Bacillus amyloliquefaciens FZB42 represses plant miR846 to induce systemic resistance via a jasmonic acid-dependent signalling pathway

Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle?

Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.

Bacillus velezensis WB induces systemic resistance in watermelon against Fusarium wilt

BACKGROUND

Our previous findings indicated that Bacillus velezensis WB could control Fusarium wilt by changing the structure of the microbial community in the watermelon rhizosphere. However, there are few studies on its mechanism in the pathogen resistance of watermelon. Therefore, in this study, we determined the mechanism of B. velezensis WB-induced systemic resistance in watermelon against Fusarium wilt through glasshouse pot experiments.

RESULTS

The results showed that B. velezensis WB significantly reduced the incidence and disease index of Fusarium wilt in watermelon. B. velezensis WB can enhance the basal immunity of watermelon plants by: increasing the activity of phenylalanine ammonia-lyase (PAL), peroxidase (POD), superoxide dismutase (SOD) and β-1,3-glucanase; accumulating lignin, salicylic acid (SA) and jasmonic acid (JA); reducing malondialdehyde (MDA) concentrations; and inducing callus deposition in watermelon plant cells. RNA-seq analysis showed that 846 watermelon genes were upregulated and 612 watermelon genes were downregulated in the WF treatment. This process led to the activation of watermelon genes associated with auxin, gibberellin, SA, ethylene and JA, and the expression of genes in the phenylalanine biosynthetic pathway was upregulated. In addition, transcription factors involved in plant resistance to pathogens, such as MYB, NAC and WRKY, were induced. Gene correlation analysis showed that Cla97C10G195840 and Cla97C02G049930 in the phenylalanine biosynthetic pathway, and Cla97C02G041360 and Cla97C10G197290 in the plant hormone signal transduction pathway showed strong correlations with other genes.

CONCLUSION

Our results indicated that B. velezensis WB is capable of inducing systemic resistance in watermelon against Fusarium wilt. © 2023 Society of Chemical Industry.

A scientific version of understanding "Why did the chickens cross the road"? - A guided journey through Bacillus spp. towards sustainable agriculture, circular economy and biofortification

The world, a famished planet with an overgrowing population, requires enormous food crops. This scenario compelled the farmers to use a high quantity of synthetic fertilizers for high food crop productivity. However, prolonged usage of chemical fertilizers results in severe adverse effects on soil and water quality. On the other hand, the growing population significantly consumes large quantities of poultry meats. Eventually, this produces a mammoth amount of poultry waste, chicken feathers. Owing to the protein value of the chicken feathers, these wastes are converted into protein hydrolysate and further extend their application as biostimulants for sustained agriculture. The protein profile of chicken feather protein hydrolysate (CFPH) produced through Bacillus spp. was the maximum compared to physical and chemical protein extraction methods. Several studies proved that the application of CFPH and active Bacillus spp. culture to soil and plants results in enhanced plant growth, phytochemical constituents, crop yield, soil nutrients, fertility, microbiome and resistance against diverse abiotic and biotic stresses. Overall, "CFPH - Jack of all trades" and "Bacillus spp. - an active camouflage to the surroundings where they applied showed profound and significant benefits to the plant growth under the most adverse conditions. In addition, Bacillus spp. coheres the biofortification process in plants through the breakdown of metals into metal ions that eventually increase the nutrient value of the food crops. However, detailed information on them is missing. This can be overcome by further real-world studies on rhizoengineering through a multi-omics approach and their interaction with plants. This review has explored the best possible and efficient strategy for managing chicken feather wastes into protein-rich CFPH through Bacillus spp. bioconversion and utilizing the CFPH and Bacillus spp. as biostimulants, biofertilizers, biopesticides and biofortificants. This paper is an excellent report on organic waste management, circular economy and sustainable agriculture research frontier.

Bacillus species as tools for biocontrol of plant diseases: A meta-analysis of twenty-two years of research, 2000-2021

The traditional way of dealing with plant diseases has been the use of chemical products, but these harm the environment and are incompatible with the global effort for sustainable development. The use of Bacillus and related species in the biological control of plant diseases is a trend in green agriculture. Many studies report the positive effect of these bacteria, but a synthesis is still necessary. So, the objective of this work is to perform a meta-analysis of Bacillus biocontrol potential and identify factors that drive its efficacy. Data were compiled from articles published in journals listed in two of the main scientific databases between 2000 and 2021. Among 6159 articles retrieved, 399 research papers met the inclusion criteria for a systematic review. Overall, Bacilli biocontrol agents reduced disease by 60% compared to control groups. Furthermore, experimental tests with higher concentrations show a strong protective effect, unlike low and single concentration essays. Biocontrol efficacy also increased when used as a protective inoculation rather than therapeutic inoculation. Inoculation directly in the fruit has a greater effect than soil drenching. The size of the effect of Bacillus-based commercial products is lower than the newly tested strains. The findings presented in this study confirm the power of Bacillus-based bioinoculants and provide valuable guidance for practitioners, researchers, and policymakers seeking effective and sustainable solutions in plant disease management.

Assessment of the phenotypic and genotypic diversity of endophytic strains of Bacillus and closely related genera from Carpinus betulus in the Hyrcanian forests of Iran

BACKGROUND

Identification and characterization of the endophytic microorganism, is gaining their underestimated significance in influencing health, performance, and other biological attributions of plants in general and forest tree species in particular. Because of the scarcity of information on the endophytic microbiome of the Hyrcanian forests species, including hornbeam (Carpinus betulus L.) trees, as a major constituent thereof, the present study aimed at the identification and partial characterization of the endophytic Bacillus species of Carpinus betulus as the first step in this context.

METHODS AND RESULTS

Shoot samples were collected from the Hyrcanian forest locations of Mazandaran and Golestan provinces in Iran. Bacterial strains were isolated from the surface-disinfected shoot segments and subjected to phenotypic characterization. Following assessment of the genetic diversity of the isolates by BOX-PCR fingerprinting, the representative isolates of each of the 15 groups were used for further characterization. Analysis of the nucleotide sequences of the 16S rDNA and HSP60 gene of the isolates led to the identification of 10 species. The predominant species was B. cereus followed by B. subtilis. The other species encountered were B. thuringiensis, Priestia filamentosa, B. velezensis, B. mojavensis, B. amyloliquefaciens, B. safensis, P. aryabhattai, and Gottfriedia acidiceleris. Most isolates possessed characteristics which could contribute to the biocontrol potential of the isolates, including formation of biofilm, production of hydrogen cyanide, tolerant to relatively high concentration of sodium chloride, and antibacterial activity.

CONCLUSIONS

Ten Bacillus species were identified as the prevailing endophytic species of C. betulus in the Hyrcanian forest of northern Iran, most turned up to possess biological activities involved in biocontrol capability of the isolates against some plant pathogens. These potentially capable bacteria could be implemented in the promotion of plant growth as well as in the biological control of pathogens. This is the first report on the characterization and elucidation of the diversity of the potentially beneficial endophytic species of Bacillus and the closely related genera living in the internal tissues of hornbeam trees.

The lncRNA20718-miR6022-RLPs module regulates tomato resistance to Phytophthora infestans

KEY MESSAGE

Sl-lncRNA20718 acts as an eTM of Sl-miR6022 regulating its expression thereby affecting SlRLP6/10 expression. SlRLP6/10 regulate PRs expression, ROS accumulation, and JA/ET content thereby affecting tomato resistance to P. infestans. Tomato (Solanum lycopersicum) is an important horticultural and cash crop whose yield and quality can be severely affected by Phytophthora infestans (P. infestans). Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are widely involved in plant defense responses against pathogens. The involvement of Sl-lncRNA20718 and Sl-miR6022 in tomato resistance to P. infestans as well as the targeting of Sl-miR6022 to receptor-like protein genes (RLPs) were predicted in our previous study. However, uncertainty exists regarding their potential interaction as well as the molecular processes regulating tomato resistance. Here, we found that Sl-lncRNA20718 and Sl-miR6022 are positive and negative regulators of tomato resistance to P. infestans by gain- and loss-of-function experiments, respectively. Overexpression of Sl-lncRNA20718 decreased the expression of Sl-miR6022, induced the expression of PRs, reduced the diameter of lesions (DOLs), thereby enhanced disease resistance. A six-point mutation in the binding region of Sl-lncRNA20718 to Sl-miR6022 disabled the interaction, indicating that Sl-lncRNA20718 acts as an endogenous target mimic (eTM) of Sl-miR6022. We demonstrated that Sl-miR6022 cleaves SlRLP6/10. Overexpression of Sl-miR6022 decreases the expression levels of SlRLP6/10, induces the accumulation of reactive oxygen species (ROS) and reduces the content of JA and ET, thus inhibiting tomato resistance to P. infestans. In conclusion, our study provides detailed information on the lncRNA20718-miR6022-RLPs module regulating tomato resistance to P. infestans by affecting the expression of disease resistance-related genes, the accumulation of ROS and the phytohormone levels, providing a new reference for tomato disease resistance breeding.

Plant-Growth-Promoting Rhizobacteria Modulate Carbohydrate Metabolism in Connection with Host Plant Defense Mechanism

Plant-growth-promoting rhizobacteria (PGPR) could potentially enhance photosynthesis and benefit plant growth by improving soil nutrient uptake and affecting plant hormone balance. Several recent studies have unveiled a correlation between alterations in photosynthesis and host plant resistance levels. Photosynthesis provides materials and energy for plant growth and immune defense and affects defense-related signaling pathways. Photosynthetic organelles, which could be strengthened by PGPR inoculation, are key centers for defense signal biosynthesis and transmission. Although endophytic PGPRs metabolize plant photosynthates, they can increase soluble sugar levels and alternate sugar type and distribution. Soluble sugars clearly support plant growth and can act as secondary messengers under stressed conditions. Overall, carbohydrate metabolism modifications induced by PGPR may also play a key role in improving plant resistance. We provide a concise overview of current knowledge regarding PGPR-induced modulation in carbohydrate metabolism under both pathogen-infected and pathogen-free conditions. We highlight PGPR application as a cost-saving strategy amidst unpredictable pathogen pressures.

Bacillus subtilis 26D Triggers Induced Systemic Resistance against Rhopalosiphum padi L. by Regulating the Expression of Genes AGO, DCL and microRNA in Bread Spring Wheat

Bacillus subtilis 26D is a plant growth-promoting endophytic bacteria capable of inducing systemic resistance through the priming mechanism, which includes plant genome reprogramming and the phenomenon of RNA interference (RNAi) and microRNA (miRNAs). The phloem-feeding insect bird cherry-oat aphid Rhopalosiphum padi L. is a serious pest that causes significant damage to crops throughout the world. However, the function of plant miRNAs in the response to aphid infestation remains unclear. The results of this work showed that B. subtilis 26D stimulated aphid resistance in wheat plants, inducing the expression of genes of hormonal signaling pathways ICS, WRKY13, PR1, ACS, EIN3, PR3, and ABI5. In addition, B. subtilis 26D activated the RNAi mechanism and regulated the expression of nine conserved miRNAs through activation of the ethylene, salicylic acid (SA), and abscisic acid (ABA) signaling pathways, which was demonstrated by using treatments with phytohormones. Treatment of plants with SA, ethylene, and ABA acted in a similar manner to B. subtilis 26D on induction of the expression of the AGO4, AGO5 and DCL2, DCL4 genes, as well as the expression of nine conserved miRNAs. Different patterns of miRNA expression were found in aphid-infested plants and in plants treated with B. subtilis 26D or SA, ethylene, and ABA and infested by aphids, suggesting that miRNAs play multiple roles in the plant response to phloem-feeding insects, associated with effects on hormonal signaling pathways, redox metabolism, and the synthesis of secondary metabolites. Our study provides new data to further elucidate the fine mechanisms of bacterial-induced priming. However, further extensive work is needed to fully unravel these mechanisms.

Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions

Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.

Transcriptomic analysis reveals that Bacillomycin D-C16 induces multiple pathways of disease resistance in cherry tomato

BACKGROUND

Bacillomycin D-C16 can induce resistance in cherry tomato against pathogens; however, the underlying molecular mechanism is poorly understood. Here, the effect of Bacillomycin D-C16 on induction of disease resistance in cherry tomato was investigated using a transcriptomic analysis.

RESULTS

Transcriptomic analysis revealed a series of obvious enrichment pathways. Bacillomycin D-C16 induced phenylpropanoid biosynthesis pathways and activated the synthesis of defense-related metabolites including phenolic acids and lignin. Moreover, Bacillomycin D-C16 triggered a defense response through both hormone signal transduction and plant-pathogen interactions pathways, and increased the transcription of several transcription factors (e.g., AP2/ERF, WRKY and MYB). These transcription factors might contribute to the further activated the expression of defense-related genes (PR1, PR10 and CHI) and stimulated the accumulation of H2O2.

CONCLUSION

Bacillomycin D-C16 can induce resistance in cherry tomato by activating the phenylpropanoid biosynthesis pathway, hormone signal transduction pathway and plant-pathogen interactions pathway, thus activating comprehensive defense reaction against pathogen invasion. These results provided a new insight into the bio-preservation of cherry tomato by the Bacillomycin D-C16.

Fengycin produced by Bacillus subtilis XF-1 plays a major role in the biocontrol of Chinese cabbage clubroot via direct effect and defense stimulation

Bacillus subtilis XF-1 is a well-investigated biocontrol agent against the biotrophic Plasmodiophora brassicae Woron., the causal agent of clubroot disease of cruciferous crops. The present study demonstrates that XF-1 could efficiently control clubroot disease via leaf spraying and provides an understanding of the biocontrol mechanisms. High-performance thin-layer chromatography (HTPLC) analysis indicated the presence of fengycin-type cyclopeptides in the supernatant. A ppsB deletion mutant of XF-1 resulted in no fengycin production, significantly reduced the lysis rate of testing spores in vitro and the primary infection rate of root hair in vivo, and decreased the protection value against clubroot disease under the greenhouse conditions. Confocal laser scanning microscopy proved that fengycin was not required for leaf internalization and root colonization. Moreover, the expression level of the ppsB gene in XF-1 was regulated by its cell density in root during interaction with P. brassicae. In addition, the ΔppsB mutant of XF-1 could not efficiently control disease because it led to a lower activation level of the jasmonic acid and salicylic acid signaling pathways in roots, which are necessary for the plant defense reaction upon pathogen invasion. Altogether, the present study provides a new understanding of specific cues in the interaction between B. subtilis and P. brassicae as well as insights into the application of B. subtilis in agriculture.

Identification of miRNAs Involved in Maize-Induced Systemic Resistance Primed by Trichoderma harzianum T28 against Cochliobolus heterostrophus

microRNAs (miRNAs) are known to play important roles in the immune response to pathogen infection in different plants. Further, Trichoderma strains are able to activate plant defense responses against pathogen attacks. However, little is known about the involvement of miRNAs in the defense response primed by Trichoderma strains. To explore the miRNAs sensitive to priming by Trichoderma, we studied the small RNAs and transcriptome changes in maize leaves that were systemically induced by seed treatment with Trichoderma harzianum (strain T28) against Cochliobolus heterostrophus (C. heterostrophus) infection in leaves. Through analysis of the sequencing data, 38 differentially expressed miRNAs (DEMs) and 824 differentially expressed genes (DEGs) were identified. GO and KEGG analyses of DEGs demonstrated that genes involved in the plant hormone signal transduction pathway and oxidation-reduction process were significantly enriched. In addition, 15 miRNA-mRNA interaction pairs were identified through the combined analysis of DEMs and DEGs. These pairs were supposed to play roles in the maize resistance primed by T. harzianum T28 to C. heterostrophus, in which miR390, miR169j, miR408b, miR395a/p, and novel miRNA (miRn5231) were more involved in the induction of maize resistance. This study provided valuable information for understanding the regulatory role of miRNA in the T. harzianum primed defense response.

Effects of Trichoderma atroviride SG3403 and Bacillus subtilis 22 on the Biocontrol of Wheat Head Blight

Wheat head blight caused by Fusarium graminearum is one of the major wheat diseases in the world; therefore, it is very significant to develop an effective and environmentally friendly microbial fungicide against it. Trichoderma atroviride and Bacillus subtilis are widely applied biocontrol microorganisms with separate advantages; however, little work has been conducted for synergistically elevating the effects of biocontrol and plant promotion through the co-cultivation of the two microorganisms. Our study demonstrated that T. atroviride SG3403 is compatible with B. subtilis 22. The co-culture metabolites contained a group of antagonistic compounds which were able to inhibit F. graminearum growth and increase the activities of pathogen G protein and mitogen-activated protein kinase (MAPK) as compared with axenic culture metabolites. Additionally, the co-culture metabolites enabled us to more significantly decrease the production of gibberellin (GA), deoxynivalenol (DON), and zearalenone (ZEN) from F. graminearum, which disorganized the subcellular structure, particularly the cytoplasm of F. graminearum hyphae, relative to the axenically cultured metabolites. Furthermore, the seed-coating agent made by the co-culture had significant effects against F. graminearum infection by triggering the expression of host plant defensive genes, including PR1, PR3, PR4, PR5, ACS, and SOD. It is suggested that jasmonic acid and ethylene (JA/ET) signaling might dominate wheat's induced systemic resistance (ISR) against wheat head blight. A dry, powdered bio-seed coating agent containing the co-culture mixtures was confirmed to be a bioavailable formulation that can be applied to control wheat head blight. Taken together, the co-culture's metabolites or the metabolites and living cells might provide a basis for the further development of a new kind of microbial bio-fungicide in the future.

Digital gene expression profiling of the transcriptional response to Sclerotinia sclerotiorum and its antagonistic bacterium Bacillus amyloliquefaciens in soybean

Soybean Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a common disease in soybean, and effective biological control is urgently needed. We have previously confirmed that Bacillus amyloliquefaciens can effectively antagonize S. sclerotiorum in a plate competition experiment and a soybean seedling inoculation experiment. In this study, the mechanisms underlying plant death caused by S. sclerotiorum and soybean resistance to S. sclerotiorum induced by B. amyloliquefaciens were evaluated. The stems of potted soybean seedlings were inoculated with S. sclerotiorum (Gm-Ss), B. amyloliquefaciens (Gm-Ba), and their combination (Gm-Ba-Ss), using scratch treatments as a control, followed by dual RNA sequencing and bioinformatics analyses. Global gene expression levels in the Gm-Ss treatment were much lower than those in the Gm-Ba, Gm-Ba-Ss, and Gm groups, suggesting that S. sclerotiorum strongly inhibited global gene expression in soybean. In a pairwise comparison of Gm-Ss vs. Gm, 19983 differentially expressed genes (DEGs) were identified. Down-regulated DEGs were involved in various KEGG pathways, including ko01110 (biosynthesis of secondary metabolites), ko01100 (metabolic pathways), ko01120 (microbial metabolism in diverse environments), ko00500 (starch and sucrose metabolism), and ko04075 (plant hormone signal transmission), suggesting that S. sclerotiorum inoculation had a serious negative effect on soybean metabolism. In Gm-Ba vs. Gm, 13091 DEGs were identified, and these DEGs were significantly enriched in ko03010 (ribosome) and ko03008 (ribosome biogenesis in eucaryotes). Our results suggest that B. amyloliquefaciens increases the expression of genes encoding the ribosomal subunit, promotes cell wall biogenesis, and induces systemic resistance. S. sclerotiorum strongly inhibited metabolism in soybean, inhibited the synthesis of the cytoskeleton, and induced the up-regulation of programmed death and senescence-related genes via an ethylene signal transduction pathway. These results improve our understanding of S. sclerotiorum-induced plant death and soybean resistance to S. sclerotiorum induced by B. amyloliquefaciens and may contribute to the improvement of strategies to avoid yield losses.

Bama Pig Manure Organic Fertilizer Regulates the Watermelon Rhizosphere Bacterial Community to Inhibit the Occurrence of Fusarium Wilt Under Continuous Cropping Conditions

Fusarium wilt caused by Fusarium oxysporum f. sp. niveum is an important manifestation of continuous cropping barrier, which causes the quality and yield of watermelon to decline. In early stage of this study, the organic fertilizer fermented by Bama pig manure applied in soil was proved to significantly inhibit the occurrence of disease by improving the structure of soil microbial community. However, the mechanism was not clear. The high-throughput sequencing technology, combined with network and PICRUSt2 function analysis was used to investigate it. MiSeq sequencing showed that the bacterial community of organic fertilizer treated soil was composed of 34 phyla and 768 genera, the number of genera was higher than that of sterile water treated soil. Fertilization significantly increased the diversity and changed the composition of bacterial community based on alpha, beta diversity, and ANOSIM/Adonis analysis. LEfSe species difference and network analysis showed that fertilization improved the relative abundance of bacteria with biological control or plant growth promotion characteristics in soil, such as Sphingomonas, Halobacillus, Nocardioides, and enhanced the interaction between rhizosphere bacteria, made the network structure more complex. PICRUSt2 also revealed fertilization promoted the bacterial function, such as metabolism and genetic information processing. These results showed that the pig manure organic fertilizer might reduce the occurrence of Fusarium wilt by regulating bacterial community, interaction, and functional metabolism in watermelon rhizosphere soil.

Extraction and characterization of cyclic lipopeptides with antifungal and antioxidant activities from Bacillus amyloliquefaciens

AIMS

This study aimed to isolate active substances from metabolites of Bacillus amyloliquefaciens SJ100001 and examine their antifungal activity against Fusarium oxysporum (F. oxysporum) SJ300024 screened from the root-soil of cucumber wilt.

METHODS AND RESULTS

An active substance, anti-SJ300024, was obtained from the fermentation broth of strain SJ100001 by reversed-phase silica gel and gel chromatography, and further got its chemical structure as cyclic lipopeptide Epichlicin through nuclear magnetic resonance (NMR) and mass spectrometry (MS). In vitro experiments showed that Epichlicin had a better inhibitory rate (67.46%) against the strain SJ300024 than the commercially available fungicide hymexazol (45.1%) at the same concentration. The MTT assays proved that Epichlicin was non-cytotoxic, besides it also had good free radical scavenging ability and total reducing ability.

CONCLUSIONS

Epichlicin isolated from strain SJ100001 can effectively control F. oxysporum SJ300024 screened from the root-soil of cucumber wilt.

SIGNIFICANCE AND IMPACT OF THE STUDY

Epichlicin may be used as an environmentally friendly and efficient biocontrol agent for controlling Fusarium wilt of cucumber and reducing crop losses. More importantly, the non-cytotoxicity of Epichlicin can avoid harm to consumers. Additionally, Epichlicin has broad application prospects in medicine due to its antioxidant properties.

Development of plant systemic resistance by beneficial rhizobacteria: Recognition, initiation, elicitation and regulation

A plant growing in nature is not an individual, but it holds an intricate community of plants and microbes with relatively stable partnerships. The microbial community has recently been demonstrated to be closely linked with plants since their earliest evolution, to help early land plants adapt to environmental threats. Mounting evidence has indicated that plants can release diverse kinds of signal molecules to attract beneficial bacteria for mediating the activities of their genetics and biochemistry. Several rhizobacterial strains can promote plant growth and enhance the ability of plants to withstand pathogenic attacks causing various diseases and loss in crop productivity. Beneficial rhizobacteria are generally called as plant growth-promoting rhizobacteria (PGPR) that induce systemic resistance (ISR) against pathogen infection. These ISR-eliciting microbes can mediate the morphological, physiological and molecular responses of plants. In the last decade, the mechanisms of microbial signals, plant receptors, and hormone signaling pathways involved in the process of PGPR-induced ISR in plants have been well investigated. In this review, plant recognition, microbial elicitors, and the related pathways during plant-microbe interactions are discussed, with highlights on the roles of root hair-specific syntaxins and small RNAs in the regulation of the PGPR-induced ISR in plants.

Induced Systemic Resistance for Improving Plant Immunity by Beneficial Microbes

Plant beneficial microorganisms improve the health and growth of the associated plants. Application of beneficial microbes triggers an enhanced resistance state, also termed as induced systemic resistance (ISR), in the host, against a broad range of pathogens. Upon the activation of ISR, plants employ long-distance systemic signaling to provide protection for distal tissue, inducing rapid and strong immune responses against pathogens invasions. The transmission of ISR signaling was commonly regarded to be a jasmonic acid- and ethylene-dependent, but salicylic acid-independent, transmission. However, in the last decade, the involvement of both salicylic acid and jasmonic acid/ethylene signaling pathways and the regulatory roles of small RNA in ISR has been updated. In this review, the plant early recognition, responsive reactions, and the related signaling transduction during the process of the plant-beneficial microbe interaction was discussed, with reflection on the crucial regulatory role of small RNAs in the beneficial microbe-mediated ISR.

Up-Regulated Salivary Proteins of Brown Marmorated Stink Bug Halyomorpha halys on Plant Growth-Promoting Rhizobacteria-Treated Plants

Plant Growth-Promoting Rhizobacteria (PGPR) induce systemic resistance (SR) in plants, decreasing the development of phytopathogens. The FZB42 strain of Bacillus velezensis is known to induce an SR against pathogens in various plant species. Previous studies suggested that it could also influence the interactions between plants and associated pests. However, insects have developed several strategies to counteract plant defenses, including salivary proteins that allow the insect escaping detection, manipulating defensive pathways to its advantage, deactivating early signaling processes, or detoxifying secondary metabolites. Because Brown Marmorated Stink Bug (BMSB) Halyomorpha halys is highly invasive and polyphagous, we hypothesized that it could detect the PGPR-induced systemic defenses in the plant, and efficiently adapt its salivary compounds to counteract them. Therefore, we inoculated a beneficial rhizobacterium on Vicia faba roots and soil, previous to plant infestation with BMSB. Salivary gland proteome of BMSB was analyzed by LC-MS/MS and a label-free quantitative proteomic method. Among the differentially expressed proteins, most were up-regulated in salivary glands of insects exposed to PGPR-treated plants for 24 h. We could confirm that BMSB was confronted with a stress during feeding on PGPR-treated plants. The to-be-confirmed defensive state of the plant would have been rapidly detected by the invasive H. halys pest, which consequently modified its salivary proteins. Among the up-regulated proteins, many could be associated with a role in plant defense counteraction, and more especially in allelochemicals detoxification or sequestration.

The Transcriptomic Profile of Watermelon Is Affected by Zinc in the Presence of Fusarium oxysporum f. sp. niveum and Meloidogyne incognita

Zinc (Zn) accumulation and deficiency affect plant response to pests and diseases differently in varying pathosystems. The concentrations of Zn in plants aid in priming defense signaling pathways and help in enhanced structural defenses against plant pathogens. Studies are lacking on how concentrations of Zn in watermelon plants influence defense against two important soil-borne pathogens: Fusarium oxysporum f. sp. niveum (FON) and southern root-knot nematode (RKN, Meloidogyne incognita). In this study a comparative transcriptomics evaluation of watermelon plants in response to high (1.2 ppm) and low (0.2 ppm) levels of Zn were determined. Differential transcript-level responses differed in watermelon plants when infected with FON or RKN or both under high- and low-Zn treatment regimes in a controlled hydroponics system. Higher numbers of differentially expressed genes (DEGs) were observed in high-Zn-treated than in low-Zn-treated non-inoculated plants, in plants inoculated with FON alone and in plants inoculated with RKN alone. However, in the co-inoculated system, low-Zn treatment had higher DEGs as compared to high-Zn treatment. In addition, most DEGs were significantly enriched in hormone signal transduction and MAPK signaling pathway, suggesting an induction of systemic resistance with high-Zn concentrations. Taken together, this study substantially expands transcriptome data resources and suggests a molecular potential framework for watermelon-Zn interaction in FON and RKN.

Bacillus subtilis SL18r Induces Tomato Resistance Against Botrytis cinerea, Involving Activation of Long Non-coding RNA, MSTRG18363, to Decoy miR1918

Mounting evidence has indicated that beneficial rhizobacteria can suppress foliar pathogen invasion via elicitation of induced systemic resistance (ISR). However, it remains elusive whether long non-coding RNAs (lncRNAs) are involved in the mediation of the rhizobacteria-primed ISR processes in plants. Herein, we demonstrated the ability of the rhizobacterial strain Bacillus subtilis SL18r to trigger ISR in tomato plants against the foliar pathogen Botrytis cinerea. Comparative transcriptome analysis was conducted to screen differentially expressed lncRNAs (DELs) between the non-inoculated and SL18r-inoculated plants. Among these DELs, four variants of MSTRG18363 possessed conserved binding sites for miR1918, which negatively regulates immune systems in tomato plants. The expression of MSTRG18363 in tomato leaves was significantly induced by SL18r inoculation. The transcription of MSTRG18363 was negatively correlated with the expression of miR1918, but displayed a positive correlation with the transcription of the RING-H2 finger gene SlATL20 (a target gene of miR1918). Moreover, MSTRG18363-overexpressing plants exhibited the enhanced disease resistance, reduction of miR1918 transcripts, and marked increases of SlATL20 expression. However, the SL18r-induced disease resistance was largely impaired in the MSTRG18363-silenced plants. VIGS-mediated SlATL20 silencing also greatly weakened the SL18r-induced disease resistance. Collectively, our results suggested that induction of MSTRG18363 expression in tomato plants by SL18r was conducive to promoting the decoy of miR1918 and regulating the expression of SlATL20, thereby provoking the ISR responses against foliar pathogen infection.

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.

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.

Induced Disease Resistance and Promotion of Shallot Growth by <i>Bacillus velezensis</i> B-27

BACKGROUND AND OBJECTIVES

Shallot is a vegetable crop with high economic value, but its productivity is still relatively low due to various limitations. One of the most hampering factors is moler disease and purple blotch disease caused by Fusarium sp. and Alternaria porri, respectively. Numerous efforts have been made to control these diseases either using chemical fungicides or through improvement of resistant cultivar. This study aimed to determine moler and purple disease suppression and improvement of plant growth by Bacillus as Plant Growth Promoting Rhizobacteria (PGPR) on shallot.

MATERIALS AND METHODS

Molecular identification of Bacillus was performed by partial gyrB gene sequencing using universal gyrB-F/gyrB-R primers. Field observation and experiments were performed using completely randomized factorial block design single factor with 3 blocks for replication.

RESULTS

The partial gyrB gene sequences showed high similarity between Bacillus isolate B-27 and Bacillus velezensis. The application of Bacillus isolate B-27 to shallots was shown to reduce the intensity of moler and purple blotch diseases by 67%. On top of that, Bacillus isolate B-27 increased the plant height up to 27.12 cm, the number of leaves up to 23 blades, tillers up to 8 bulbs and the tuber weight during harvest time up to 33.64 kg.

CONCLUSION

Molecular identification based on partial gyrB gene sequence analysis suggested that Bacillus isolate B-27 has close relationship with Bacillus velezensis. Besides, the application of Bacillus isolate B-27 on shallot could reduce the disease intensity and increase height, number of tillers and plant yield significantly.

Current Utility of Plant Growth-Promoting Rhizobacteria as Biological Control Agents towards Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPN) are among the most economically and ecologically damaging pests, causing severe losses of crop production worldwide. Chemical-based nematicides have been widely used, but these may have adverse effects on human health and the environment. Hence, biological control agents (BCAs) have become an alternative option for controlling PPN, since they are environmentally friendly and cost effective. Lately, a major effort has been made to evaluate the potential of a commercial grade strain of plant growth-promoting rhizobacteria (PGPR) as BCAs, because emerging evidence has shown that PGPR can reduce PPN in infested plants through direct and/or indirect antagonistic mechanisms. Direct antagonism occurs by predation, release of antinematicidal metabolites and semiochemicals, competition for nutrients, and niche exclusion. However, the results of direct antagonism may be inconsistent due to unknown endogenous and exogenous factors that may prevent PGPR from colonizing plant's roots. On the other hand, indirect antagonism may occur from the induced systemic resistance (ISR) that primes whole plants to better fight against various biotic and abiotic constraints, actuating faster and/or stronger defense responses (adaption), enhancing their promise as BCAs. Hence, this review will briefly revisit (i) two modes of PGPR in managing PPN, and (ii) the current working models and many benefits of ISR, in the aim of reassessing current progresses and future directions for isolating more effective BCAs and/or developing better PPN management strategy.

The Prevention of Bio-Organic Fertilizer Fermented from Cow Manure Compost by Bacillus sp. XG-1 on Watermelon Continuous Cropping Barrier

The continuous cropping barrier is an important factor leading to the decline of watermelon quality and yield. In this study, we focused on a bio-organic fertilizer prepared with one bacterial strain, Bacillus sp. XG-1, to prevent the occurrence of the continuous cropping barrier. The strain XG-1 was isolated from watermelon rhizosphere soil, and promoted the growth of watermelon by producing phytase (0.19 U/mL), indole-3-acetic acid (IAA, 7.31 mg/L), and gibberellins (GA3, 2.47 mg/L). In addition, the strain also possessed a strong antagonistic effect against the pathogen Fusarium oxysporum f. sp. niveum (Fon) by inhibiting conidia germination with an inhibition ratio of 85.3% and mycelium growth. The bio-organic fertilizer fermented by XG-1, based on cow manure compost and rapeseed meal (85:15, w/w) under optimal conditions, was mixed in soil (watermelon had been planted for two consecutive years). After the cultivation of watermelon for 50 d, a higher density of XG-1 (9.79 × 10⁵ colony-forming units (CFU)/g) and one order of magnitude lower of Fon (1.29 × 10³ copies/g) were detected in the rhizosphere soil compared with soils without bio-organic fertilizer (7.59 × 10⁴ copies/g for Fon), leading to an 86.4% control efficiency of watermelon caused by Fusarium wilt. The application of bio-organic fertilizer enriched soil nutrients, including the organic matter (13.2%), total nitrogen (13.9%), total phosphorus (20.5%), and total potassium (3.77%), adjusted the soil pH from 6.69 to 7.01, and significantly improved the watermelon growth in terms of the seedling height, root length, fresh weight of seedling and root with increase of 78.8%, 72.2%, 84.6%, and 96.4%, respectively. This study regarded the watermelon continuous cropping soil as the research point, and focused on inhibiting Fon, regulating soil properties and enhancing watermelon growth to eliminate the continuous cropping barrier through a combination of compost and functional strains, demonstrating the potential application value in watermelon production.

High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection

MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in Arabidopsis-Phytophthora capsici (P. capsici) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from Arabidopsis thaliana leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with P. capsici. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to P. capsici infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by P. capsici. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to Phytophthora species in other crops.

Induced Systemic Resistance by a Plant Growth-Promoting Rhizobacterium Impacts Development and Feeding Behavior of Aphids

The effects of microorganisms on plant-insect interactions have usually been underestimated. While plant growth-promoting rhizobacteria (PGPR) are known to induce plant defenses, endosymbiotic bacteria hosted by herbivorous insects are often beneficial to the host. Here, we aimed to assess whether PGPR-induced defenses in broad bean plants impact the pea aphid, depending on its genotype and the presence of endosymbionts. We estimated aphid reproduction, quantified defense- and growth-related phytohormones by GC-MS, and measured different plant growth and physiology parameters, after PGPR treatment. In addition, we recorded the feeding behavior of aphids by electropenetrography. We found that the PGPR treatment of broad bean plants reduced the reproduction of one of the pea aphid clones. We highlighted a phenomenon of PGPR-induced plant defense priming, but no noticeable plant growth promotion. The main changes in aphid probing behavior were related to salivation events into phloem sieve elements. We suggest that the endosymbiont Hamiltonella defensa played a key role in plant-insect interactions, possibly helping aphids to counteract plant-induced resistance and allowing them to develop normally on PGPR-treated plants. Our results imply that plant- and aphid-associated microorganisms add greater complexity to the outcomes of aphid-plant interactions.

Biocontrol Potential of Sclerotinia sclerotiorum and Physiological Changes in Soybean in Response to Butia archeri Palm Rhizobacteria

Sclerotinia sclerotiorum is a necrotrophic parasitic fungus that causes Sclerotinia stem rot (SSR), which is currently one of the most difficult agronomic crop diseases to control. A number of plants of the Brazilian Cerrado biome have been shown to be important sources of symbiotic microorganisms with biotechnological potential, so we decided to test the potential of bacteria isolated from the dwarf jelly palm, Butia archeri (Arecaceae) for the control of the pathogenic effects provoked by S. sclerotiorum. For this, we bioprimed seeds and evaluated the effects of this biopriming on the OJIP transient patterns prior to and following infection by the phytopathogen. Plants treated with the BA48R strain of Enterobacter sp., and in particular, those treated with the BA88R strain of Bacillus cereus presented the best results in terms of the loss/gain of the physiological and symptomatological variables evaluated. The plants bioprimed with BA88R presented high post-infection levels of total chlorophyll (33.35 FCIs) and chlorophyll a (26.39 FCIs), maintained a high Nitrogen Balance Index (NBI = 18.87), and synthesized low concentrations of flavonoids (1.39). These plants also maintained high levels of PI_ABS (1.111) and PI_TOTAL (1.300) following infection, and low levels of Di₀/RC (0.602), which indicates that, in the presence S. sclerotiorum, the efficiency of the photosynthesis in the plants treated with these bacteria was less affected in the reaction centers, as confirmed by the negative amplitude recorded in the L band. The present study reconfirms the importance of the use of chlorophyll fluorescence for the diagnosis of disease and conditions of stress in crop plants, in addition to demonstrating the effectivenesss of the BA48R bacterial strain and, in particular, the BA88R strain on systemic resistance induction and suppression of S. sclerotiorum in Glycine max plants, with enormous potential for the development of more sustainable agricultural processes.

High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection

MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in Arabidopsis-Phytophthora capsici (P. capsici) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from Arabidopsis thaliana leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with P. capsici. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to P. capsici infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by P. capsici. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to Phytophthora species in other crops.

Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms

Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.

Two rapid and sensitive methods based on TaqMan qPCR and droplet digital PCR assay for quantitative detection of Bacillus subtilis in rhizosphere

AIMS

Bacillus subtilis, a typical plant growth-promoting rhizobacteria, can benefit plant through promoting growth and reducing disease. The colonization intensity of B. subtilis in rhizosphere is a key factor for improving their effectiveness of field application. In this study, we developed a rapid and sensitive method for detecting B. subtilis in rhizosphere via TaqMan qPCR and droplet digital PCR (ddPCR) methods.

METHODS AND RESULTS

The primers/probe set targeting gyrB gene could successfully distinguish B. subtilis from its close-related species. Both the TaqMan qPCR and ddPCR methods exhibited a good linear relationship in the sensitivity assay, suggesting the developed method was specific, effective and reliable. Finally, the two methods were used to detect the colonization dynamic of B. subtilis within Arabidopsis rhizosphere. Both of them showed a consistent trend compared with the traditional cultivation-based and microscopy-based methods.

CONCLUSIONS

The TaqMan qPCR and droplet digital PCR (ddPCR) methods we developed could be used to rapidly detect B. subtilis in rhizosphere.

SIGNIFICANCE AND IMPACT OF THE STUDY

The TaqMan qPCR and ddPCR methods developed in this study can be applied to rapid quantitative detection of B. subtilis populations, and will be helpful to evaluate their effectiveness of field application.

Identification of miRNAs Involved in Bacillus velezensis FZB42-Activated Induced Systemic Resistance in Maize

Bacillus velezensis FZB42 is able to activate induced systemic resistance (ISR) to enhance plant defense response against pathogen infections. Though the roles of microRNAs (miRNAs) in Bacillus-triggered ISR have been reported in Arabidopsis, the maize miRNAs responsible for the Bacillus-activated ISR process have not been discovered. To explore the maize miRNAs involved in ISR, maize miRNAs in response to FZB42 (ISR activating), FZB42△sfp△alss (deficient in triggering ISR), and a control for 12 h were sequenced. A total of 146 known miRNAs belonging to 30 miRNA families and 217 novel miRNAs were identified. Four miRNAs specifically repressed in FZB42-treatment were selected as candidate ISR-associated miRNAs. All of them contained at least one defense response-related cis-element, suggesting their potential roles in activating the ISR process. Interestingly, three of the four candidate ISR-associated miRNAs belong to the conserved miR169 family, which has previously been confirmed to play roles in abiotic stress response. Moreover, 52 mRNAs were predicted as potential targets of these candidate ISR-associated miRNAs through TargetFinder software and degradome sequencing. Gene Ontology (GO) and network analyses of target genes showed that these differentially expressed miRNA might participate in the ISR process by regulating nuclear factor Y transcription factor. This study is helpful in better understanding the regulatory roles of maize miRNAs in the Bacillus-activated ISR process.

Arabidopsis thaliana Seedlings Influence Bacillus subtilis Spore Formation

Bacillus subtilis is a Gram-positive plant-growth-promoting rhizobacterium exerting many beneficial effects on plant health. Because they secrete antimicrobial compounds and elicit induced systemic resistance, B. subtilis and phylogenetically related species are of particular interest as antifungals in organic agriculture. These bacteria are also known for their capacity to differentiate phenotypically into endospores able to withstand many environmental stresses. However, although B. subtilis is often inoculated on plants as spores, dynamics of germination and sporulation on roots remain unexplored. Using a hydroponic culture system and a soil system for Arabidopsis thaliana, we observed that B. subtilis spores germinate rapidly on contact with plants. However, the vegetative cells are abundant on roots for only a few days before reversing back to spores. We observed that the germinant receptor GerK and sporulation kinases KinA and KinB identified in vitro control sporulation dynamics on plants. Surprisingly, when plants are inoculated with B. subtilis, free-living cells sporulate more rapidly than plant-associated cells. However, direct contact between plant and bacteria is required for the induction of sporulation in the surrounding B. subtilis. This study has fundamental implications for our understanding of interactions between Bacillus spp. and plants, and particularly for a more efficient usage of B. subtilis as a biofertilizer or biofungicide.

Mannan oligosaccharides trigger multiple defence responses in rice and tobacco as a novel danger-associated molecular pattern

Oligosaccharide, a typical danger-associated molecular pattern (DAMP), has been studied and applied as plant defence elicitor for several years. Here, we report a novel oligosaccharide, mannan oligosaccharide (MOS) with a degree of polymerization of 2-6, which was hydrolysed from locust bean gum by a newly reported enzyme, BpMan5. The MOS treatment can significantly enhance the generation of signalling molecules such as intracellular Ca2+ and reactive oxygen species. Subsequent defence events like stomata closure and cell death were also caused by MOS, eventually leading to the prevention of pathogen invasion or expansion. Transcriptional expression assay indicated that MOS activated mitogen-activated protein kinase cascades in tobacco and rice via different cascading pathways. The expression levels of the defence-related genes PR-1a and LOX were both up-regulated after MOS treatment, suggesting that MOS may simultaneously activate salicylic acid and jasmonic acid-dependent signalling pathways. Furthermore, liquid chromatography-mass spectrometry analysis showed that MOS led to the accumulation of four phytoalexins (momilactone A, phytocassane A, phytocassane D, and phytocassane E) in rice seedling leaves within 12-24 h. Finally, MOS conferred resistance in rice and tobacco against Xanthomonas oryzae and Phytophthora nicotianae, respectively. Taken together, our results indicated that MOS, a novel DAMP, could trigger multiple defence responses to prime plant resistance and has a great potential as plant defence elicitor for the management of plant disease.

Imidazole and Methoxybenzylamine Growth Inhibitors Reduce Salmonella Persistence in Tomato Plant Tissues

HIGHLIGHTS

Small molecules (SMs) 1, 3, 4, and 5 are novel growth inhibitors of Salmonella enterica. These SMs are not toxic to tomato plant tissues including fruits. Combining biocontrol agents and SMs enhanced the control of Salmonella in infected plants. These SMs may be safe bactericides against Salmonella and phytopathogens in produce.

Co-cultivation of Trichoderma asperellum GDFS1009 and Bacillus amyloliquefaciens 1841 Causes Differential Gene Expression and Improvement in the Wheat Growth and Biocontrol Activity

In an effort to balance the demands of plant growth promoting and biological control agents in a single product, the technology on the co-cultivation of two microbes, Trichoderma asperellum GDFS1009 and Bacillus amyloliquefaciens 1841 has been developed and demonstrated its effectiveness in synergistic interactions and its impact on the plant growth and biocontrol potential. In this study, optimization of T. asperellum and B. amyloliquefaciens growth in a single medium was carried out using response surface methodology (RSM). The optimal medium for enhanced growth was estimated as 2% yeast extract, 2% molasses and 2% corn gluten meal. T. asperellum evolved the complicated molecular mechanisms in the co-culture by the induction of BLR-1/BLR-2, VELVET, and NADPH oxidases genes. In performance with these genes, conserved signaling pathways, such as heterotrimeric G proteins and mitogen-activated protein kinases (MAPKs) had also involved in this molecular orchestration. The co-cultivation induced the expression of T. asperellum genes related to secondary metabolism, mycoparasitism, antioxidants and plant growth. On the other hand, the competition during co-cultivation induced the production of new compounds that are not detected in axenic cultures. In addition, the co-culture significantly enhanced the plant growth and protection against Fusarium graminearum. The present study demonstrated the potential of co-cultivation technology could be a used to grow the T. asperellum GDFS1009 and B. amyloliquefaciens 1841 synergistically to improve the production of mycoparasitism related enzymes, secondary metabolites, and plant growth promoting compounds to significantly enhance the plant growth and protection against plant pathogens.

Microbial Consortia versus Single-Strain Inoculants: An Advantage in PGPM-Assisted Tomato Production?

The use of biostimulants with plant growth-promoting properties, but without significant input of nutrients, is discussed as a strategy to increase stress resistance and nutrient use efficiency of crops. However, limited reproducibility under real production conditions remains a major challenge. The use of combination products based on microbial and non-microbial biostimulants or microbial consortia, with the aim to exploit complementary or synergistic interactions and increase the flexibility of responses under different environmental conditions, is discussed as a potential strategy to overcome this problem. This study aimed at comparing the efficiency of selected microbial single-strain inoculants with proven plant-growth promoting potential versus consortium products under real production conditions in large-scale tomato cultivation systems, exposed to different environmental challenges. In a protected greenhouse production system at Timisoara, Romania, with composted cow manure, guano, hair-, and feather-meals as major fertilizers, different fungal and bacterial single-strain inoculants, as well as microbial consortium products, showed very similar beneficial responses. Nursery performance, fruit setting, fruit size distribution, seasonal yield share, and cumulative yield (39–84% as compared to the control) were significantly improved over two growing periods. By contrast, superior performance of the microbial consortia products (MCPs) was recorded under more challenging environmental conditions in an open-field drip-fertigated tomato production system in the Negev desert, Israel with mineral fertilization on a high pH (7.9), low fertility, and sandy soil. This was reflected by improved phosphate (P) acquisition, a stimulation of vegetative shoot biomass production and increased final fruit yield under conditions of limited P supply. Moreover, MCP inoculation was associated with selective changes of the rhizosphere-bacterial community structure particularly with respect to Sphingobacteriia and Flavobacteria, reported as salinity indicators and drought stress protectants. Phosphate limitation reduced the diversity of bacterial populations at the root surface (rhizoplane) and this effect was reverted by MCP inoculation, reflecting the improved P status of the plants. The results support the hypothesis that the use of microbial consortia can increase the efficiency and reproducibility of BS-assisted strategies for crop production, particularly under challenging environmental conditions.

Complete genome sequence of Caulobacter flavus RHGG3T, a type species of the genus Caulobacter with plant growth-promoting traits and heavy metal resistance

Caulobacter flavus RHGG3^T, a novel type species in the genus Caulobacter, originally isolated from rhizosphere soil of watermelon (Citrullus lanatus), has the ability to improve the growth of watermelon seedling and tolerate heavy metals. In vitro, C. flavus RHGG3^T was able to solubilize phosphate (80.56 mg L^-1), produce indole-3-acetic acid (IAA) (11.58 mg L^-1) and was resistant to multiple heavy metals (copper, zinc, cadmium, cobalt and lead). Inoculating watermelon with this strain increased shoot and root length by 22.1% and 43.7%, respectively, and the total number of lateral roots by 55.9% compared to non-inoculated watermelon. In this study, we present the complete genome sequence of C. flavus RHGG3^T, which was comprised of a single circular chromosome of 5,659,202 bp with a G + C content of 69.25%. An annotation analysis revealed that the C. flavus RHGG3^T genome contained 5172 coding DNA sequences, 9 rRNA and 55 tRNA genes. Genes related to plant growth promotion (PGP), such as those associated with phosphate solubilization, nitrogen fixation, IAA, phenazine, volatile compounds, spermidine and cobalamin synthesis, were found in the C. flavus RHGG3^T genome. Some genes responsible for heavy metal tolerance were also identified. The genome sequence of strain RHGG3^T reported here provides new insight into the molecular mechanisms underlying the promotion of plant growth and the resistance to heavy metals in C. flavus. This study will be valuable for further exploration of the biotechnological applications of strain RHGG3^T in agriculture.

Epsc Involved in the Encoding of Exopolysaccharides Produced by Bacillus amyloliquefaciens FZB42 Act to Boost the Drought Tolerance of Arabidopsis thaliana

Bacillus amyloliquefaciens FZB42 is a plant growth-promoting rhizobacteria that stimulates plant growth, and enhances resistance to pathogens and tolerance of salt stress. Instead, the mechanistic basis of drought tolerance in Arabidopsis thaliana induced by FZB42 remains unexplored. Here, we constructed an exopolysaccharide-deficient mutant epsC and determined the role of epsC in FZB42-induced drought tolerance in A. thaliana. Results showed that FZB42 significantly enhanced growth and drought tolerance of Arabidopsis by increasing the survival rate, fresh and dry shoot weights, primary root length, root dry weight, lateral root number, and total lateral root length. Coordinated changes were also observed in cellular defense responses, including elevated concentrations of proline and activities of superoxide dismutase and peroxidase, decreased concentrations of malondialdehyde, and accumulation of hydrogen peroxide in plants treated with FZB42. The relative expression levels of drought defense-related marker genes, such as RD29A, RD17, ERD1, and LEA14, were also increased in the leaves of FZB42-treated plants. In addition, FZB42 induced the drought tolerance in Arabidopsis by the action of both ethylene and jasmonate, but not abscisic acid. However, plants inoculated with mutant strain epsC were less able to resist drought stress with respect to each of these parameters, indicating that epsC are required for the full benefit of FZB42 inoculation to be gained. Moreover, the mutant strain was less capable of supporting the formation of a biofilm and of colonizing the A. thaliana root. Therefore, epsC is an important factor that allows FZB42 to colonize the roots and induce systemic drought tolerance in Arabidopsis.

Expression of a maize NBS gene ZmNBS42 enhances disease resistance in Arabidopsis

Expression of the ZmNBS42 in Arabidopsis plants conferred resistance to bacterial pathogens, providing potential resistance enhancement of maize in further genetic breeding. Nucleotide-binding site (NBS) domain proteins play critical roles in disease resistance. In this study, we isolate a novel NBS gene ZmNBS42 from maize and systematically investigate its function on disease resistance. We find that the expression levels of ZmNBS42 in maize leaf were strikingly increased in response to Bipolaris maydis inoculation and SA treatment. The spatial expression pattern analysis reveals that, during development, ZmNBS42 is ubiquitously highly expressed in maize root, leaf, stem, internode and seed, but lowly expressed in pericarp and embryo. To better understand the roles of ZmNBS42, we overexpressed ZmNBS42 in heterologous systems. Transient overexpression of ZmNBS42 in the leaves of Nicotiana benthamiana induces a hypersensitive response. ZmNBS42 overexpression (ZmNBS42-OE) Arabidopsis plants produced more SA content than Col-0 plants, and increased the expression levels of some defense-responsive genes compared to Col-0 plants. Moreover, the ZmNBS42-OE Arabidopsis plants displayed enhanced resistance against Pseudomonas syringae pathovar tomato DC3000 (Pst DC3000). These results together suggest that ZmNBS42 can serve as an important regulator in disease resistance, thus better understanding of ZmNBS42 would benefit the resistance enhancement in maize breeding programs.

The Maize NBS-LRR Gene ZmNBS25 Enhances Disease Resistance in Rice and Arabidopsis

Nucleotide-binding site-leucine-rich repeat (NBS-LRR) domain proteins are immune sensors and play critical roles in plant disease resistance. In this study, we cloned and characterized a novel NBS-LRR gene ZmNBS25 in maize. We found that ZmNBS25 could response to pathogen inoculation and salicylic acid (SA) treatment in maize, and transient overexpression of ZmNBS25 induced a hypersensitive response in tobacco. High-performance liquid chromatography (HPLC) analysis showed that, compared to control plants, ZmNBS25 overexpression (ZmNBS25-OE) in Arabidopsis and rice resulted in higher SA levels. By triggering the expression of certain defense-responsive genes, ZmNBS25-OE enhanced the resistance of Arabidopsis and rice to Pseudomonas syringae pv. tomato DC3000 and sheath blight disease, respectively. Moreover, we found little change of grain size and 1000-grain weight between ZmNBS25-OE rice lines and controls. Together, our results suggest that ZmNBS25 can function as a disease resistance gene across different species, being a valuable candidate for engineering resistance in breeding programs.