Modulation of host immunity by beneficial microbes

Impact of microplastics on plant biogenic volatile organic compounds emission: A preliminary study

Plants produce biogenic volatile organic compounds (BVOCs) that are essential for interacting with the environment. As emerging pollutants, microplastics (MPs) may influence BVOCs emissions, yet their effects remain poorly underexplored. This study employed headspace solid phase microextraction coupled with gas chromatography - mass spectrum to investigate the impact of MPs on the BVOC emission profiles of lettuce (Lactuca sativa). Our results demonstrated that polystyrene (PS) MPs exposure, even at environmental concentrations (0.5-2 mg/L), significantly altered BVOC profiles, with a marked increase in aldehydes and ketones. A 7-fold increase in phenylacetaldehyde and benzaldehyde at 50 mg/L indicated stress-related metabolic changes, which also evidenced by reduced superoxide dismutase (SOD) activity and shifts in root microbial communities. The key discriminating BVOCs identified suggest that the presence of MPs impact plant survival and adaptability, with emissions originating from various metabolic pathways, including phenylpropanoid, lipoxygenase, and terpenoid synthesis pathways. Furthermore, variations in type, size, and aging treatment of MPs influenced BVOCs emission patterns. Our findings underscore the significance of BVOCs as indicators of exposure risks associated with MPs and highlight the ecological threats posed by these pollutants.

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

How different stress responses by male and female plants are influenced by interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant and quantified biotic associations between microorganisms to explore the relationship between microbial associations and plant adaptation. We propose a health index (HI) to comprehensively characterize the physiological characteristics and adaptive capacity of plants under stress. It was found that male poplars demonstrated higher salt stress tolerance than females, and root-secreted citric acid was significantly higher in the rhizospheres of male poplars. Positive biotic association among bacteria increased poplar HI significantly under salt stress, while fungal and cross-domain biotic association (bacteria-fungi) did not. We further identified a keystone bacterial taxon regulating bacterial biotic association, ASV_22706, which was itself regulated by citric acid and significantly positively correlated with host HI. The abundance of keystone fungal taxa was positively correlated with HI of male poplars and negatively correlated with HI of female poplars. Compared with female poplars, male poplars enriched more prebiotics and probiotics under stress. This work primarily reveals the relationship between adaptation differences and microbial interactions in dioecious plants, which suggests a microbial approach to improve plant adaptability to stress conditions.

Unlocking the potential of ecofriendly guardians for biological control of plant diseases, crop protection and production in sustainable agriculture

Several beneficial microbial strains inhibit the growth of different phytopathogens and commercialized worldwide as biocontrol agents (BCAs) for plant disease management. These BCAs employ different strategies for growth inhibition of pathogens, which includes production of antibiotics, siderophores, lytic enzymes, bacteriocins, hydrogen cyanide, volatile organic compounds, biosurfactants and induction of systemic resistance. The efficacy of antagonistic strains could be further improved through genetic engineering for better disease suppression in sustainable farming practices. Some antagonistic microbial strains also possess plant-growth-promoting activities and their inoculation improved plant growth in addition to disease suppression. This review discusses the characterization of antagonistic microbes and their antimicrobial metabolites, and the application of these BCAs for disease control. The present review also provides a comprehensive summary of the genetic organization and regulation of the biosynthesis of different antimicrobial metabolites in antagonistic strains. Use of molecular engineering to improve production of metabolites in BCAs and their efficacy in disease control is also discussed. The application of these biopesticides will reduce use of conventional pesticides in disease control and help in achieving sustainable and eco-friendly agricultural systems.

Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

Gaeumannomyces tritici is responsible for take-all disease, one of the most important wheat root threats worldwide. High-quality annotated genome resources are sorely lacking for this pathogen, as well as for the closely related antagonist and potential wheat take-all biocontrol agent, G. hyphopodioides. As such, we know very little about the genetic basis of the interactions in this host-pathogen-antagonist system. Using PacBio HiFi sequencing technology we have generated nine near-complete assemblies, including two different virulence lineages for G. tritici and the first assemblies for G. hyphopodioides and G. avenae (oat take-all). Genomic signatures support the presence of two distinct virulence lineages in G. tritici (types A and B), with A strains potentially employing a mechanism to prevent gene copy-number expansions. The CAZyme repertoire was highly conserved across Gaeumannomyces, while candidate secreted effector proteins and biosynthetic gene clusters showed more variability and may distinguish pathogenic and non-pathogenic lineages. A transition from self-sterility (heterothallism) to self-fertility (homothallism) may also be a key innovation implicated in lifestyle. We did not find evidence for transposable element and effector gene compartmentalisation in the genus, however the presence of Starship giant transposable elements may contribute to genomic plasticity in the genus. Our results depict Gaeumannomyces as an ideal system to explore interactions within the rhizosphere, the nuances of intraspecific virulence, interspecific antagonism, and fungal lifestyle evolution. The foundational genomic resources provided here will enable the development of diagnostics and surveillance of understudied but agriculturally important fungal pathogens.

Half-Century Scientometric Analysis: Unveiling the Excellence of Fungi as Biocontrol Agents and Biofertilisers

Reducing the use of chemical inputs is becoming a major challenge in developing sustainable agriculture. Fungi, known as biocontrol agents (BCAs) and biofertilisers, are crucial in scientific research and are celebrated for their efficacy, eco-friendliness, and multifaceted roles. In this study, a bibliometric analysis was conducted on 5349 articles related to fungi as BCAs and biofertilisers over the past half-century using the Web of Science Core Collection (WoSCC) database. The publications on fungi, such as BCAs and biofertilisers, have increased significantly over the last 20 years, with a maximum growth rate of 33.7%. The USA and China lead in this field. Keyword clustering analysis revealed that entomopathogenic fungi, including Hemiptera, Coleoptera, and Lepidoptera, can be used to manage plant pests. It also showed that fungi can be used as biofertilisers to promote plant growth. The analysis of research trends shows that Beauveria bassiana in biological control is highly significant. This study also showed that entomopathogenic fungi control plant pests by infiltrating the insect cuticles. Trichoderma spp. exert biocontrol effects by producing antibiotics. Arbuscular mycorrhizal fungi can trigger plant defence mechanisms by modulating secondary metabolite synthesis. This study contributes to the current knowledge of fungi as BCAs and biofertilisers and can guide future research.

Lotus resistance against Ralstonia is enhanced by Mesorhizobium and does not impair mutualism

Legumes establish nitrogen-fixing symbioses with rhizobia. On the contrary, they can be attacked concomitantly by pathogens, raising the question of potential trade-offs between mutualism and immunity. In order to study such trade-offs, we used a tripartite system involving the model legume Lotus japonicus, its rhizobial symbiont Mesorhizobium loti and the soilborne pathogen Ralstonia solanacearum. We investigated the impact of mutualism on plant defense and the reciprocal influence of plant defense on mutualism. We found that Lotus age-related resistance against Ralstonia was improved by the interaction with rhizobia especially when nodulation is triggered. Conversely, age-related resistance did not compromise nodule organogenesis or functioning under pathogen attack. Proteomic characterization indicates that this resistance is associated with distinct proteome modifications in roots and nodules. This resistance questions the concept of interference between efficient defense reactions and mutualistic interactions and is of great interest for agricultural purposes as it not only restricts pathogen colonization, but would also preserve nitrogen fixation and yield.

Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Effects of endophytes on early growth and ascorbate metabolism in Brassica napus

Understanding the early interactions between plants and endophytes will contribute to a more systematic approach to enhancing endophyte-mediated effects on plant growth and environmental stress resistance. This study examined very early growth and ascorbate metabolism after seed treatment of Brassica napus with three different endophytes. The three endophytes used were Bacillus amyloliquefaciens pb1(Bapb1), Micrococcus luteus (Ml) and Pseudomonas fluorescens SLB4 (SLB4). Seeds of Brassica napus cv. trophy were surface sterilized and plated on 1/2 MS Basal salts (pH 5.7 -5.8) + 0.8% agarose. Under sterile conditions, endophyte suspensions or sterile distilled water (controls) were applied to plated seeds. After two days, all plates were scanned to produce digital images for subsequent growth analysis. Then, seedlings were gently removed from the plates and placed in sterile microfuge tubes. For biochemical analyses, extracts were prepared from samples and assayed spectrophotometrically. We detected slight changes in seedling root tip and/or primary root growth with Bapb1 and Ml. Seedlings treated with SLB4 exhibited significantly increased primary root and root tip length after two days of growth. Ascorbate oxidation, however, was the primary significant change common to all endophyte-treated seedlings. In relation to ascorbate oxidation, soluble ascorbate oxidase (AO) was slightly reduced in Bapb1 and Ml-treated seedlings, whereas ionically-bound AO was reduced in Bapb1 and SLB4-treated seedlings. Total AO activity was significantly reduced in Bapb1-treated seedlings. There were no differences in cytosolic APX activity or glutathione levels between endophyte-treated seedlings and controls. Like pathogens, endophytes can trigger an oxidative burst in the plant. A level of ascorbate oxidation seems required to propagate ROS as signaling molecules as part of the plant immune response. The slight to moderate reductions in plant AO activity that we found mimic the inhibitory effects of pathogens on AO activity, but there was still a level of AO activity that may have been sufficient for the apoplastic ascorbate oxidation required for subsequent ROS signaling. Other studies have suggested that endophytes may elicit a more moderate plant immune response relative to pathogens to facilitate colonization. The AO, APX, and glutathione results would be consistent with a moderate plant immune response to endophytes.

Triple interactions for induced systemic resistance in plants

Induced systemic resistance (ISR) is a crucial concept in modern agriculture, explaining plant defense mechanisms primed by rhizosphere stimuli and activated by subsequent infections. Biological factors contributing to ISR generally include plant growth-promoting microbes3 (PGPM). Bacillus spp., Pseudomonas spp., and Trichoderma spp. have been extensively studied for their plant growth-promoting characteristics and ISR effect against above-ground pathogens and insect infestations. These phenomena elucidate the bottom-up effects of how beneficial rhizosphere microbes help plants resist above-ground attacks. Conversely, soil microbiome analysis in the rhizosphere of plants infected by above-ground pathogens has shown increased beneficial microbes in the soil, a phenomenon termed 'soil legacy effects'. This represents the top-down effects of above-ground attackers on plants' rhizosphere environments. Interestingly, recent studies have shown that above-ground stimuli not only recruit PGPM in the rhizosphere but also that these PGPM influence plant defense responses against subsequent pathogen infections. This can be seen as a four-step plant defense mechanism involving above-ground attackers, host plants, rhizosphere microbes, and subsequent attacks. This represents an active defense mechanism that overcomes the limitations of sessile plants. This review summarizes plant ISR mechanisms in terms of triple inter-organism interactions and provides molecular evidence for each step.

Mechanisms of rhizosphere plant-microbe interactions: molecular insights into microbial colonization

The rhizosphere, as the "frontline" of plant life, connects plant roots, rhizosphere microorganisms, and surrounding soil, plays a crucial role in plant growth and health, particularly in sustainable agriculture. Despite the well-established contribution of plant-microbe interactions to plant health, the specific molecular mechanisms remain insufficiently understood. This review aims to summarize the physiological adjustments and signal modulation that both plants and microorganisms undergo within this unique ecological niche to ensure successful colonization. By analyzing key processes such as chemotaxis, root attachment, immune evasion, and biofilm formation, we uncover how plants precisely modulate root exudates to either recruit or repel specific microorganisms, thereby shaping their colonization patterns. These findings provide new insights into the complexity of plant-microbe interactions and suggest potential directions for future research in sustainable agriculture.

Flue-cured tobacco intercropping with insectary floral plants improves rhizosphere soil microbial communities and chemical properties of flue-cured tobacco

BACKGROUND

Continuous cropping of the same crop leads to land degradation. This is also called the continuous-cropping obstacle. Currently, intercropping tobacco with other crops can serve as an effective strategy to alleviate continuous cropping obstacles.

RESULTS

In this study, tobacco K326 and insectary floral plants were used as materials, and seven treatments of tobacco monoculture (CK), tobacco intercropped with Tagetes erecta, Vicia villosa, Fagopyrum esculentum, Lobularia maritima, Trifolium repens, and Argyranthemum frutescens respectively, were set up to study their effects on rhizosphere soil chemical properties and composition and structure of rhizosphere soil microbial community of tobacco. The 16 S rRNA gene and ITS amplicons were sequenced using Illumina high-throughput sequencing. tobacco/insectary floral plants intercropping can influence rhizosphere soil chemical properties, which also change rhizosphere microbial communities. The CK and treatment groups tobacco rhizosphere soil microorganisms had significantly different genera, such as tobacco intercropping with T. repens and A. frutescens significantly increased the number of Fusarium and intercropping T. erecta, V. villosa, L. maritima, T. repens, and A. frutescens significantly increased the number of Sphingomonas and unknown Gemmatimonadaceae. Additionally, intercropping T. erecta, V. villosa and L. maritima changed the rhizosphere fungal and bacteria community and composition of tobacco and the positive correlation between tobacco rhizosphere the genera of fungi and bacterial were greater than CK. The pathway of the carbohydrate metabolism, amino acid metabolism, and energy metabolism in rhizosphere bacteria were significantly decreased after continuous cropping. Fungal symbiotic trophic and saprophytic trophic were significantly increased after intercropping V. villosa, L. maritima and plant pathogen and animal pathogen were increased after intercropping T. repens and A. frutescens. Additionally, bacterial and fungal communities significantly correlated with soil chemical properties, respectively.

CONCLUSION

This study reveals that intercropping tobacco with insectary floral plants, particularly T. erecta, V. villosa, L. maritima and A. frutescens significantly affects soil chemical properties and alters rhizosphere microbial communities, increasing the abundance of certain microbial genera. Additionally, intercropping enhances pathways related to carbohydrate, amino acid, and energy metabolism in rhizosphere bacteria. These findings suggest that intercropping could provide a promising strategy to overcome challenges associated with continuous tobacco cropping by regulating the rhizosphere environment.

Arbuscular mycorrhizal fungi influence belowground interactions between a specialist root-feeder and its natural enemy

As primary producers, plants play a central role in mediating interactions across trophic levels. Although plants are the primary food source for herbivorous insects, they can protect themselves from herbivore damage. Many plants produce toxic compounds that directly reduce herbivore feeding, but plants also protect themselves indirectly by attracting natural enemies of the attacking herbivore through volatile signaling. These so-called tri-trophic interactions have historically been documented aboveground in aerial plant parts but are also known to occur belowground in root systems. In addition to herbivores, plants directly interact with other organisms, which can influence the outcomes of tri-trophic interactions. Arbuscular mycorrhizal fungi (AMF) are symbiotic soil microbes that colonize the roots of plants and facilitate nutrient uptake. These microbes can alter plant chemistry and subsequent resistance to herbivores. Few studies, however, have shown how AMF affect tri-trophic interactions above- or belowground. This study examines how AMF colonization affects the emission of root volatiles when plants are under attack by western corn rootworm, a problematic pest of corn, and subsequent attraction of entomopathogenic nematodes, a natural enemy of western corn rootworm. Mycorrhizal fungi increased rootworm survival but decreased larval weight. Differences were detected across root volatile profiles, but there was not a clear link between volatile signaling and nematode behavior. Nematodes were more attracted to non-mycorrhizal plants without rootworms and AMF alone in soil, suggesting that AMF may interfere with cues that are used in combination with volatiles which nematodes use to locate prey.

Microbe-Friendly Plants Enable Beneficial Interactions with Soil Rhizosphere Bacteria by Lowering Their Defense Responses

The use of plant growth-promoting rhizobacteria presents a promising addition to conventional mineral fertilizer use and an alternative strategy for sustainable agricultural crop production. However, genotypic variations in the plant host may result in variability of the beneficial effects from these plant-microbe interactions. This study examined growth promotion effects of commercial vegetable crop cultivars of tomato, cucumber and broccoli following application with five rhizosphere bacteria. Biochemical assays revealed that the bacterial strains used possess several nutrient acquisition traits that benefit plants, including nitrogen fixation, phosphate solubilization, biofilm formation, and indole-3-acetic acid (IAA) production. However, different host cultivars displayed genotype-specific responses from the inoculations, resulting in significant (p < 0.05) plant growth promotion in some cultivars but insignificant (p > 0.05) or no growth promotion in others. Gene expression profiling in tomato cultivars revealed that these cultivar-specific phenotypes are reflected in differential expressions of defense and nutrient acquisition genes, suggesting that plants can be categorized into "microbe-friendly" cultivars (with little or no defense responses against beneficial microbes) and "microbe-hostile" cultivars (with strong defense responses). These results validate the notion that "microbe-friendly" (positive interaction with rhizosphere microbes) should be considered an important trait in breeding programs when developing new cultivars which could result in improved crop yields.

Selection and application of methanol-utilizing bacteria from tomato leaves for biocontrol of gray mold

Gray mold, caused by Botrytis cinerea, is a significant threat to tomato production. Traditional chemical control methods have become increasingly ineffective because of the development of resistance. This study aimed to isolate methanol-utilizing bacteria from tomato leaves and evaluate their biocontrol potential against gray mold. To obtain bacterial suspensions, tomato leaf samples were collected and washed. We analyzed the microbial communities of these samples using 16S rRNA amplicon sequencing and identified several methylotrophic strains. Among these, 405 isolated strains were cultivated on a solid low-nutrient inorganic salt medium containing methanol, and 7 strains exhibiting considerable antifungal activity against B. cinerea were identified. Greenhouse tests revealed that two strains-SY163 and SY183-significantly reduced the severity of gray mold on tomato leaves. Disease index scores and the area under the disease progress curve values confirmed the efficacy of these strains as biocontrol agents. Statistical analysis indicated the effectiveness of pre- and co-application of these strains with B. cinerea. Phylogenetic analysis identified Serratia rubidaea as the inhibitory strain. The biocontrol activity is likely mediated through the production of antifungal compounds and suppression of B. cinerea sporulation. This study provides the basis for developing a technology of gray mold suppression by controlling the abundance of S. rubidaea in plant microbial communities.

Gene expression signatures of mutualism and pathogenesis in flax roots

Introduction

Fusarium wilt, a devastating soil-borne fungal disease in flax (Linum usitatissimum), is caused by Fusarium oxysporum f. sp. lini, a hemibiotrophic plant pathogen that penetrates plant roots. There are several reports of the molecular response of L. usitatissimum to F. oxysporum f. sp. lini; however, comparisons of the effects of mutualistic and pathogenic fungi on plants are more limited.

Methods

In this study, we have integrated phenotyping and RNA-Seq approaches to examine the response of flax to F. oxysporum f.sp. lini and to a mutualistic arbuscular mycorrhizal fungus (AMF) Rhizoglomus irregulare. R. irregulare is a common soil fungus and also widely used as a commercial inoculant to improve plant growth. We measured flax growth parameters after plant inoculation with each or both fungi, in comparison with non-inoculated control. We performed transcriptome analysis of root tissues collected at 9 and 14 days post-inoculation.

Results

We identified several differentially expressed genes (DEGs) in response to pathogenic and mutualistic fungi. These included genes related to ethylene and salicylic acid biosynthesis, carbohydrate binding, oxidoreductases, and sugar transmembrane transporters. Genes related to calcium signaling, nutrient transport, lipid metabolism, cell wall, and polysaccharide-modifying were up-regulated by R. irregulare; however, the same genes were down-regulated by F. oxysporum f. sp. lini when treated independently. In the combined treatment, genes related to cell wall modifications, hormone regulation and nutrient uptake were up-regulated. These results suggest that inoculation with R. irregulare reduced gene expression related to F. oxysporum f. sp. lini infection, leading to a reduced response to the pathogen. In response to AMF, flax prioritized mutualism-related gene expression over defense, reversing the growth inhibition caused by F. oxysporum f. sp.lini in the combined treatment.

Discussion

This research provides insights into the protective effects of AMF, revealing the pre-symbiotic gene expression profile of flax in response to mutualism in comparison with pathogenicity. Potential target genes for crop improvement were identified, especially defense related genes.

RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions

BACKGROUND

Small RNA (sRNAs)- mediated RNA silencing is emerging as a key player in host-microbe interactions. However, its role in fungus-plant interactions relevant to biocontrol of plant diseases is yet to be explored. This study aimed to investigate Dicer (DCL)-mediated endogenous and cross-kingdom gene expression regulation in the biocontrol fungus Clonostachys rosea and wheat roots during interactions.

RESULTS

C. rosea Δdcl2 strain exhibited significantly higher root colonization than the WT, whereas no significant differences were observed for Δdcl1 strains. Dual RNA-seq revealed the upregulation of CAZymes, membrane transporters, and effector coding genes in C. rosea, whereas wheat roots responded with the upregulation of stress-related genes and the downregulation of growth-related genes. The expression of many of these genes was downregulated in wheat during the interaction with DCL deletion strains, underscoring the influence of fungal DCL genes on wheat defense response. sRNA sequencing identified 18 wheat miRNAs responsive to C. rosea, and three were predicted to target the C. rosea polyketide synthase gene pks29. Two of these miRNAs (mir_17532_x1 and mir_12061_x13) were observed to enter C. rosea from wheat roots with fluorescence analyses and to downregulate the expression of pks29, showing plausible cross-kingdom RNA silencing of the C. rosea gene by wheat miRNAs.

CONCLUSIONS

We provide insights into the mechanisms underlying the interaction between biocontrol fungi and plant roots. Moreover, the study sheds light on the role of sRNA-mediated gene expression regulation in C. rosea-wheat interactions and provides preliminary evidence of cross-kingdom RNA silencing between plants and biocontrol fungi.

The Structural and Functional Responses of Rhizosphere Bacteria to Biodegradable Microplastics in the Presence of Biofertilizers

Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach.

Transcriptome analysis unravels the biocontrol mechanism of Serratia plymuthica A30 against potato soft rot caused by Dickeya solani

Endophytic bacterium Serratia plymuthica A30 was identified as a superior biocontrol agent due to its effective colonization of potato tuber, tolerance to cold conditions, and strong inhibitory action against various soft rot pathogens, including Dickeya solani. We characterized transcriptome changes in potato tubers inoculated with S. plymuthica A30, D. solani, or both at the early and the late phases of interaction. At the early phase and in the absence of the pathogen, A30 influenced the microbial recognition system to initiate plant priming. In the presence of the pathogen alongside biocontrol strain, defense signaling was highly stimulated, characterized by the induction of genes involved in the detoxification system, reinforcement of cell wall structure, and production of antimicrobial metabolites, highlighting A30's role in enhancing the host resistance against pathogen attack. This A30-induced resistance relied on the early activation of jasmonic acid signaling and its production in tubers, while defense signaling mediated by salicylic acid was suppressed. In the late phase, A30 actively interferes with plant immunity by inhibiting stress- and defense-related genes expression. Simultaneously, the genes involved in cell wall remodeling and indole-3-acetic acid signaling were activated, thereby enhancing cell wall remodeling to establish symbiotic relationship with the host. The endophytic colonization of A30 coincided with the induction of genes involved in the biosynthesis and signaling of ethylene and abscisic acid, while downregulating those related to gibberellic acid and cytokinin. This combination suggested fitness benefits for potato tubers by preserving dormancy, and delaying sprouting, which affects durability of tubers during storage. This study contributes valuable insights into the tripartite interaction among S. plymuthica A30, D. solani, and potato tubers, facilitating the development of biocontrol system for soft rot pathogens under storage conditions.

Enhancing Resistance to Cercospora Leaf Spot in Mung Bean (Vigna radiata L.) through Bradyrhizobium sp. DOA9 Priming: Molecular Insights and Bio-Priming Potential

Mung bean (Vigna radiata L.), a vital legume in Asia with significant nutritional benefits, is highly susceptible to Cercospora leaf spot (CLS) caused by Cercospora canescens, leading to significant yield losses. As an alternative to chemical fungicides, bio-priming with rhizobacteria can enhance plant resistance. This study explores the potential of Bradyrhizobium sp. strain DOA9 to augment resistance in mung bean against CLS via root priming. The results reveal that short (3 days) and double (17 and 3 days) priming with DOA9 before fungal infection considerably reduces lesion size on infected leaves by activating defense-related genes, including Pti1, Pti6, EDS1, NDR1, PR-1, PR-2, Prx, and CHS, or by suppressing the inhibition of PR-5 and enhancing peroxidase (POD) activity in leaves. Interestingly, the Type 3 secretion system (T3SS) of DOA9 may play a role in establishing resistance in V. radiata CN72. These findings suggest that DOA9 primes V. radiata CN72's defense mechanisms, offering an effective bio-priming strategy to alleviate CLS. Hence, our insights propose the potential use of DOA9 as a bio-priming agent to manage CLS in V. radiata CN72, providing a sustainable alternative to chemical fungicide applications.

From trade-off to synergy: microbial insights into enhancing plant growth and immunity

The reduction in crop yield caused by pathogens and pests presents a significant challenge to global food security. Genetic engineering, which aims to bolster plant defence mechanisms, emerges as a cost-effective solution for disease control. However, this approach often incurs a growth penalty, known as the growth-defence trade-off. The precise molecular mechanisms governing this phenomenon are still not completely understood, but they generally fall under two main hypotheses: a "passive" redistribution of metabolic resources, or an "active" regulatory choice to optimize plant fitness. Despite the knowledge gaps, considerable practical endeavours are in the process of disentangling growth from defence. The plant microbiome, encompassing both above- and below-ground components, plays a pivotal role in fostering plant growth and resilience to stresses. There is increasing evidence which indicates that plants maintain intimate associations with diverse, specifically selected microbial communities. Meta-analyses have unveiled well-coordinated, two-way communications between plant shoots and roots, showcasing the capacity of plants to actively manage their microbiota for balancing growth with immunity, especially in response to pathogen incursions. This review centers on successes in making use of specific root-associated microbes to mitigate the growth-defence trade-off, emphasizing pivotal advancements in unravelling the mechanisms behind plant growth and defence. These findings illuminate promising avenues for future research and practical applications.

Symphony of survival: Insights into cross-talk mechanisms in plants, bacteria, and fungi for strengthening plant immune responses

Plants coexist with a diverse array of microorganisms, predominantly bacteria and fungi, in both natural and agricultural environments. While some microorganisms positively influence plant development and yield, others can cause harm to the host, leading to significant adverse impacts on the environment and the economy. Plant growth-promoting microorganisms (PGPM), including plant growth-promoting bacteria, arbuscular mycorrhizal fungus (AMF), and rhizobia, have been found to increase plant biomass production by synthesizing hormones, fixing nitrogen, and solubilizing phosphate and potassium. Numerous studies have contributed to unraveling the complex process of plant-microbe interactions in recent decades. In light of the increasing global challenges such as population growth, climate change, and resource scarcity, it has become imperative to explore the potential of plant-bacteria-fungi crosstalk in promoting sustainability. This review aims to bridge existing knowledge gaps, providing a roadmap for future research in this dynamic field by synthesizing current knowledge and identifying emerging trends.

Molecular Insights into the Defense of Dioscorea opposita Cultivar Tiegun Callus Against Pathogenic and Endophytic Fungal Infection Through Transcriptome Analysis

Dioscorea opposita cultivar Tiegun is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of Tiegun were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, whereas P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase, peroxidase, and catalase; thus, the degree of damage to the callus caused by P. halotolerans was weaker than that caused by A. alternata. RNA sequencing analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the mitogen-activated protein kinase signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism, and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.

Plant growth-promoting rhizobacteria modulate induced corn defense against Spodoptera litura (Lepidoptera: Noctuidae)

Common cutworm, Spodoptera litura is an important pest of corn causing significant crop yield loss. Synthetic insecticides have mostly been used to combat this pest, raising human and environmental health concerns. Plant growth-promoting rhizobacteria (PGPR) could compensate for or augment the harmful effects of agrochemicals. Herein, we aimed to assess whether PGPR-induced defenses in corn plants impact the host-plant selection behavior of S. litura. Headspace volatile organic compounds were analyzed using gas chromatography-mass spectrometry. Larvae fed inoculated corn exhibited lower weights and relative growth rate than noninoculated plants. Under choice experiments, PGPR-treated plants significantly reduced percentage leaf damage area and oviposition rate compared to untreated plants. Volatile organic compound ratio emission varied significantly between control and PGPR treatments, which, in part, explains feeding and oviposition deterrence in PGPR-treated plants. The results demonstrate that PGPR inoculation can enhance corn resistance to S. litura, making it a promising candidate for crop protection strategies.

Effects of wheat intercropping on growth and occurrence of Fusarium wilt in watermelon

Watermelon is commonly affected by Fusarium wilt in a monoculture cropping system. Wheat intercropping alleviates the affection of Fusarium wilt of watermelon. The objective of this study was to determine the effects of wheat and watermelon intercropping on watermelon growth and Fusarium wilt. Our results showed that wheat and watermelon intercropping promoted growth, increased chlorophyll content, and photosynthesis of watermelon. Meanwhile, wheat and watermelon intercropping inhibited watermelon Fusarium wilt occurrence, decreased spore numbers, increased root vigor, increased antioxidant enzyme activities, and decreased malondialdehyde (MDA) content in watermelon roots. Additionally, wheat and watermelon intercropping enhanced the bacterial colonies and total microbes growth in soil, decreased fungi and Fusarium oxysporum f. sp. niveum (FON) colonies, and increased soil enzyme activities in watermelon rhizosphere soil. Our results indicated that wheat and watermelon intercropping enhanced watermelon growth and decreased the incidence of Fusarium wilt in watermelon. These effects could be due to intercropping inducing physiological changes, regulating soil enzyme activities, and/or modulating soil microbial communities.

Arbuscular Mycorrhizal Fungi as Biostimulant and Biocontrol Agents: A Review

Arbuscular mycorrhizal fungi (AMF) are soil microorganisms living in symbiosis with most terrestrial plants. They are known to improve plant tolerance to numerous abiotic and biotic stresses through the systemic induction of resistance mechanisms. With the aim of developing more sustainable agriculture, reducing the use of chemical inputs is becoming a major concern. After providing an overview on AMF history, phylogeny, development cycle and symbiosis benefits, the current review aims to explore the potential of AMF as biostimulants and/or biocontrol agents. Nowadays, AMF inoculums are already increasingly used as biostimulants, improving mineral nutrient plant acquisition. However, their role as a promising tool in the biocontrol market, as an alternative to chemical phytosanitary products, is underexplored and underdiscussed. Thus, in the current review, we will address the mechanisms of mycorrhized plant resistance to biotic stresses induced by AMF, and highlight the various factors in favor of inoculum application, but also the challenges that remain to be overcome.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Root endophyte-mediated alteration in plant H2O2 homeostasis regulates symbiosis outcome and reshapes the rhizosphere microbiota

Endophytic symbioses between plants and fungi are a dominant feature of many terrestrial ecosystems, yet little is known about the signaling that defines these symbiotic associations. Hydrogen peroxide (H2O2) is recognized as a key signal mediating the plant adaptive response to both biotic and abiotic stresses. However, the role of H2O2 in plant-fungal symbiosis remains elusive. Using a combination of physiological analysis, plant and fungal deletion mutants, and comparative transcriptomics, we reported that various environmental conditions differentially affect the interaction between Arabidopsis and the root endophyte Phomopsis liquidambaris, and link this process to alterations in H2O2 levels and H2O2 fluxes across root tips. We found that enhanced H2O2 efflux leading to a moderate increase in H2O2 levels at the plant-fungal interface is required for maintaining plant-fungal symbiosis. Disturbance of plant H2O2 homeostasis compromises the symbiotic ability of plant roots. Moreover, the fungus-regulated H2O2 dynamics modulate the rhizosphere microbiome by selectively enriching for the phylum Cyanobacteria, with strong antioxidant defenses. Our results demonstrated that the regulation of H2O2 dynamics at the plant-fungal interface affects the symbiotic outcome in response to external conditions and highlight the importance of the root endophyte in reshaping the rhizosphere microbiota.

Evaluation of Tunisian wheat endophytes as plant growth promoting bacteria and biological control agents against Fusarium culmorum

Plant growth-promoting rhizobacteria (PGPR) applications have emerged as an ideal substitute for synthetic chemicals by their ability to improve plant nutrition and resistance against pathogens. In this study, we isolated fourteen root endophytes from healthy wheat roots cultivated in Tunisia. The isolates were identified based from their 16S rRNA gene sequences. They belonged to Bacillota and Pseudomonadota taxa. Fourteen strains were tested for their growth-promoting and defense-eliciting potentials on durum wheat under greenhouse conditions, and for their in vitro biocontrol power against Fusarium culmorum, an ascomycete responsible for seedling blight, foot and root rot, and head blight diseases of wheat. We found that all the strains improved shoot and/or root biomass accumulation, with Bacillus mojavensis, Paenibacillus peoriae and Variovorax paradoxus showing the strongest promoting effects. These physiological effects were correlated with the plant growth-promoting traits of the bacterial endophytes, which produced indole-related compounds, ammonia, and hydrogen cyanide (HCN), and solubilized phosphate and zinc. Likewise, plant defense accumulations were modulated lastingly and systematically in roots and leaves by all the strains. Testing in vitro antagonism against F. culmorum revealed an inhibition activity exceeding 40% for five strains: Bacillus cereus, Paenibacillus peoriae, Paenibacillus polymyxa, Pantoae agglomerans, and Pseudomonas aeruginosa. These strains exhibited significant inhibitory effects on F. culmorum mycelia growth, sporulation, and/or macroconidia germination. P. peoriae performed best, with total inhibition of sporulation and macroconidia germination. These finding highlight the effectiveness of root bacterial endophytes in promoting plant growth and resistance, and in controlling phytopathogens such as F. culmorum. This is the first report identifying 14 bacterial candidates as potential agents for the control of F. culmorum, of which Paenibacillus peoriae and/or its intracellular metabolites have potential for development as biopesticides.

Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions

Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.

Amphibian skin bacteria display antifungal activity and induce plant defense mechanisms against Botrytis cinerea

Botrytis cinerea is the causal agent of gray mold, which affects a wide variety of plant species. Chemical agents have been used to prevent the disease caused by this pathogenic fungus. However, their toxicity and reduced efficacy have encouraged the development of new biological control alternatives. Recent studies have shown that bacteria isolated from amphibian skin display antifungal activity against plant pathogens. However, the mechanisms by which these bacteria act to reduce the effects of B. cinerea are still unclear. From a diverse collection of amphibian skin bacteria, three proved effective in inhibiting the development of B. cinerea under in vitro conditions. Additionally, the individual application of each bacterium on the model plant Arabidopsis thaliana, Solanum lycopersicum and post-harvest blueberries significantly reduced the disease caused by B. cinerea. To understand the effect of bacteria on the host plant, we analyzed the transcriptomic profile of A. thaliana in the presence of the bacterium C32I and the fungus B. cinerea, revealing transcriptional regulation of defense-related hormonal pathways. Our study shows that bacteria from the amphibian skin can counteract the activity of B. cinerea by regulating the plant transcriptional responses.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Emerging Roles of Epigenetics in Grapevine and Winegrowing

Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype-environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.

Antivirulence effects of cell-free culture supernatant of endophytic bacteria against grapevine crown gall agent, Agrobacterium tumefaciens, and induction of defense responses in plantlets via intact bacterial cells

BACKGROUND

Crown gall disease caused by Agrobacterium tumefaciens is a very destructive affliction that affects grapevines. Endophytic bacteria have been discovered to control plant diseases via the use of several mechanisms. This research examined the potential for controlling crown gall by three endophytic bacteria that were previously isolated from healthy cultivated and wild grapevines including Pseudomonas kilonensis Ba35, Pseudomonas chlororaphis Ba47, and Serratia liquefaciens Ou55.

RESULT

At various degrees, three endophytic bacteria suppressed the populations of A. tumefaciens Gh1 and greatly decreased the symptoms of crown gall. Furthermore, biofilm production and motility behaviors of A. tumefaciens Gh1were greatly inhibited by the Cell-free Culture Supernatant (CFCS) of endophytic bacteria. According to our findings, CFCS may reduce the adhesion of A. tumefaciens Gh1 cells to grapevine cv. Rashe root tissues as well as their chemotaxis motility toward the extract of the roots. When compared to the untreated control, statistical analysis showed that CFCS significantly reduced the swimming, twitching, and swarming motility of A. tumefaciens Gh1. The findings demonstrated that the endophytic bacteria effectively stimulated the production of plant defensive enzymes including superoxide dismutase (SOD), polyphenol oxidase (PPO), peroxidase (POD), phenylalanine ammonia lyase (PAL), and total soluble phenols at different time intervals in grapevine inoculated with A. tumefaciens Gh1. The Ba47 strain markedly increased the expression levels of defense genes associated with plant resistance. The up-regulation of PR1, PR2, VvACO1, and GAD1 genes in grapevine leaves indicates the activation of SA and JA pathways, which play a role in enhancing resistance to pathogen invasion. The results showed that treating grapevine with Ba47 increased antioxidant defense activities and defense-related gene expression, which reduced oxidative damage caused by A. tumefaciens and decreased the incidence of crown gall disease.

CONCLUSION

This is the first study on how A. tumefaciens, the grapevine crown gall agent, is affected by CFCS generated by endophytic bacteria in terms of growth and virulence features. To create safer plant disease management techniques, knowledge of the biocontrol processes mediated by CFCS during microbial interactions is crucial.

Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture

In the rhizosphere, the activities within all processes and functions are primarily influenced by plant roots, microorganisms present in the rhizosphere, and the interactions between roots and microorganisms. The rhizosphere, a dynamic zone surrounding the roots, provides an ideal environment for a diverse microbial community, which significantly shapes plant growth and development. Microbial activity in the rhizosphere can promote plant growth by increasing nutrient availability, influencing plant hormonal signaling, and repelling or outcompeting pathogenic microbial strains. Understanding the associations between plant roots and soil microorganisms has the potential to revolutionize crop yields, improve productivity, minimize reliance on chemical fertilizers, and promote sustainable plant growth technologies. The rhizosphere microbiome could play a vital role in the next green revolution and contribute to sustainable and eco-friendly agriculture. However, there are still knowledge gaps concerning plant root-environment interactions, particularly regarding roots and microorganisms. Advances in metabolomics have helped to understand the chemical communication between plants and soil biota, yet challenges persist. This article provides an overview of the latest advancements in comprehending the communication and interplay between plant roots and microbes, which have been shown to impact crucial factors such as plant growth, gene expression, nutrient absorption, pest and disease resistance, and the alleviation of abiotic stress. By improving these aspects, sustainable agriculture practices can be implemented to increase the overall productivity of plant ecosystems.

Plant growth-promoting rhizobacterium Bacillus cereus AR156 induced systemic resistance against multiple pathogens by priming of camalexin synthesis

Phytoalexins play a crucial role in plant immunity. However, the mechanism of how phytoalexin is primed by beneficial microorganisms against broad-spectrum pathogens remains elusive. This study showed that Bacillus cereus AR156 could trigger ISR against broad-spectrum disease. RNA-sequencing and camalexin content assays showed that AR156-triggered ISR can prime the accumulation of camalexin synthesis and secretion-related genes. Moreover, it was found that AR156-triggered ISR elevates camalexin accumulation by increasing the expression of camalexin synthesis genes upon pathogen infection. We observed that the priming of camalexin accumulation by AR156 was abolished in cyp71a13 and pad3 mutants. Further investigations reveal that in the wrky33 mutant, the ability of AR156 to prime camalexin accumulation is abolished, and the mediated ISR against the three pathogens is significantly compromised. Furthermore, PEN3 and PDR12, acting as camalexin transporters, participate in AR156-induced ISR against broad-spectrum pathogens differently. In addition, salicylic acid and JA/ET signalling pathways participate in AR156-primed camalexin synthesis to resist pathogens in different forms depending on the pathogen. In summary, B. cereus AR156 triggers ISR against Botrytis cinerea, Pst DC3000 and Phytophthora capsici by priming camalexin synthesis. Our study provides deeper insights into the significant role of camalexin for AR156-induced ISR against broad-spectrum pathogens.

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

Erwinia amylovora Type III Secretion System Inhibitors Reduce Fire Blight Infection Under Field Conditions

Fire blight, caused by Erwinia amylovora, is an economically important disease in apples and pears worldwide. This pathogen relies on the type III secretion system (T3SS) to cause disease. Compounds that inhibit the function of the T3SS (T3SS inhibitors) have emerged as alternative strategies for bacterial plant disease management, as they block bacterial virulence without affecting growth, unlike traditional antibiotics. In this study, we investigated the mode of action of a T3SS inhibitor named TS108, a plant phenolic acid derivative, in E. amylovora. We showed that adding TS108 to an in vitro culture of E. amylovora repressed the expression of several T3SS regulon genes, including the master regulator gene hrpL. Further studies demonstrated that TS108 negatively regulates CsrB, a global regulatory small RNA, at the posttranscriptional level, resulting in a repression of hrpS, which encodes a key activator of hrpL. Additionally, TS108 has no impact on the expression of T3SS in Dickeya dadantii or Pseudomonas aeruginosa, suggesting that its inhibition of the E. amylovora T3SS is likely species specific. To better evaluate the performance of T3SS inhibitors in fire blight management, we conducted five independent field experiments in four states (Michigan, New York, Oregon, and Connecticut) from 2015 to 2022 and observed reductions in blossom blight incidence as high as 96.7% compared with untreated trees. In summary, the T3SS inhibitors exhibited good efficacy against fire blight.

The Complex Interplay between Arbuscular Mycorrhizal Fungi and Strigolactone: Mechanisms, Sinergies, Applications and Future Directions

Plants, the cornerstone of life on Earth, are constantly struggling with a number of challenges arising from both biotic and abiotic stressors. To overcome these adverse factors, plants have evolved complex defense mechanisms involving both a number of cell signaling pathways and a complex network of interactions with microorganisms. Among these interactions, the relationship between symbiotic arbuscular mycorrhizal fungi (AMF) and strigolactones (SLs) stands as an important interplay that has a significant impact on increased resistance to environmental stresses and improved nutrient uptake and the subsequent enhanced plant growth. AMF establishes mutualistic partnerships with plants by colonizing root systems, and offers a range of benefits, such as increased nutrient absorption, improved water uptake and increased resistance to both biotic and abiotic stresses. SLs play a fundamental role in shaping root architecture, promoting the growth of lateral roots and regulating plant defense responses. AMF can promote the production and release of SLs by plants, which in turn promote symbiotic interactions due to their role as signaling molecules with the ability to attract beneficial microbes. The complete knowledge of this synergy has the potential to develop applications to optimize agricultural practices, improve nutrient use efficiency and ultimately increase crop yields. This review explores the roles played by AMF and SLs in plant development and stress tolerance, highlighting their individual contributions and the synergistic nature of their interaction.

Characterization of endophytic bacteria isolated from root nodules of lentil in intercropping with durum wheat

Legumes improve soil fertility by interacting symbiotically with nitrogen-fixing rhizobia allocated in root nodules. Some bacterial endophytes can coexist with rhizobia in nodules and might help legumes by enhancing stress tolerance, producing hormones stimulating plant growth, and increasing plant nutrient intake. Twenty-six bacterial endophytes from Lens culinaris root nodules cultivated in intercropping with Triticum durum were identified and characterized molecularly and biochemically. Potential plant growth-promoting strains have been selected according to the indole acetic acid and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, and for their inorganic phosphate solubilization ability. The presence of genes associated to ACC deaminase and nitrogenase was evaluated. Six selected strains were grown with varying NaCl and polyethylene glycol concentrations to test their salt and osmotic stress tolerance. Priestia megaterium 11NL3 and Priestia aryabhattai 19NL1, resulted to be tolerant to salinity and osmotic stress, were tested on four genotypes of T. durum seeds in different stress conditions. The effect of strain inoculation on seed germination, vigor, and root-to-shoot ratio varied depending on the type of stress and on the durum wheat genotypes. For future research, it will be necessary to test the selected bacterial strains at different plant phenological stages and to clarify the mechanisms involved in the different outcomes of plant-microbe interactions.

Dual RNA-Seq Analysis Pinpoints a Balanced Regulation between Symbiosis and Immunity in Medicago truncatula-Sinorhizobium meliloti Symbiotic Nodules

Legume-rhizobial symbiosis initiates the formation of root nodules, within which rhizobia reside and differentiate into bacteroids to convert nitrogen into ammonium, facilitating plant growth. This process raises a fundamental question: how is plant immunity modulated within nodules when exposed to a substantial number of foreign bacteria? In Medicago truncatula, a mutation in the NAD1 (Nodules with Activated Defense 1) gene exclusively results in the formation of necrotic nodules combined with activated immunity, underscoring the critical role of NAD1 in suppressing immunity within nodules. In this study, we employed a dual RNA-seq transcriptomic technology to comprehensively analyze gene expression from both hosts and symbionts in the nad1-1 mutant nodules at different developmental stages (6 dpi and 10 dpi). We identified 89 differentially expressed genes (DEGs) related to symbiotic nitrogen fixation and 89 DEGs from M. truncatula associated with immunity in the nad1-1 nodules. Concurrently, we identified 27 rhizobial DEGs in the fix and nif genes of Sinorhizobium meliloti. Furthermore, we identified 56 DEGs from S. meliloti that are related to stress responses to ROS and NO. Our analyses of nitrogen fixation-defective plant nad1-1 mutants with overactivated defenses suggest that the host employs plant immunity to regulate the substantial bacterial colonization in nodules. These findings shed light on the role of NAD1 in inhibiting the plant's immune response to maintain numerous rhizobial endosymbiosis in nodules.

Counter-attack of biocontrol agents: Environmentally benign Approaches against Root-knot nematodes (Meloidogyne spp.) on Agricultural crops

Root-knot nematodes (Meloidogyne spp.) are obligate sedentary endoparasites, considered severe crop-damaging taxa among all plant-parasitic nematodes globally. Their attacks through parasitic proteins alter the physiology and machinery of the host cells to favour parasitism and reduction in crop yield. Currently, the use of excessive pesticides as a fast remedy to manage this pest is hazardous for both the environment and humans. Keeping this view in mind, there is an urgent need for developing efficient eco-friendly strategies. Bio-control as an eco-friendly is considered the best approach to manage nematodes without disturbing non-target microbes. In bio-control, living agents such as fungi and bacteria are the natural enemies of nematodes and the best substitute for pesticides. Fungi, including nematode-trapping fungi, can sense host signals and produce special trapping devices viz., constricting rings and adhesive knobs/loops, to capture nematodes and kill them. Whereas, endo-parasitic fungi kill nematodes by enzymatic secretions and spore adhesion through their hyphae. Bacteria can also control nematodes by producing antibiotic compounds, competing for nutrients and rhizosphere, production of hydrolytic enzymes viz., chitinases, proteases, lipases, and induction of systemic resistance (ISR) in host plants. Scientists throughout the world are trying to evolve environmentally benign methods that sustain agricultural production and keep nematodes below a threshold level. Whatever methods evolve, in the future the focus should be on important aspects like green approaches for managing nematodes without disturbing human health and the environment.

Fossil-fuel-dependent scenarios could lead to a significant decline of global plant-beneficial bacteria abundance in soils by 2100

Exploiting the potential benefits of plant-associated microbes represents a sustainable approach to enhancing crop productivity. Plant-beneficial bacteria (PBB) provide multiple benefits to plants. However, the biogeography and community structure remain largely unknown. Here we constructed a PBB database to couple microbial taxonomy with their plant-beneficial traits and analysed the global atlas of potential PBB from 4,245 soil samples. We show that the diversity of PBB peaks in low-latitude regions, following a strong latitudinal diversity gradient. The distribution of potential PBB was primarily governed by environmental filtering, which was mainly determined by local climate. Our projections showed that fossil-fuel-dependent future scenarios would lead to a significant decline of potential PBB by 2100, especially biocontrol agents (-1.03%) and stress resistance bacteria (-0.61%), which may potentially threaten global food production and (agro)ecosystem services.

Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato

Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant-fungus relationship. In the early stages of colonization (5-7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12-19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.

A Symbiotic Fungus Sistotrema Benefits Blueberry Rejuvenation and Abiotic Stress Tolerance

Blueberry (Vaccinium spp.) rhizosphere microorganisms can significantly increase the absorption area and improve the efficiency of rhizospheric nutrient uptake. However, there has been little research on blueberry rhizosphere microorganisms, especially those that can complement root function deficiency. In this study, we analyzed the rhizosphere fungi of 'O'Neal,' 'Sharpblue,' and 'Premier' blueberry cultivars and found that 'Premier' blueberries showed strong growth potential and relatively high root regulation ability. The dominant symbiotic fungus Sistotrema was correlated with the strong growth of 'Premier' and was directionally screened and isolated based on conserved gene structures and COG function analysis. This fungus was reinoculated onto the roots of 'Gulfcoast' and 'Star' blueberry cultivars. Sistotrema promoted the growth of blueberries and improved their ability to resist stress and grow under adverse conditions, as indicated by maintained or increased chlorophyll content under such conditions. Further analyses showed that Sistotrema has certain functional characteristics such as the ability to dissolve iron in its insoluble form and then release it, to fix nitrogen, and to inhibit nitrification in soil. Thus, it effectively doubled the soil nitrogen content and increased the soluble iron content in soil by 50%. This investigation indicates sistotrema inoculation as an approach to increase blueberry stress tolerance and complete their root nutrition deficiency.

Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion

Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.

Temporal and spatial changes in rhizosphere bacterial diversity of mountain Rhododendron mucronulatum

To better conserve the ecology of the wild Rhododendron mucronulatum range, we studied the rhizosphere microenvironment of R. mucronulatum in Beijing's Yunmeng Mountain National Forest Park. R. mucronulatum rhizosphere soil physicochemical properties and enzyme activities changed significantly with temporal and elevational gradients. The correlations between soil water content (SWC), electrical conductivity (EC), organic matter content (OM), total nitrogen content (TN), catalase activity (CAT), sucrose-converting enzyme activity (INV), and urease activity (URE) were significant and positive in the flowering and deciduous periods. The alpha diversity of the rhizosphere bacterial community was significantly higher in the flowering period than in the deciduous period, and the effect of elevation was insignificant. The diversity of the R. mucronulatum rhizosphere bacterial community changed significantly with the change in the growing period. A network analysis of the correlations revealed stronger linkages between the rhizosphere bacterial communities in the deciduous period than in the flowering period. Rhizomicrobium was the dominant genus in both periods, but its relative abundance decreased in the deciduous period. Changes in the relative abundance of Rhizomicrobium may be the main factor influencing the changes in the R. mucronulatum rhizosphere bacterial community. Moreover, the R. mucronulatum rhizosphere bacterial community and soil characteristics were significantly correlated. Additionally, the influence of soil physicochemical properties on the rhizosphere bacterial community was larger than that of enzyme activity on the bacterial community. We mainly analyzed the change patterns in the rhizosphere soil properties and rhizosphere bacterial diversity of R. mucronulatum during temporal and spatial variation, laying the foundation for further understanding of the ecology of wild R. mucronulatum.

The Rice Endophyte-Derived α-Mannosidase ShAM1 Degrades Host Cell Walls To Activate DAMP-Triggered Immunity against Disease

Endophytes play an important role in shaping plant growth and immunity. However, the mechanisms for endophyte-induced disease resistance in host plants remain unclear. Here, we screened and isolated the immunity inducer ShAM1 from the endophyte Streptomyces hygroscopicus OsiSh-2, which strongly antagonizes the pathogen Magnaporthe oryzae. Recombinant ShAM1 can trigger rice immune responses and induce hypersensitive responses in various plant species. After infection with M. oryzae, blast resistance was dramatically improved in ShAM1-inoculated rice. In addition, the enhanced disease resistance by ShAM1 was found to occur through a priming strategy and was mainly regulated through the jasmonic acid-ethylene (JA/ET)-dependent signaling pathway. ShAM1 was identified as a novel α-mannosidase, and its induction of immunity is dependent on its enzyme activity. When we incubated ShAM1 with isolated rice cell walls, the release of oligosaccharides was observed. Notably, extracts from the ShAM1-digested cell wall can enhance the disease resistance of the host rice. These results indicated that ShAM1 triggered immune defense against pathogens by damage-associated molecular pattern (DAMP)-related mechanisms. Our work provides a representative example of endophyte-mediated modulation of disease resistance in host plants. The effects of ShAM1 indicate the promise of using active components from endophytes as plant defense elicitors for the management of plant disease. IMPORTANCE The specific biological niche inside host plants allows endophytes to regulate plant disease resistance effectively. However, there have been few reports on the role of active metabolites from endophytes in inducing host disease resistance. In this study, we demonstrated that an identified α-mannosidase protein, ShAM1, secreted by the endophyte S. hygroscopicus OsiSh-2 could activate typical plant immunity responses and induce a timely and cost-efficient priming defense against the pathogen M. oryzae in rice. Importantly, we revealed that ShAM1 enhanced plant disease resistance through its hydrolytic enzyme (HE) activity to digest the rice cell wall and release damage-associated molecular patterns. Taken together, these findings provide an example of the interaction mode of endophyte-plant symbionts and suggest that HEs derived from endophytes can be used as environmentally friendly and safe prevention agent for plant disease control.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Plant-Fungi Interactions: Where It Goes?

Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.

New insights into the occurrence of continuous cropping obstacles in pea (Pisum sativum L.) from soil bacterial communities, root metabolism and gene transcription

BACKGROUND

Continuous cropping is a significant obstacle to sustainable development in the pea (Pisum sativum L.) industry, but the underlying mechanisms of this remain unclear. In this study, we used 16 S rDNA sequencing, transcriptomics, and metabolomics to analyze the response mechanism of roots and soil bacteria to continuous cropping and the relationship between soil bacteria and root phenotypes of different pea genotypes (Ding wan 10 and Yun wan 8).

RESULTS

Continuous cropping inhibited pea growth, with a greater effect on Ding wan 10 than Yun wan 8. Metabolomics showed that the number of differentially accumulated metabolites (DAMs) in pea roots increased with the number of continuous cropping, and more metabolic pathways were involved. Transcriptomics revealed that the number of differentially expressed genes (DEGs) increased with the number of continuous cropping. Continuous cropping altered the expression of genes involved in plant-pathogen interaction, MAPK signal transduction, and lignin synthesis pathways in pea roots, with more DEGs in Ding wan 10 than in Yun wan 8. The up-regulated expression of genes in the ethylene signal transduction pathway was evident in Ding wan 10. Soil bacterial diversity did not change, but the relative abundance of bacteria significantly responded to continuous cropping. Integrative analysis showed that the bacteria with significant relative abundance in the soil were strongly associated with the antioxidant synthesis and linoleic acid metabolism pathway of pea roots under continuous cropping once. Under continuous cropping twice, the bacteria with significant relative abundance changes were strongly associated with cysteine and methionine metabolism, fatty acid metabolism, phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, linoleic acid, and amino sugar and nucleotide sugar metabolism.

CONCLUSION

Ding wan 10 was more sensitive to continuous cropping than Yun wan 8. Continuous cropping times and pea genotypes determined the differences in root metabolic pathways. There were common metabolic pathways in the two pea genotypes in response to continuous cropping, and the DEGs and DAMs in these metabolic pathways were strongly associated with the bacteria with significant changes in relative abundance in the soil. This study provides new insights into obstacles to continuous cropping in peas.