference genome. The analysis revealed that 548 genes (332 upregulated and 216 downregulated) in the resistant genotype (Ana) and 1115 genes (595 upregulated and 520 downregulated) in the susceptible genotype (Hashem) were differentially expressed under Fusarium wilt (FW) disease stress caused by Foc race 6. The expression patterns of some differentially expressed genes (DEGs) were validated using quantitative real-time PCR. A total of 131 genes were exclusively upregulated under FW stress in the resistant cultivar, including several genes involved in sensing (e.g., CaNLR-RPM1, CaLYK5-RLK, CaPR5-RLK, CaLRR-RLK, and CaRLP-EIX2), signaling (e.g., CaPP7, CaEPS1, CaSTY13, and CaPR-1), transcription regulation (e.g., CaMYBs, CaGLK, CaERFs, CaZAT11-like, and CaNAC6) and cell wall integrity (e.g., CaPGI2-like, CaEXLs, CaCSLD and CaCYP73A100-like).

CONCLUSIONS

The achieved results could provide insights into the molecular mechanism underlying resistance to FW and could be valuable for breeding programs aimed at developing FW-resistant chickpea varieties.

Trade-offs between Cd bioconcentration and translocation and underlying physiological and rhizobacterial mechanisms in Phragmites australis

Cadmium (Cd) pollution poses a significant threat to wetland ecosystems. Phragmites australis, a species with intraspecific ploidy diversity, is commonly used in constructed wetlands for pollution remediation. However, little is known about how the ploidy variation of P. australis influences the phytoremediation processes via physiological and rhizosphere regulations. Here, we used P. australis from two major lineages in China (i.e., tetraploid lineage O and octoploid lineage P) and applied three Cd treatments (control, low Cd concentration, and high Cd concentration). We found that the lineage O had a bioconcentration factor of Cd approximately 40% higher than that of the lineage P. The translocation factor of the lineage P was about 300% higher than that of the lineage O. These suggest that the lower ploidy lineage exhibited a greater capacity to absorb Cd from the environment into the underground part compared to the higher ploidy lineage, and the higher ploidy lineage demonstrated a superior ability in transferring Cd from the underground to the aboveground part. The advanced transpiration system in the higher ploidy lineage can contribute to its enhanced ability to translocate Cd, as the translocation factor of Cd was significantly correlated with the base shoot diameter and the transpiration rate, both notably higher in the lineage P. The rhizobacterial community associated with the lineage P displayed a more intense response to Cd, characterized by an increase in both the diversity of the community and the number of varied bacterial functions following the addition of Cd. Our study offers profound insights into the ecological consequences of intraspecific polyploidization and the application of intraspecific ploidy variation in environmental management and wetland restoration.

Decoding the biochemical dialogue: metabolomic insights into soybean defense strategies against diverse pathogens

Soybean, a crucial global leguminous crop, confronts persistent threats from diverse pathogens, exerting a profound impact on global yields. While genetic dimensions of soybean-pathogen interactions have garnered attention, the intricate biochemical responses remain poorly elucidated. In this study, we applied targeted and untargeted liquid chromatography coupled to mass spectrometry (LC-MS) metabolite profiling to dissect the complex interplay between soybeans and five distinct pathogens. Our analysis uncovered 627 idMS/MS spectra, leading to the identification of four main modules, encompassing flavonoids, isoflavonoids, triterpenoids, and amino acids and peptides, alongside other compounds such as phenolics. Profound shifts were observed in both primary and secondary metabolism in response to pathogenic infections. Particularly notable were the bidirectional changes in total flavonoids across diverse pathogenic inoculations, while triterpenoids exhibited a general declining trend. Noteworthy among the highly inducible total flavonoids were known representative anti-pathogen compounds (glyceollin I), backbone forms of isoflavonoids (daidzein, genistein, glycitein, formononetin), and newly purified compounds in this study (prunin). Subsequently, we delved into the biological roles of these five compounds, validating their diverse functions against pathogens: prunin significantly inhibited the vegetative growth and virulence of Phytophthora sojae; genistein exhibited a pronounced inhibitory effect on the vegetative growth and virulence of Phomopsis longicolla; daidzein and formononetin displayed significant repressive effects on the virulence of P. longicolla. This study underscores the potent utility of metabolomic tools, providing in-depth insights into plant-pathogen interactions from a biochemical perspective. The findings not only contribute to plant pathology but also offer strategic pathways for bolstering plant resistance against diseases on a broader scale.

Biocontrol Potential of Bacillus strains against soybean cyst nematode (Heterodera glycines) and for promotion of soybean growth

The soybean cyst nematode (SCN, Heterodera glycines) is the most yield-limiting pathogen in soybeans worldwide. Using chemical pesticides to control this disease is harmful to human and environment. It is urgent to develop environment-friendly nematicides. The aim of this study was to discover novel biocontrol agents on H. glycines control and soybean growth under greenhouse and field conditions Eight Bacillus strains were isolated from soil rhizosphere soils and the stability and efficiency of H. glycines was assessed in greenhouse and field experiments in 2021 and 2022. In particular, the Ba2-6 strain had the highest potential, because it was a biocontrol agent against H. glycines shown to cause 93.85% juvenile mortality. Furthermore, strains Ba 1-7, Ba2-4, and Ba2-6 effectively reduced the number of females and improved the soybean seed number per plant. Based on their morphological, physiological, biochemical and molecular (16 S rRNA) characteristics, the three strains were identified as B. aryabhattai (Ba1-7), B. megatherium (Ba2-4), and B. halotolerans (Ba2-6). The ability of Ba2-6 to induce systemic resistance to H. glycines in soybeans was investigated by the split-root system and real-time quantitative PCR experiments. The results indicated that the Ba2-6 strain induced systemic resistance to suppress the penetration of H. glycines, and enhanced gene expression of PR1, PR3a, PR5, and NPR1-2, involved in the salicylic acid and jasmonic acid pathways. The study suggests that the strains of B. aryabhattai Ba1-7, B. megatherium Ba2-4, and B. halotolerans Ba2-6 can be considered as effective biocontrol agents to control H. glycines. Further, B. halotolerans Ba2-6 not only promotes soybean growth but also enhances resistance to H. glycines by regulating defense-related gene expression and inducing systemic resistance in soybean.

Research on the mechanism of Bacillus velezensis A-27 in enhancing the resistance of red kidney beans to soybean cyst nematode based on TMT proteomics analysis

Soybean cyst nematode (SCN) poses a significant challenge to red kidney beans cultivation, resulting in yield losses and quality deterioration. This study investigates the molecular mechanisms using Tandem Mass Tag (TMT) based proteomics technology to explore how the plant growth-promoting rhizobacterium (PGPR) Bacillus velezensis A-27 enhances the resistance of red kidney beans against SCN. The results revealed that out of 1,374 differentially expressed proteins (DEPs) in the red kidney beans roots, 734 DEPs were upregulated and 640 DEPs were downregulated in the A-27 + J2 vs J2 treatment group. KEGG analysis revealed that 14 DEPs were involved in the α-LeA metabolic pathway, crucial for the biosynthesis of jasmonic acid (JA) in plants. Quantitative real-time PCR (qRT-PCR) confirmed the upregulation of 4 key genes (PLA1, AOS, AOC, ACX) in the JA biosynthesis pathway, while enzyme-linked immunosorbent assay (ELISA) demonstrated a significant increase in JA content in the roots. The study demonstrates that B. velezensis A-27 stimulates induced systemic resistance (ISR) in red kidney beans, and induce JA biosynthesis by regulating the expression of key enzymes in the α-LeA metabolic pathway. This enhances the plant's defense against SCN, providing a theoretical foundation for the potential use of B. velezensis A-27 as a biocontrol agent for managing SCN in leguminous crops.

The Effects of Bacillus subtilis Expressing a Plant Elicitor Peptide on Nematode Infection on Soybean

There is a pressing need to develop alternative management strategies for the soybean cyst nematode (Heterodera glycines), the most costly pathogen to soybeans. Plant elicitor peptides (PEPs), which are produced by plants in response to stress and stimulate broad-spectrum disease resistance, were previously shown to reduce soybean cyst nematode infection on soybeans when applied as a seed treatment. Here, we introduce an alternative method to deliver PEPs to soybean using a common plant growth-promoting rhizobacterium, Bacillus subtilis, as a bacterial expression system. Similar to the empty vector control, B. subtilis engineered to express a PEP from soybean (GmPEP3) was able to colonize soybean roots and persisted on roots more than a month after treatment. Compared with water or the empty vector control, plants that received a seed treatment with B. subtilis expressing GmPEP3 (B.+GmPEP3) were significantly taller early in vegetative growth (V1 stage) and had lower chlorophyll content in the reproductive stage (R3/R4); these results suggest that GmPEP3 may hasten growth and subsequent senescence. When plants were inoculated with soybean cyst nematode at the V1 stage, those pretreated with B.+GmPEP3 supported significantly fewer nematode eggs at the reproductive stage (R3/R4) than plants treated with water or the empty vector. The effects of B.+GmPEP3 on nematode infection and plant growth appeared to be due primarily to the peptide itself because no significant differences were observed between plants treated with water or with B. subtilis expressing the empty vector. These results indicate the ability of B. subtilis to deliver defense activators for nematode management on soybean.

Plant-nematode battle: engagement of complex signaling network

Plant-parasitic nematodes (PPNs) are widely distributed and highly adaptable. To evade the invasion and infection of PPNs, plants initiate a series of defense responses. In turn, PPNs secrete effectors into the host tissues to suppress plant defense. In this ongoing battle between PPNs and plants, complex signal transduction processes are typically involved. This article aims to review the plant signaling network involved in host perception by the nematode, nematode perception, and downstream activation of plant defense signaling and how nematodes attempt to interfere with this network. Our goal is to establish a foundation for elucidating the signaling and regulatory mechanisms of plant-nematode interactions, and to provide insights and tools for developing PPN-resistant crops and technologies.

Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

Transcriptomic changes in soybean underlying growth promotion and defense against cyst nematode after Bacillus simplex Sneb545 treatment

Bacillus simplex Sneb45 is a plant-growth-promoting rhizobacterium that promotes soybean growth and systemic resistance to cyst nematode. To investigate transcriptional changes in soybean roots in response to B. simplex Sneb45 treatment, transcriptome analysis and quantitative real-time PCR were conducted to detect and validate the differentially expressed genes (DEGs). In total, 19,109 DEGs were obtained. After B. simplex Sneb545 treatment, 970 and 1265 genes were up- and down-regulated at 5 days post-inoculation (dpi), respectively, and 142 and 47 genes were up- and down-regulated at 10 dpi, respectively, compared with untreated soybean roots. Functional annotation of DEGs indicated that B. simplex Sneb545 regulated soybean growth and defense against cyst nematode possibly through genes related to auxin, gibberellin, and NB-LRR protein. In addition, GO and KEGG enrichment analyses indicated that the DEGs were enriched in metabolism, signal transduction, and plant-pathogen interaction pathways. Moreover, the auxin and gibberellin contents were lower in B. simplex Sneb545-treated soybean roots than in untreated roots at 5 dpi. B. simplex Sneb545 possibly altered the expression of wound-induced protein and NAC transcription factor to regulate soybean growth and defense against cyst nematode. Our study provided deep insights into the alterations in soybean transcriptome after exposure to B. simplex Sneb45 and a theoretical basis for further exploring molecular functions underlying the biological control activity of B. simplex Sneb545.

The Roles of Mepiquate Chloride and Melatonin in the Morpho-Physiological Activity of Cotton under Abiotic Stress

Cotton growth and yield are severely affected by abiotic stress worldwide. Mepiquate chloride (MC) and melatonin (MT) enhance crop growth and yield by reducing the negative effects of abiotic stress on various crops. Numerous studies have shown the pivotal role of MC and MT in regulating agricultural growth and yield. Nevertheless, an in-depth review of the prominent performance of these two hormones in controlling plant morpho-physiological activity and yield in cotton under abiotic stress still needs to be documented. This review highlights the effects of MC and MT on cotton morpho-physiological and biochemical activities; their biosynthetic, signaling, and transduction pathways; and yield under abiotic stress. Furthermore, we also describe some genes whose expressions are affected by these hormones when cotton plants are exposed to abiotic stress. The present review demonstrates that MC and MT alleviate the negative effects of abiotic stress in cotton and increase yield by improving its morpho-physiological and biochemical activities, such as cell enlargement; net photosynthesis activity; cytokinin contents; and the expression of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. MT delays the expression of NCED1 and NCED2 genes involved in leaf senescence by decreasing the expression of ABA-biosynthesis genes and increasing the expression of the GhYUC5, GhGA3ox2, and GhIPT2 genes involved in indole-3-acetic acid, gibberellin, and cytokinin biosynthesis. Likewise, MC promotes lateral root formation by activating GA20x genes involved in gibberellin catabolism. Overall, MC and MT improve cotton's physiological activity and antioxidant capacity and, as a result, improve the ability of the plant to resist abiotic stress. The main purpose of this review is to present an in-depth analysis of the performance of MC and MT under abiotic stress, which might help to better understand how these two hormones regulate cotton growth and productivity.

Simply Versatile: The Use of Peribacillus simplex in Sustainable Agriculture

Peribacillus simplex is a Gram-positive, spore-forming bacterium derived from a vast range of different origins. Notably, it is part of the plant-growth-promoting rhizobacterial community of many crops. Although members of the Bacillaceae family have been widely used in agriculture, P. simplex has, so far, remained in the shadow of its more famous relatives, e.g., Bacillus subtilis or Bacillus thuringiensis. Recent studies have, however, started to uncover the bacterium's highly promising and versatile properties, in particular in agricultural and environmental applications. Hence, here, we review the plant-growth-promoting features of P. simplex, as well as its biocontrol activity against a variety of detrimental plant pests in different crops. We further highlight the bacterium's potential as a bioremediation agent for environmental contaminants, such as metals, pesticide residues, or (crude) oil. Finally, we examine the recent developments in the European regulatory landscape to facilitate the use of microorganisms in plant protection products. Undoubtedly, further studies on P. simplex will reveal additional benefits for agricultural and environmentally friendly applications.

Metabolome and transcriptome reprogramming underlying tomato drought resistance triggered by a Pseudomonas strain

Although amelioration of drought stress by Plant Growth Promoting Rhizobacteria (PGPR) is a well-documented phenomenon, the combined molecular and metabolic mechanisms governing this process remain unclear. In these lines, the present study aimed to provide new insights in the underlying drought attenuating mechanisms of tomato plants inoculated with a PGP Pseudomonas putida strain, by using a combination of metabolomic and transcriptomic approaches. Following Differentially Expressed Gene analysis, it became evident that inoculation resulted in a less disturbed plant transcriptome upon drought stress. Untargeted metabolomics highlighted the differential metabolite accumulation upon inoculation, as well as the less metabolic reprograming and the lower accumulation of stress-related metabolites for inoculated stressed plants. These findings were in line with morpho-physiological evidence of drought stress mitigation in the inoculated plants. The redox state modulation, the more efficient nitrogen assimilation, as well as the differential changes in amino acid metabolism, and the induction of the phenylpropanoid biosynthesis pathway, were the main drought-attenuating mechanisms in the SAESo11-inoculated plants. Shifts in pathways related to hormonal signaling were also evident upon inoculation at a transcript level and in conjunction with carbon metabolism regulation, possibly contributed to a drought-attenuation preconditioning. The identified signatory molecules of SAESo11-mediated priming against drought included aspartate, myo-inositol, glutamate, along with key genes related to trehalose, tryptophan and cysteine synthesis. Taken together, SAESo11-inoculation provides systemic effects encompassing both metabolic and regulatory functions, supporting both seedling growth and drought stress amelioration.

Genetic analysis of protein content and oil content in soybean by genome-wide association study

Soybean seed protein content (PC) and oil content (OC) have important economic value. Detecting the loci/gene related to PC and OC is important for the marker-assisted selection (MAS) breeding of soybean. To detect the stable and new loci for PC and OC, a total of 320 soybean accessions collected from the major soybean-growing countries were used to conduct a genome-wide association study (GWAS) by resequencing. The PC ranged from 37.8% to 46.5% with an average of 41.1% and the OC ranged from 16.7% to 22.6% with an average of 21.0%. In total, 23 and 29 loci were identified, explaining 3.4%-15.4% and 5.1%-16.3% of the phenotypic variations for PC and OC, respectively. Of these, eight and five loci for PC and OC, respectively, overlapped previously reported loci and the other 15 and 24 loci were newly identified. In addition, nine candidate genes were identified, which are known to be involved in protein and oil biosynthesis/metabolism, including lipid transport and metabolism, signal transduction, and plant development pathway. These results uncover the genetic basis of soybean protein and oil biosynthesis and could be used to accelerate the progress in enhancing soybean PC and OC.

Phosphorus and Serendipita indica synergism augments arsenic stress tolerance in rice by regulating secondary metabolism related enzymatic activity and root metabolic patterns

The multifarious problems created by arsenic (As), for collective environment and human health, serve a cogent case for searching integrative agricultural approaches to attain food security. Rice (Oryza sativa L.) acts as a sponge for heavy metal(loid)s accretion, specifically As, due to anaerobic flooded growth conditions facilitating its uptake. Acclaimed for their positive impact on plant growth, development and phosphorus (P) nutrition, 'mycorrhizas' are able to promote stress tolerance. Albeit, the metabolic alterations underlying Serendipita indica (S. indica; S.i) symbiosis-mediated amelioration of As stress along with nutritional management of P are still understudied. By using biochemical, RT-qPCR and LC-MS/MS based untargeted metabolomics approach, rice roots of ZZY-1 and GD-6 colonized by S. indica, which were later treated with As (10 µM) and P (50 µM), were compared with non-colonized roots under the same treatments with a set of control plants. The responses of secondary metabolism related enzymes, especially polyphenol oxidase (PPO) activities in the foliage of ZZY-1 and GD-6 were enhanced 8.5 and 12-fold, respectively, compared to their respective control counterparts. The current study identified 360 cationic and 287 anionic metabolites in rice roots, and the commonly enriched pathway annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was biosynthesis of phenylalanine, tyrosine and tryptophan, which validated the results of biochemical and gene expression analyses associated with secondary metabolic enzymes. Particularly under As+S.i+P comparison, both genotypes exhibited an upregulation of key detoxification and defense related metabolites, including fumaric acid, L-malic acid, choline, 3,4-dihydroxybenzoic acid, to name a few. The results of this study provided the novel insights into the promising role of exogenous P and S. indica in alleviating As stress.

Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications

In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.

Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1

INTRODUCTION

The soybean cyst nematode (SCN) is a major disease in soybean production thatseriously affects soybean yield. At present, there are no studies on weighted geneco-expression network analysis (WGCNA) related to SCN resistance.

METHODS

Here, transcriptome data from 36 soybean roots under SCN HG Type 0 (race 3) stresswere used in WGCNA to identify significant modules.

RESULTS AND DISCUSSION

A total of 10,000 differentially expressed genes and 21 modules were identified, of which the module most related to SCN was turquoise. In addition, the hub gene GmHg1 with high connectivity was selected, and its function was verified. GmHg1 encodes serine/threonine protein kinase (PK), and the expression of GmHg1 in SCN-resistant cultivars ('Dongnong L-204') and SCN-susceptible cultivars ('Heinong 37') increased significantly after HG Type 0 stress. Soybean plants transformed with GmHg1-OX had significantly increased SCN resistance. In contrast, the GmHg1-RNAi transgenic soybean plants significantly reduced SCN resistance. In transgenic materials, the expression patterns of 11 genes with the same expression trend as the GmHg1 gene in the 'turquoise module' were analyzed. Analysis showed that 11genes were co-expressed with GmHg1, which may be involved in the process of soybean resistance to SCN. Our work provides a new direction for studying the Molecular mechanism of soybean resistance to SCN.

Transcriptomic and Metabolomic Analyses Reveal That Fullerol Improves Drought Tolerance in Brassica napus L

Carbon nanoparticles have potential threats to plant growth and stress tolerance. The polyhydroxy fullerene-fullerol (one of the carbon nanoparticles) could increase biomass accumulation in several plants subjected to drought; however, the underlying molecular and metabolic mechanisms governed by fullerol in improving drought tolerance in Brassica napus remain unclear. In the present study, exogenous fullerol was applied to the leaves of B. napus seedlings under drought conditions. The results of transcriptomic and metabolomic analyses revealed changes in the molecular and metabolic profiles of B. napus. The differentially expressed genes and the differentially accumulated metabolites, induced by drought or fullerol treatment, were mainly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbohydrate metabolism (e.g., "carbon metabolism" and "galactose metabolism"), amino acid metabolism (e.g., "biosynthesis of amino acids" and "arginine and proline metabolism"), and secondary metabolite metabolism (e.g., "biosynthesis of secondary metabolites"). For carbohydrate metabolism, the accumulation of oligosaccharides (e.g., sucrose) was decreased, whereas that of monosaccharides (e.g., mannose and myo-inositol) was increased by drought. With regard to amino acid metabolism, under drought stress, the accumulation of amino acids such as phenylalanine and tryptophan decreased, whereas that of glutamate and proline increased. Further, for secondary metabolite metabolism, B. napus subjected to soil drying showed a reduction in phenolics and flavonoids, such as hyperoside and trans-3-coumaric acid. However, the accumulation of carbohydrates was almost unchanged in fullerol-treated B. napus subjected to drought. When exposed to water shortage, the accumulation of amino acids, such as proline, was decreased upon fullerol treatment. However, that of phenolics and flavonoids, such as luteolin and trans-3-coumaric acid, was enhanced. Our findings suggest that fullerol can alleviate the inhibitory effects of drought on phenolics and flavonoids to enhance drought tolerance in B. napus.

Impact of key parameters involved with plant-microbe interaction in context to global climate change

Anthropogenic activities have a critical influence on climate change that directly or indirectly impacts plant and microbial diversity on our planet. Due to climate change, there is an increase in the intensity and frequency of extreme environmental events such as temperature rise, drought, and precipitation. The increase in greenhouse gas emissions such as CO2, CH4, NOx, water vapor, increase in global temperature, and change in rainfall patterns have impacted soil–plant-microbe interactions, which poses a serious threat to food security. Microbes in the soil play an essential role in plants’ resilience to abiotic and biotic stressors. The soil microbial communities are sensitive and responsive to these stressors. Therefore, a systemic approach to climate adaptation will be needed which acknowledges the multidimensional nature of plant-microbe-environment interactions. In the last two scores of years, there has been an enhancement in the understanding of plant’s response to microbes at physiological, biochemical, and molecular levels due to the availability of techniques and tools. This review highlights some of the critical factors influencing plant-microbe interactions under stress. The association and response of microbe and plants as a result of several stresses such as temperature, salinity, metal toxicity, and greenhouse gases are also depicted. New tools to study the molecular complexity of these interactions, such as genomic and sequencing approaches, which provide researchers greater accuracy, reproducibility, and flexibility for exploring plant-microbe–environment interactions under a changing climate, are also discussed in the review, which will be helpful in the development of resistant crops/plants in present and future.

Molecular Breeding to Overcome Biotic Stresses in Soybean: Update

Soybean (Glycine max (L.) Merr.) is an important leguminous crop and biotic stresses are a global concern for soybean growers. In recent decades, significant development has been carried outtowards identification of the diseases caused by pathogens, sources of resistance and determination of loci conferring resistance to different diseases on linkage maps of soybean. Host-plant resistance is generally accepted as the bestsolution because of its role in the management of environmental and economic conditions of farmers owing to low input in terms of chemicals. The main objectives of soybean crop improvement are based on the identification of sources of resistance or tolerance against various biotic as well as abiotic stresses and utilization of these sources for further hybridization and transgenic processes for development of new cultivars for stress management. The focus of the present review is to summarize genetic aspects of various diseases caused by pathogens in soybean and molecular breeding research work conducted to date.

Metabolome Profiling: A Breeding Prediction Tool for Legume Performance under Biotic Stress Conditions

Legume crops such as common bean, pea, alfalfa, cowpea, peanut, soybean and others contribute significantly to the diet of both humans and animals. They are also important in the improvement of cropping systems that employ rotation and fix atmospheric nitrogen. Biotic stresses hinder the production of leguminous crops, significantly limiting their yield potential. There is a need to understand the molecular and biochemical mechanisms involved in the response of these crops to biotic stressors. Simultaneous expressions of a number of genes responsible for specific traits of interest in legumes under biotic stress conditions have been reported, often with the functions of the identified genes unknown. Metabolomics can, therefore, be a complementary tool to understand the pathways involved in biotic stress response in legumes. Reports on legume metabolomic studies in response to biotic stress have paved the way in understanding stress-signalling pathways. This review provides a progress update on metabolomic studies of legumes in response to different biotic stresses. Metabolome annotation and data analysis platforms are discussed together with future prospects. The integration of metabolomics with other “omics” tools in breeding programmes can aid greatly in ensuring food security through the production of stress tolerant cultivars.

Comparative Transcriptome Analysis Reveals the Specific Activation of Defense Pathways Against Globodera pallida in Gpa2 Resistant Potato Roots

Cyst nematodes are considered a dominant threat to yield for a wide range of major food crops. Current control strategies are mainly dependent on crop rotation and the use of resistant cultivars. Various crops exhibit single dominant resistance (R) genes that are able to activate effective host-specific resistance to certain cyst nematode species and/or populations. An example is the potato R gene Gpa2, which confers resistance against the potato cyst nematode (PCN), Globodera pallida population D383. Activation of Gpa2 results in a delayed resistance response, which is characterized by a layer of necrotic cells formed around the developing nematode feeding structure. However, knowledge about the Gpa2-induced defense pathways is still lacking. Here, we uncover the transcriptional changes and gene expression network induced upon Gpa2 activation in potato roots infected with G. pallida. To this end, in vitro-grown Gpa2-resistant potato roots were infected with the avirulent population D383 and virulent population Rookmaker. Infected root segments were harvested at 3 and 6 dpi and sent for RNA sequencing. Comparative transcriptomics revealed a total of 1,743 differentially expressed genes (DEGs) upon nematode infection, of which 559 DEGs were specifically regulated in response to D383 infection. D383-specific DEGs associated with Gpa2-mediated defense mainly relates to calcium-binding activity, salicylic acid (SA) biosynthesis, and systemic acquired resistance (SAR). These data reveal that cyst nematode resistance in potato roots depends on conserved downstream signaling pathways involved in plant immunity, which are also known to contribute to R genes-mediated resistance against other pathogens with different lifestyles.

High-throughput plant phenotyping: a role for metabolomics?

High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype-phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response

Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant-pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein-protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN-soybean interaction mechanism as a model will present more understanding of other plant-nematode interactions.

RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars

Potato (Solanum tuberosum L.) is an important food crop worldwide, and potato cyst nematodes (PCNs) are among the most serious pests. The identification of disease resistance genes and molecular markers for PCN infestation can aid in crop improvement research programs against PCN infestation. In the present study, we used high-throughput RNA sequencing to investigate the comprehensive resistance mechanisms induced by PCN infestation in the resistant cultivar Kufri Swarna and the susceptible cultivar Kufri Jyoti. PCN infestation induced 791 differentially expressed genes in resistant cultivar Kufri Swarna, comprising 438 upregulated and 353 downregulated genes. In susceptible cultivar Kufri Jyoti, 2225 differentially expressed genes were induced, comprising 1247 upregulated and 978 downregulated genes. We identified several disease resistance genes (KIN) and transcription factors (WRKY, HMG, and MYB) that were upregulated in resistant Kufri Swarna. The differentially expressed genes from several enriched KEGG pathways, including MAPK signaling, contributed to the disease resistance in Kufri Swarna. Functional network analysis showed that several cell wall biogenesis genes were induced in Kufri Swarna in response to infestation. This is the first study to identify underlying resistance mechanisms against PCN and host interaction in Indian potato varieties.

A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode

Plant pathogens greatly impact food security of the ever-growing human population. Breeding resistant crops is one of the most sustainable strategies to overcome the negative effects of these biotic stressors. In order to efficiently breed for resistant plants, the specific plant-pathogen interactions should be understood. Soybean is a short-day legume that is a staple in human food and animal feed due to its high nutritional content. Soybean cyst nematode (SCN) is a major soybean stressor infecting soybean worldwide including in China, Brazil, Argentina, USA and Canada. There are many Quantitative Trait Loci (QTLs) conferring resistance to SCN that have been identified; however, only two are widely used: rhg1 and Rhg4. Overuse of cultivars containing these QTLs/genes can lead to SCN resistance breakdown, necessitating the use of additional strategies. In this manuscript, a literature review is conducted on research related to soybean resistance to SCN. The main goal is to provide a current understanding of the mechanisms of SCN resistance and list the areas of research that could be further explored.

Soybean miR159-GmMYB33 Regulatory Network Involved in Gibberellin-Modulated Resistance to Heterodera glycines

Soybean cyst nematode (SCN, Heterodera glycines) is an obligate sedentary biotroph that poses major threats to soybean production globally. Recently, multiple miRNAome studies revealed that miRNAs participate in complicated soybean-SCN interactions by regulating their target genes. However, the functional roles of miRNA and target genes regulatory network are still poorly understood. In present study, we firstly investigated the expression patterns of miR159 and targeted GmMYB33 genes. The results showed miR159-3p downregulation during SCN infection; conversely, GmMYB33 genes upregulated. Furthermore, miR159 overexpressing and silencing soybean hairy roots exhibited strong resistance and susceptibility to H. glycines, respectively. In particular, miR159-GAMYB genes are reported to be involve in GA signaling and metabolism. Therefore, we then investigated the effects of GA application on the expression of miR159-GAMYB module and the development of H. glycines. We found that GA directly controls the miR159-GAMYB module, and exogenous GA application enhanced endogenous biologically active GA1 and GA3, the abundance of miR159, lowered the expression of GmMYB33 genes and delayed the development of H. glycines. Moreover, SCN infection also results in endogenous GA content decreased in soybean roots. In summary, the soybean miR159-GmMYB33 module was directly involved in the GA-modulated soybean resistance to H. glycines.

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

Evaluation of Scopoletin from Penicillium janthinellum Snef1650 for the Control of Heterodera glycines in Soybean

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is responsible for causing a major soybean disease globally. The fungal strain Penicillium janthinellum Snef1650 was evaluated against H. glycines. However, the effective determinants of the P. janthinellum strain are unknown. By performing pot experiments, a functioning compound was isolated from P. janthinellum Snef1650 through organic solvent extraction, semi-preparative HPLC, Sephadex LH-20 column chromatography, and silica gel column chromatography, and the isolated compound was identified to be scopoletin through 1H NMR, 13C NMR, and HPLC–MS. The pot experiments indicated that the treatment of soybean seeds with scopoletin drastically reduced the SCN population. The field experiments performed in 2017 and 2018 revealed that scopoletin decreased over 43.7% juveniles in the roots and over 61.55% cysts in the soil. Scopoletin treatment also promoted soybean growth and improved its yield, with an increase in plot yield by >5.33%. Scopoletin obtained from P. janthinellum Snef1650 could be used as an anti-H. glycines biocontrol agent.

Re-vitalizing of endophytic microbes for soil health management and plant protection

Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.

Soybean Metabolomics Based in Mass Spectrometry: Decoding the Plant's Signaling and Defense Responses under Biotic Stress

Metabolomics is an omics technology that is extremely valuable to analyze all small-molecule metabolites in organisms. Recent advances in analytical instrumentation, such as mass spectrometry combined with data processing tools, chemometrics, and spectral data libraries, allow plant metabolomics studies to play a fundamental role in the agriculture field and food security. Few studies are found in the literature using the metabolomics approach in soybean plants on biotic stress. In this review, we provide a new perspective highlighting the potential of metabolomics-based mass spectrometry for soybean in response to biotic stress. Furthermore, we highlight the response and adaptation mechanisms of soybean on biotic stress about primary and secondary metabolism. Consequently, we provide subsidies for further studies of the resistance and improvement of the crop.

Metabolomics as a Tool to Study Underused Soy Parts: In Search of Bioactive Compounds

The valorization of agri-food by-products is essential from both economic and sustainability perspectives. The large quantity of such materials causes problems for the environment; however, they can also generate new valuable ingredients and products which promote beneficial effects on human health. It is estimated that soybean production, the major oilseed crop worldwide, will leave about 597 million metric tons of branches, leaves, pods, and roots on the ground post-harvesting in 2020/21. An alternative for the use of soy-related by-products arises from the several bioactive compounds found in this plant. Metabolomics studies have already identified isoflavonoids, saponins, and organic and fatty acids, among other metabolites, in all soy organs. The present review aims to show the application of metabolomics for identifying high-added-value compounds in underused parts of the soy plant, listing the main bioactive metabolites identified up to now, as well as the factors affecting their production.

Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7

BACKGROUND

Soybean cyst nematode, Heterodera glycines, is one of the most devastating pathogens of soybean and causes severe annual yield losses worldwide. Different soybean varieties exhibit different responses to H. glycines infection at various levels, such as the genomic, transcriptional, proteomic and metabolomic levels. However, there have not yet been any reports of the differential responses of incompatible and compatible soybean varieties infected with H. glycines based on combined metabolomic and transcriptomic analyses.

RESULTS

In this study, the incompatible soybean variety PI437654 and three compatible soybean varieties, Williams 82, Zhonghuang 13 and Hefeng 47, were used to clarify the differences in metabolites and transcriptomics before and after the infection with HG1.2.3.5.7. A local metabolite-calibrated database was used to identify potentially differential metabolites, and the differences in metabolites and metabolic pathways were compared between the incompatible and compatible soybean varieties after inoculation with HG1.2.3.5.7. In total, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories: metabolites/pathways overlapped in the incompatible and compatible soybeans, and metabolites/pathways specific to either the incompatible or compatible soybean varieties. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specific differential metabolites (such as significantly up-regulated nicotine and down-regulated D-aspartic acid) and their associated KEGG pathways (such as the tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolism, sphingolipid metabolism and arginine biosynthesis) were significantly altered and abundantly enriched in the incompatible soybean variety PI437654, and likely played pivotal roles in defending against HG1.2.3.5.7 infection. Three key metabolites (N-acetyltranexamic acid, nicotine and D,L-tryptophan) found to be significantly up-regulated in the incompatible soybean variety PI437654 infected by HG1.2.3.5.7 were classified into two types and used for combined analyses with the transcriptomic expression profiling. Associated genes were predicted, along with the likely corresponding biological processes, cellular components, molecular functions and pathways.

CONCLUSIONS

Our results not only identified potential novel metabolites and associated genes involved in the incompatible response of PI437654 to soybean cyst nematode HG1.2.3.5.7, but also provided new insights into the interactions between soybeans and soybean cyst nematodes.

iTRAQ-Based Proteomic Analysis Reveals the Role of the Biological Control Agent, Sinorhizobium fredii Strain Sneb183, in Enhancing Soybean Resistance Against the Soybean Cyst Nematode

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, poses a serious threat to soybean production worldwide. Biological control agents have become eco-friendly candidates to control pathogens. Our previous study indicated that the biocontrol agent, Sinorhizobium fredii strain Sneb183, may induce soybean resistance to SCN. To study the mechanisms underlying induced disease resistance in the plant by Sneb183, an iTRAQ (isobaric tag for relative and absolute quantitation)-based proteomics approach was used to identify proteomic changes in SCN-infected soybean roots derived from seeds coated with the Sneb183 fermentation broth or water. Among a total of 456 identified differentially expressed proteins, 212 and 244 proteins were upregulated and downregulated, respectively, in Sneb183 treated samples in comparison to control samples. Some identified differentially expressed proteins are likely to be involved in the biosynthesis of phenylpropanoid, flavone, flavanol, and isoflavonoid and have a role in disease resistance and adaptation to environmental stresses. We used quantitative real-time PCR (qRT-PCR) to analyze key genes, including GmPAL (phenylalanine ammonia-lyase), GmCHR (chalcone reductase), GmCHS (chalcone synthase), and GmIFS (isoflavone synthase), that are involved in isoflavonoid biosynthesis in Sneb183-treated and control samples. The results showed that these targeted genes have higher expression levels in Sneb183-treated than in control samples. High performance liquid chromatography (HPLC) analysis further showed that the contents of daidzein in Sneb183-treated samples were 7.24 times higher than those in control samples. These results suggested that the Sinorhizobium fredii strain Sneb183 may have a role in inducing isoflavonoid biosynthesis, thereby resulting in enhanced resistance to SCN infection in soybean.

Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress

Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.

A Phytochemical Perspective on Plant Defense Against Nematodes

Given the large yield losses attributed to plant-parasitic nematodes and the limited availability of sustainable control strategies, new plant-parasitic nematode control strategies are urgently needed. To defend themselves against nematode attack, plants possess sophisticated multi-layered immune systems. One element of plant immunity against nematodes is the production of small molecules with anti-nematode activity, either constitutively or after nematode infection. This review provides an overview of such metabolites that have been identified to date and groups them by chemical class (e.g., terpenoids, flavonoids, glucosinolates, etc.). Furthermore, this review discusses strategies that have been used to identify such metabolites and highlights the ways in which studying anti-nematode metabolites might be of use to agriculture and crop protection. Particular attention is given to emerging, high-throughput approaches for the identification of anti-nematode metabolites, in particular the use of untargeted metabolomics techniques based on nuclear magnetic resonance (NMR) and mass spectrometry (MS).

Comparative transcriptomic analysis reveals that multiple hormone signal transduction and carbohydrate metabolic pathways are affected by Bacillus cereus in Nicotiana tabacum

Bacillus cereus is thought to be a beneficial bacterium for plants in several aspects, such as promoting plant growth and inducing plant disease resistance. However, there is no detailed report on the effect of Bacillus cereus acting on Nicotiana tabacum. In the present study, RNA-based sequencing (RNA-seq) was used to identify the molecular mechanisms of the interaction between B. cereus CGMCC 5977 and N. tabacum. A total of 7345 and 5604 differentially expressed genes (DEGs) were identified from leaves inoculated with Bacillus cereus at 6 and 24 hpi, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the most DEGs could be significantly enriched in hormone signal transduction, the MAPK signaling pathway, photosynthesis, oxidative stress, and amino sugar, and nucleotide sugar metabolism. Furthermore, glycolysis/gluconeogenesis was severely affected by inoculation with Bacillus cereus. In the hormone signal pathway, multiple DEGs were involved in plant defense-related major hormones, including activation of jasmonic acid (JA), salicylic acid (SA), and ethylene (Eth). Further analyses showed that other hormone-related genes involved in abscisic acid (ABA), gibberellin (GA), auxin (AUX), and cytokinin (CK) also showed changes. Notably, a large number of genes associated with glycolysis/gluconeogenesis, catabolism of starch and oxidative stress were induced. In addition, the majority of DEGs related to nucleic acid sugar metabolism were also significantly upregulated. Biochemical assays showed that the starch content of B. cereus-treated leaves was reduced to 2.51 mg/g and 2.38 mg/g at 6 and 24 hpi, respectively, while that of the control sample was 5.42 mg/g. Overall, our results demonstrated that multiple hormone signal transduction and carbohydrate metabolic pathways are involved in the interaction of tobacco and B. cereus.

Isolation and identification of induced systemic resistance determinants from Bacillus simplex Sneb545 against Heterodera glycines

Heterodera glycines is one of the most destructive pathogens of soybean. Soybean seeds coated with Bacillus simplex Sneb545 have shown resistance to H. glycines as a result of induced systemic resistance (ISR) in the plants. In this study, we aimed to identify the resistance-inducing determinants from this B. simplex strain. Combining the ISR bioassay, six ISR-active compounds were isolated from a culture of B. simplex Sneb545 using organic solvent gradient extraction, silica gel column chromatography, Sephadex LH-20 column chromatography, and semi-preparative high-performance liquid chromatography (HPLC), and all systems were based on activity tracking. The compounds were determined as cyclic(Pro-Tyr), cyclic(Val-Pro), cyclic(Leu-Pro), uracil, phenylalanine, and tryptophan using 1H NMR and 13C NMR. In plants from seeds coated with Bacillus simplex Sneb545, these six ISR-active compounds delayed the development of H. glycines in soybean roots. Moreover, cyclic(Pro-Tyr), cyclic(Val-Pro), and tryptophan reduced the number of nematodes in soybean roots. The expression levels of defense-related genes with cyclic(Val-Pro), tryptophan and uracil treatment soybean analysed using Quantitative real-time PCR (qRT-PCR). The results indicate cyclic(Val-Pro), tryptophan and uracil induced the expression of defense-related genes involved in the SA- and JA-pathways to against H. glycines. Our research results provide new agents for the control of H. glycines.

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.

Plant Dynamic Metabolic Response to Bacteriophage Treatment After Xanthomonas campestris pv. campestris Infection

Periodic epidemics of black rot disease occur worldwide causing substantial yield losses. Xanthomonas campestris pv. campestris (Xcc) represents one of the most common bacteria able to cause the above disease in cruciferous plants such as broccoli, cabbage, cauliflower, and Arabidopsis thaliana. In agriculture, several strategies are being developed to contain the Xanthomonas infection. The use of bacteriophages could represent a valid and efficient approach to overcome this widespread phenomenon. Several studies have highlighted the potential usefulness of implementing phage therapy to control plant diseases as well as Xcc infection. In the present study, we characterized the effect of a lytic phage on the plant Brassica oleracea var. gongylodes infected with Xcc and, for the first time, the correlated plant metabolic response. The results highlighted the potential benefits of bacteriophages: reduction of bacterium proliferation, alteration of the biofilm structure and/or modulation of the plant metabolism and defense response.

Microbes Attaching to Endoparasitic Phytonematodes in Soil Trigger Plant Defense Upon Root Penetration by the Nematode

Root-knot nematodes (Meloidogyne spp.) are among the most aggressive phytonematodes. While moving through soil to reach the roots of their host, specific microbes attach to the cuticle of the infective second-stage juveniles (J2). Reportedly, the attached microorganisms affect nematodes and reduce their performance on the host plants. We have previously shown that some non-parasitic bacterial strains isolated from the cuticle of Meloidogyne hapla in different soils affected J2 mortality, motility, hatching, and root invasion. Here we tested whether cuticle-attached microbes trigger plant defenses upon penetration of J2. In in vitro assays, M. hapla J2-attached microbes from a suppressive soil induced pathogen-associated molecular pattern-triggered immunity (PTI) in tomato roots. All tested PTI-responsive defense genes were upregulated after root invasion of J2 with attached microbes, compared to surface-sterilized J2, particularly the jasmonic acid-mediated PTI marker genes TFT1 and GRAS4.1. The strain Microbacterium sp. K6, that was isolated from the cuticle, significantly reduced root invasion when attached to the J2. Attached K6 cells supported plant defense and counteracted suppression of plant basal defense in roots by invaded J2. The plant response to the J2-attached K6 cells was stronger in leaves than in roots, and it increased from 1 to 3 days post inoculation (dpi). At 1 dpi, the plant responded to J2-attached K6 cells by ameliorating the J2-triggered down-regulation of defense genes mostly in roots, while at 3 dpi this response was systemic and more pronounced in leaves. In a reactive oxygen species (ROS) assay, the compounds released from J2 with attached K6 cells triggered a stronger ROS burst in tomato roots than the compounds from nematodes without K6, or the metabolites released from strain K6 alone. Leaves showed a 100 times more sensitive response than roots, and the metabolites of K6 with or without J2 induced strong ROS bursts. In conclusion, our results suggest the importance of microorganisms that attach to M. hapla in suppressive soil, inducing early basal defenses in plants and suppressing nematode performance in roots.

Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

Biocontrol potential of Microbacterium maritypicum Sneb159 against Heterodera glycines

BACKGROUND

The soybean cyst nematode Heterodera glycines (Ichinohe) is the most devastating pathogen affecting soybean production worldwide. Biocontrol agents have become eco-friendly candidates to control pathogens. The aim of this study was to discover novel biocontrol agents against H. glycines.

RESULTS

Microbacterium maritypicum Sneb159, screened from 804 strains, effectively reduced the number of females in field experiments conducted in 2014 and 2015. The stability and efficiency of H. glycines control by Sneb159 was further assessed in growth chamber and field experiments. Sneb159 decreased H. glycines population densities, especially the number of females by 43.9%-67.7%. To confirm Sneb159 induced plant resistance, a split-root assay was conducted. Sneb159 induced local and systemic resistance to suppress the penetration and development of H. glycines, and enhanced the gene expression of PR2, PR3b, and JAZ1, involved in the salicylic acid and jasmonic acid pathways.

CONCLUSION

This is the first report of M. maritypicum Sneb159 suppressing H. glycines infection. This effect may be the result of Sneb159-induced resistance. Our study indicates that M. maritypicum Sneb159 is a promising biocontrol agent against H. glycines. © 2019 Society of Chemical Industry.

Bacillus amyloliquefaciens inoculation alters physiology of rice (Oryza sativa L. var. IR-36) through modulating carbohydrate metabolism to mitigate stress induced by nutrient starvation

To avoid disproportionate usage of chemicals in agriculture, an alternative eco-friendly strategy is required to improve soil fertility, and enhance crop productivity. Therefore, the present study demonstrates the role of plant beneficial rhizobacteria viz., Paenibacillus lentimorbus B-30488 (B-30488), Bacillus amyloliquefaciens SN13 (SN13), and their consortium in rice (Oryza sativa L. var. IR-36) facing nutrient deprivation. Parameters such as proline, total soluble sugar, relative water content, electrolytic leakage and malondialdehyde content were modulated in control rice seedlings as compared to treated under nutrient starved conditions. Bacterial inoculation not only significantly improved the agronomic parameters but also concentrations, uptake and partitioning of macro-micro nutrients. To disclose PGPR induced mechanisms to low nutrient stress tolerance, GC-MS analysis was performed. Overall 43 differential metabolites were characterized. Proline, glutamine, linolenic acid, malic acid, ribitol, propanoic acid and serine were accumulated in seedlings exposed to nutrient starvation. In PGPR inoculated rice glucose, fructose, mannose, glucitol, oleic acid, gulonic acid, raffinose, inositol were accumulated that induce metabolic and physiological parameters to reduce the impact of stress. Based on results SN13 was selected for gene expression analysis of metabolism-related genes that further affirmed the ability of PGPR to modulate carbohydrate metabolism in rice seedlings under suboptimum nutrient level.

Phytobiome metabolism: beneficial soil microbes steer crop plants' secondary metabolism

Crops are negatively affected by abiotic and biotic stresses, however, plant-microbe cooperation allows prompt buffering of these environmental changes. Microorganisms exhibit an extensive metabolic capability to assist plants in reducing these burdens. Interestingly, beneficial microbes may also trigger, at the host side, a sequence of events from signal perception to metabolic responses leading to stress tolerance or protection against biotic threats. Although plants are well known for their vast chemical diversity, plant-microbial interactions often stimulate the production of a rich and different repertoire of metabolites in plants. The targeted microbial-plant interactions reprogramming plant metabolism represent potential means to foster various pest managements. However, the molecular mechanisms of microbial modulation of plant metabolic plasticity are still poorly understood. Here, we review an increasing amount of reports providing evidence for alterations to plant metabolism caused by beneficial microbial colonization. In addition, we highlight the vital importance of these metabolic reprograms for plants under stress erratic conditions. © 2019 Society of Chemical Industry.