Natural rice rhizospheric microbes suppress rice blast infections

Dihydroorotase MoPyr4 is required for development, pathogenicity, and autophagy in rice blast fungus

Dihydroorotase (DHOase) is the third enzyme in the six enzymatic reaction steps of the endogenous pyrimidine nucleotide de novo biosynthesis pathway, which is a metabolic pathway conserved in both bacteria and eukaryotes. However, research on the biological function of DHOase in plant pathogenic fungi is very limited. In this study, we identified and named MoPyr4, a homologous protein of Saccharomyces cerevisiae DHOase Ura4, in the rice blast fungus Magnaporthe oryzae and investigated its ability to regulate fungal growth, pathogenicity, and autophagy. Deletion of MoPYR4 led to defects in growth, conidiation, appressorium formation, the transfer and degradation of glycogen and lipid droplets, appressorium turgor accumulation, and invasive hypha expansion in M. oryzae, which eventually resulted in weakened fungal pathogenicity. Long-term replenishment of exogenous uridine-5'-phosphate (UMP) can effectively restore the phenotype and virulence of the ΔMopyr4 mutant. Further study revealed that MoPyr4 also participated in the regulation of the Pmk1-MAPK signaling pathway, co-localized with peroxisomes for the oxidative stress response, and was involved in the regulation of the Osm1-MAPK signaling pathway in response to hyperosmotic stress. In addition, MoPyr4 interacted with MoAtg5, the core protein involved in autophagy, and positively regulated autophagic degradation. Taken together, our results suggested that MoPyr4 for UMP biosynthesis was crucial for the development and pathogenicity of M. oryzae. We also revealed that MoPyr4 played an essential role in the external stress response and pathogenic mechanism through participation in the Pmk1-MAPK signaling pathway, peroxisome-related oxidative stress response mechanism, the Osm1-MAPK signaling pathway and the autophagy pathway.

Risk assessment of pesticide compounds: IPT and TCZ cause hepatotoxicity, activate stress pathway and affect the composition of intestinal flora in red swamp crayfish (Procambarusclarkii)

Isoprothiolane (IPT) and tricyclazole (TCZ) are widely used in rice farming and recently in combined rice-fish farming. However, co-cultured animals are affected by these pesticides. To investigate the organismal effects and toxicity of pesticides, crayfish were exposed to 0, 1, 10, or 100 ppt TCZ or IPT for 7 days. Pesticide bioaccumulation, survival rate, metabolic parameters, structure of intestinal flora, and antioxidant-, apoptosis-, and HSP-related gene expression were determined. Pesticide exposure caused bioaccumulation of IPT or TCZ in the hepatopancreas and muscles of crayfish; however, IPT bioaccumulation was higher than that of TCZ. Both groups showed significant changes in hepatopancreatic serum biochemical parameters. Mitochondrial damage and chromosomal agglutination were observed in hepatopancreatic cells exposed to 100 ppt IPT or TCZ. IPT induced more significant changes in serum biochemical parameters than TCZ. The results of intestinal flora showed that Vibro, Flavobacterium, Anaerorhabdus and Shewanella may have potential for use as a bacterial marker of TCZ and IPT. Antioxidant-, apoptosis-, and HSP-related gene expression was disrupted by pesticide exposure, and was more seriously affected by IPT. The results suggest that IPT or TCZ induce hepatopancreatic cell toxicity; however, IPT or TCZ content in dietary crayfish exposed to 1 ppt was below the food safety residue standard. The data indicated that IPT exposure may be more toxic than TCZ exposure in hepatopancreas and intestines and toxicity of organism are alleviated by activating the pathway of stress-response, providing an understanding of pesticide compounds in rice-fish farming and food safety.

Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach

Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.

Pontibacter kalidii sp. nov., isolated from rhizosphere soil of Kalidium foliatum

A Gram-negative, aerobic, gliding motile, rod-shaped bacterium, designated XAAS-72T, was isolated from the rhizosphere soil of Kalidium foliatum sampled in the Xinjiang Uyghur Autonomous Region, PR China. Cells grew at 4-45 °C, pH 5.0-8.0 and 0-8% NaCl, with optimal growth at 20-30 °C, pH 6.0-7.0 and 1-2 % NaCl. Strain XAAS-72T is closely related to members of the genus Pontibacter, namely Pontibacter korlensis CCTCC AB 206081T (97.6%) and Pontibacter flavimaris ACCC 19859T (97.2 %), and <94.6 % related to other currently described Pontibacter strains. The average nucleotide identity values between XAAS-72T and P. korlensis CCTCC AB 206081T and P. flavimaris ACCC 19859T were 77.9 and 86.9 %, respectively; the corresponding digital DNA-DNA hybridization values were 21.7 and 31.8 %. Menaquinone-7 was the predominant respiratory menaquinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified glycolipids and five unidentified lipids. The major cellular fatty acids were summed feature 4 (containing iso-C17 : 1 I/anteiso-C17 : 1 B), summed feature 3 (containing C16 : 1  ω7c/C16 : 1  ω6c) and iso-C15 : 0. The genome length of strain XAAS-72T was 5 054 860 bp with a genomic DNA G+C content of 54.5 mol%. The phenotypic and genotypic data suggest that strain XAAS-72T represents a novel species of the genus Pontibacter, for which the name Pontibacter kalidii sp. nov. is proposed. The strain is XAAS-72T (CGMCC 16594T=KCTC 72095T).

Biocontrol of Diseases Caused by Phytophthora capsici and P. parasitica in Pepper Plants

The main objective of this study was to evaluate the ability of Trichoderma aggressivum f. europaeum, T. longibrachiatum, Paecilomyces variotii, and T. saturnisporum as biological control agents (BCAs) against diseases caused by P. capsici and P. parasitica in pepper. For this purpose, their antagonistic activities were evaluated both in vitro and in vivo. We analysed the expression patterns of five defence related genes, CaBGLU, CaRGA1, CaBPR1, CaPTI1, and CaSAR8.2, in leaves. All BCAs showed a high in vitro antagonistic activity, significantly reducing the mycelial growth of P. capsici and P. parasitica. The treatments with T. aggressivum f. europaeum, T. longibrachiatum, and P. variotii substantially reduced the severity of the disease caused by P. capsici by 54, 76, and 70%, respectively, and of the disease caused by P. parasitica by 66, 55, and 64%, respectively. T. saturnisporum had the lowest values of disease reduction. Reinoculation with the four BCAs increased the control of both plant pathogens. Markedly different expression patterns were observed in the genes CaBGLU, CaRGA1, and CaSAR8.2. Based on the results, all four BCAs under study could be used as a biological alternative to chemicals for the control of P. capsici and P. parasitica in pepper with a high success rate.

Oxidative Status of Medicago truncatula Seedlings after Inoculation with Rhizobacteria of the Genus Pseudomonas, Paenibacillus and Sinorhizobium

An increasing number of scientists working to raise agricultural productivity see the potential in the roots and the soil adjacent to them, together with a wealth of micro-organisms. The first mechanisms activated in the plant during any abiotic or biotic stress concern changes in the oxidative status of the plant. With this in mind, for the first time, an attempt was made to check whether the inoculation of seedlings of the model plant Medicago truncatula with rhizobacteria belonging to the genus Pseudomonas (P. brassicacearum KK5, P. corrugata KK7), Paenibacillus borealis KK4 and a symbiotic strain Sinorhizobium meliloti KK13 would change the oxidative status in the days following inoculation. Initially, an increase in H₂O₂ synthesis was observed, which led to an increase in the activity of antioxidant enzymes responsible for regulating hydrogen peroxide levels. The main enzyme involved in the reduction of H₂O₂ content in the roots was catalase. The observed changes indicate the possibility of using the applied rhizobacteria to induce processes related to plant resistance and thus to ensure protection against environmental stress factors. In the next stages, it seems reasonable to check whether the initial changes in the oxidative state affect the activation of other pathways related to plant immunity.

Impacts of Binary Oxide Nanoparticles on the Soybean Plant and Its Rhizosphere, Associated Phytohormones, and Enzymes

The utilization of binary oxide nanoparticles is geometrically increasing due to their numerous applications. Their intentional or accidental release after usage has led to their omnipresence in the environment. The usage of sludge or fertilizer containing binary oxide nanoparticles is likely to increase the chance of the plants being exposed to these binary oxide nanoparticles. The aim of the present review is to assess the detailed positive and negative impacts of these oxide nanoparticles on the soybean plants and its rhizosphere. In this study, methods of synthesizing binary oxide nanoparticles, as well as the merits and demerits of these methods, are discussed. Furthermore, various methods of characterizing the binary oxide nanoparticles in the tissues of soybean are highlighted. These characterization techniques help to track the nanoparticles inside the soybean plant. In addition, the assessment of rhizosphere microbial communities of soybean that have been exposed to these binary oxide nanoparticles is discussed. The impacts of binary oxide nanoparticles on the leaf, stem, root, seeds, and rhizosphere of soybean plant are comprehensively discussed. The impacts of binary oxides on the bioactive compounds such as phytohormones are also highlighted. Overall, it was observed that the impacts of the oxide nanoparticles on the soybean, rhizosphere, and bioactive compounds were dose-dependent. Lastly, the way forward on research involving the interactions of binary oxide nanoparticles and soybean plants is suggested.

Regulatory strategies for inhibiting horizontal gene transfer of ARGs in paddy and dryland soil through computer-based methods

Antibiotic resistance genes (ARGs) have been regarded as emerging pollutants due to their potential risk of resistance. Horizontal gene transfer (HGT) is the main pathway for ARGs to lead to environmental threats. Therefore, the inhabitation of ARGs' HGT can effectively inhibit ARGs' potential drug resistance risk within a single strain. In this paper, the characteristics of ARGs' HGT in paddy and dryland soils were identified and regulated by a combination of ARGs' HGT feature identification, transfer mechanism analysis and transfer process regulation. The homology modeling algorithm was used to simulate the construction of the Tn5 plasmid transposase of Escherichia coli (E. coli) for identifying ARGs' HGT characteristics. The GCG (212.617 Å) was thus determined as the target codon. Through integrated computer-based methods, results showed that the most important environmental disturbance factors for the HGT of ARGs in the paddy and dryland soils were rough farmyard manure/sewage irrigation and mining pollution, respectively. Under the disturbance of key environmental factors, the inhibitory effect of HGT of ARGs in paddy and dryland soil was reduced by 35.01 % and 34.74 %, respectively. Results demonstrated that the proposed theoretical mechanism and control strategies could effectively inhibit the HGT of E. coli ARGs in the soil environment.

The power of the smallest: The inhibitory activity of microbial volatile organic compounds against phytopathogens

Plant diseases caused by phytopathogens result in huge economic losses in agriculture. In addition, the use of chemical products to control such diseases causes many problems to the environment and to human health. However, some bacteria and fungi have a mutualistic relationship with plants in nature, mainly exchanging nutrients and protection. Thus, exploring those beneficial microorganisms has been an interesting and promising alternative for mitigating the use of agrochemicals and, consequently, achieving a more sustainable agriculture. Microorganisms are able to produce and excrete several metabolites, but volatile organic compounds (VOCs) have huge biotechnology potential. Microbial VOCs are small molecules from different chemical classes, such as alkenes, alcohols, ketones, organic acids, terpenes, benzenoids and pyrazines. Interestingly, volatilomes are species-specific and also change according to microbial growth conditions. The interaction of VOCs with other organisms, such as plants, insects, and other bacteria and fungi, can cause a wide range of effects. In this review, we show that a large variety of plant pathogens are inhibited by microbial VOCs with a focus on the in vitro and in vivo inhibition of phytopathogens of greater scientific and economic importance in agriculture, such as Ralstonia solanacearum, Botrytis cinerea, Xanthomonas and Fusarium species. In this scenario, some genera of VOC-producing microorganisms stand out as antagonists, including Bacillus, Pseudomonas, Serratia and Streptomyces. We also highlight the known molecular and physiological mechanisms by which VOCs inhibit the growth of phytopathogens. Microbial VOCs can provoke many changes in these microorganisms, such as vacuolization, fungal hyphal rupture, loss of intracellular components, regulation of metabolism and pathogenicity genes, plus the expression of proteins important in the host response. Furthermore, we demonstrate that there are aspects to investigate by discussing questions that are still not very clear in this research area, especially those that are essential for the future use of such beneficial microorganisms as biocontrol products in field crops. Therefore, we bring to light the great biotechnological potential of VOCs to help make agriculture more sustainable.

Bio-Functionalized Manganese Nanoparticles Suppress Fusarium Wilt in Watermelon (Citrullus lanatus L.) by Infection Disruption, Host Defense Response Potentiation, and Soil Microbial Community Modulation

The use of nanofabricated materials is being explored for the potential in crop disease management. Chemically synthesized micronutrient nanoparticles (NPs) have been shown to reduce crop diseases; however, the potential of biogenic manganese NPs (bio-MnNPs) in disease control is unknown. Here, the potential and mechanism of bio-MnNPs in suppression of watermelon Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon) are reported. Bio-MnNPs are synthesized by cell-free cultural filtrate of a waterrmelon rhizosphere bacterial strain Bacillus megaterium NOM14, and are found spherical in shape with a size range of 27.0-65.7 nm. Application of bio-MnNPs at 100 µg mL^-1 increases Mn content in watermelon roots/shoots and improves growth performance through enhancing multiple physiological processes, including antioxidative capacity. Bio-MnNPs at 100 µg mL^-1 suppress Fusarium wilt through inhibiting colonization and invasive growth of Fon in watermelon roots/stems, and inhibit Fon vegetative growth, conidiation, conidial morphology, and cellular integrity. Bio-MnNPs potentiate watermelon systemic acquired resistance by triggering the salicylic acid signaling upon Fon infection, and reshape the soil microbial community by improving fungal diversity. These findings demonstrate that bio-MnNPs suppress watermelon Fusarium wilt by multiple ex planta and in planta mechanisms, and offer a promising nano-enabled strategy for the sustainable management of crop diseases.

Piper caninum extract and Brevibacillus agri mixture suppresses rice leaf spot pathogen; Nigrospora oryzae and improves the production of red rice (Oryza sativa L)

Under the guise of enhancing productivity, using pesticides and artificial fertilizers in agriculture affects both the environment and living things. High chemical residues in food and the environment disrupt the health of consumers. One of the solutions that can bring about a reduction in the use of pesticides and chemicals is switching to organic fertilizers. The application of biopesticides originating from biological sources such as plant extracts and the use of microbes is gaining global acceptance. Therefore, this study aimed to obtain the best biopesticides and biostimulants that could suppress the leaf spot pathogen, Nigrospora oryzae, and increase the growth and yield of Bali red rice. The study contained four treatments, namely untreated control (F0), Piper caninum leaf extract (F1), Brevibacillus agri (F2), and fermented P. caninum leaf extract plus B. agri (F3). The treatments were arranged in a randomized complete block design, and each treatment was replicated three times. The parameters measured were the number of tillers per plant, number of leafs per plant, chlorophyll content, number of grains per panicle, grain weight, and grain yield. Furthermore, antimicrobial and antioxidants were assayed using SEM. GC-MS. At the end of the experiment, the disease index of the leaf spot was measured. The results showed that F3 significantly suppressed leaf spots caused by N. oryzae compared to other treatments, including untreated control in red rice. Additionally, the F3 significantly increased the number of productive tillers, number of grains per panicle, and grain yield compared to all other treatments. The F3 enhanced the crop yield at 6.19 tons/ha, an increase of 50% compared to the untreated control. The SEM.GC-MS results showed the presence of 2.3 butanediol, tetra-decanoic acid, butanoic acid, ethyl ester, benzene propanal, 3-(1,1-dimethylethyl)-a-methyl, a-N-Normethadol in treated plants with P. canicum plus B. agri.

Phytoremediation potential of Gossypium hirsutum on abandoned polluted chromium sludge soil with the amalgamation of Streptomyces tritici D5

The phytoremediation potency of Gossypium hirsutum was explored in this research under the influence of pre-identified metal tolerant Streptomyces tritici D5 in Cr enriched sludge soil using various treatment sets (I to V) in a greenhouse setting. Interestingly, the G. hirsutum remarkable remediate the Cr metal from the Cr enriched sludge soil under diluted (50:50) condition in 90 days of greenhouse experiment. The S. tritici D5 also effectively support the growth and phytoremediation competence of G. hirsutum. This was evidenced by the under the diluted (set III) condition the growth and major biomolecules such as protein, carbohydrate, and chlorophyll content of G. hirsutum were considerably increased in quantity. Hence, the phytoremediation potential of G. hirsutum was effective at soil diluted with fertile and xenobiotics free soil with dilution ratio of 50:50 (set III) and followed by 75:25 (set II) ratio. Thus, under diluted conditions (50:50) G. hirsutum seed coated with S. tritici D5 showed an outstanding phytoremediation process. Therefore, this method can be implemented to the field level study to assess the metal removal prospects of this environmentally friendly method.

Reconstruction of a Soil Microbial Network Induced by Stress Temperature

The microbial community is viewed as a network of diverse microorganisms connected by various interspecific interactions. While the stress gradient hypothesis (SGH) predicts that positive interactions are favored in more stressful environments, the prediction has been less explored in complex microbial communities due to the challenges of identifying interactions. Here, by applying a nonlinear time series analysis to the amplicon-based diversity time series data of the soil microbiota cultured under less stressful (30°C) or more stressful (37°C) temperature conditions, we show how the microbial network responds to temperature stress. While the genera that persisted only under the less stressful condition showed fewer positive effects, the genera that appeared only under the more stressful condition received more positive effects, in agreement with SGH. However, temperature difference also induced reconstruction of the community network, leading to an increased proportion of negative interactions at the whole-community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities. IMPORTANCE By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.

Beneficial Effect and Potential Risk of Pantoea on Rice Production

Bacteria from the genus Pantoea have been reported to be widely distributed in rice paddy environments with contradictory roles. Some strains promoted rice growth and protected rice from pathogen infection or abiotic stress, but other strain exhibited virulence to rice, even causing severe rice disease. In order to effectively utilize Pantoea in rice production, this paper analyzed the mechanisms underlying beneficial and harmful effects of Pantoea on rice growth. The beneficial effect of Pantoea on rice plants includes growth promotion, abiotic alleviation and disease inhibition. The growth promotion may be mainly attributed to nitrogen-fixation, phosphate solubilization, plant physiological change, the biosynthesis of siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylic acid deaminase and phytohormones, including cytokinin, indole-3-acetic acid (IAA), auxins, abscisic acid and gibberellic acid, while the disease inhibition may be mainly due to the induced resistance, nutrient and spatial competition, as well as the production of a variety of antibiotics. The pathogenic mechanism of Pantoea can be mainly attributed to bacterial motility, production of phytohormones such as IAA, quorum sensing-related signal molecules and a series of cell wall-degrading enzymes, while the pathogenicity-related genes of Pantoea include genes encoding plasmids, such as the pPATH plasmid, the hypersensitive response and pathogenicity system, as well as various types of secretion systems, such as T3SS and T6SS. In addition, the existing scientific problems in this field were discussed and future research prospects were proposed.

Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa

The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal–Wallis test was used to test samples’ diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.

Biocontrol of Wilt disease of rice seedlings incited by Fusarium oxysporum through soil application of Streptomyces chilikensis RC1830

The genus Streptomyces includes many antifungal metabolite producing novel strains. Fusarium oxysporum a soil-inhabiting pathogenic fungi, that affects rice to cause wilt disease. This work demonstrates the efficacy of novel Streptomyces chilikensis strain RC1830, previously isolated from estuarine habitat Chilika Lake in preventing the F. oxysporum wilting/root rot disease and promoting the growth of rice (Var. Swarna) seedlings. A total of 25 different compounds were identified from crude extracts of S. chilikensis RC1830 by GC-MS. In pot trial experiments, Streptomyces treated rice seedlings showed significantly reduced Disease severity index (DSI) by 80.51%. The seedlings growth parameters (root length, root fresh weight and root dry weight )were also increased by 53.91%, 62.5%, 73.46% respectively in Streptomyces treated groups of seedlings compared to Fusarium infected seedlings. Similarly, the shoot length, shoot dry weight and shoot fresh weight were also increased by 26%, 58% and 34.4% respectively in Streptomyces treated groups of seedlings compared to Fusarium infected seedlings. Formulations of the strain were prepared using seven organic & inorganic wastes as the carrier material and the shelf lives of the propagules were also monitored. Vermiculite and activated charcoal formulations stored at 4°C exhibited a higher viable cell count after 3 months of storage.

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs. rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications.

The influence of endophytes on rice fitness under environmental stresses

KEY MESSAGE

Endophytes are crucial for the promotion of rice growth and stress tolerance and can be used to increase rice crop yield. Endophytes can thus be exploited in biotechnology and genetic engineering as eco-friendly and cost-effective means for the development of high-yielding and stress-tolerant rice plants. Rice (Oryza sativa) crop is continuously subjected to biotic and abiotic stresses, compromising growth and consequently yield. The situation is exacerbated by climate change impacting on ecosystems and biodiversity. Genetic engineering has been used to develop stress-tolerant rice, alongside physical and chemical methods to mitigate the effect of these stresses. However, the success of these strategies has been hindered by short-lived field success and public concern on adverse effects associated. The limited success in the field of stress-tolerant cultivars developed through breeding or transgenic approaches is due to the complex nature of stress tolerance as well as to the resistance breakdown caused by accelerated evolution of pathogens. It is therefore necessary to develop novel and acceptable strategies to enhance rice stress tolerance and durable resistance and consequently improve yield. In the last decade, plant growth promoting (PGP) microbes, especially endophytes, have drawn the attention of agricultural scientists worldwide, due to their ability to mitigate environmental stresses in crops, without causing adverse effects. Increasing evidence indicates that endophytes effectively confer fitness benefits also to rice under biotic and abiotic stress conditions. Endophyte-produced metabolites can control the expression of stress-responsive genes and improve the physiological performance and growth of rice plants. This review highlights the current evidence available for PGP microbe-promoted tolerance of rice to abiotic stresses such as salinity and drought and to biotic ones, with special emphasis on endophytes. Associated molecular mechanisms are illustrated, and prospects for sustainable rice production also in the light of the impending climate change, discussed.

Multi-Omics Techniques for Analysis Antifungal Mechanisms of Lipopeptides Produced by Bacillus velezensis GS-1 against Magnaporthe oryzae In Vitro

Magnaporthe oryzae is a fungal pathogen that causes rice blast, a highly destructive disease. In the present study, the bacteria strain GS-1 was isolated from the rhizosphere soil of ginseng and identified as Bacillus velezensis through 16S rRNA gene sequencing, whole genome assembly, and average nucleotide identity analysis. B. velezensis strain GS-1 exhibited significant antagonistic activity to several plant fungal pathogens. Through whole genome sequencing, 92 Carbohydrate-Active Enzymes and 13 gene clusters that encoded for secondary metabolites were identified. In addition, strain GS-1 was able to produce the lipopeptide compounds, surfactin, fengycin, and plantazolicin. The inhibitory effects of lipopeptide compounds on M. oryzae were confirmed, and the antagonistic mechanism was explored using transcriptomics and metabolomics analysis. Differential expressed genes (DEGs) and differential accumulated metabolites (DAMs) revealed that the inhibition of M. oryzae by lipopeptide produced by GS-1 downregulated the expression of genes involved in amino acid metabolism, sugar metabolism, oxidative phosphorylation, and autophagy. These results may explain why GS-1 has antagonistic activity to fungal pathogens and revealed the mechanisms underlying the inhibitory effects of lipopeptides produced by GS-1 on fungal growth, which may provide a theoretical basis for the potential application of B. velezensis GS-1 in future plant protection.

Phosphorylation of CAD1, PLDdelta, NDT1, RPM1 Proteins Induce Resistance in Tomatoes Infected by Ralstonia solanacearum

Ralstonia solanacaerum is one of the most devastating bacteria causing bacterial wilt disease in more than 200 species of plants, especially those belonging to the family Solanaceae. To cope with this pathogen, plants have evolved different resistance mechanisms depending on signal transduction after perception. Phosphorylation is the central regulatory component of the signal transduction pathway. We investigated a comparative phosphoproteomics analysis of the stems of resistant and susceptible tomatoes at 15 min and 30 min after inoculation with Ralstonia solanacearum to determine the phosphorylated proteins involved in induced resistance. Phosphoprotein profiling analyses led to the identification of 969 phosphoproteins classified into 10 functional categories. Among these, six phosphoproteins were uniquely identified in resistant plants including cinnamyl alcohol dehydrogenase 1 (CAD1), mitogen-activated protein kinase kinase kinase 18 (MAPKKK18), phospholipase D delta (PLDDELTA), nicotinamide adenine dinucleotide transporter 1 (NDT1), B3 domain-containing transcription factor VRN1, and disease resistance protein RPM1 (RPM1). These proteins are typically involved in defense mechanisms across different plant species. qRT-PCR analyses were performed to evaluate the level of expression of these genes in resistant and susceptible tomatoes. This study provides useful data, leading to an understanding of the early defense mechanisms of tomatoes against R. solanacearum.

Quantitative detection of induced systemic resistance genes of potato roots upon ethylene treatment and cyst nematode, Globodera rostochiensis, infection during plant–nematode interactions

Potato cyst nematodes caused by Globodera rostochiensis, are quarantine-restricted pests causing significant yield losses to potato growers. The phytohormone ethylene play significant roles in various plant-pathogen interactions, however, the molecular knowledge of how ethylene influences potato–nematode interaction is still lacking. Precise detection of potato-induced genes is essential for recognizing plant-induced systemic resistance (ISR). Candidate genes or PR- proteins with putative functions in modulating the response to potato cyst nematode stress were selected and functionally characterized. Using real-time polymerase chain reaction (RT-PCR), we measured the quantified expression of four pathogenesis-related (PR) genes, PR2, PR3, peroxidase, and polyphenol oxidase. The activation of these genes is intermediate during the ISR signaling in the root tissues. Using different ethylene concentrations could detect and induce defense genes in infected potato roots compared to the control treatment. The observed differences in the gene expression of treated infected plants are because of different concentrations of ethylene treatment and pathogenicity. Besides, the overexpressed or suppressed of defense- related genes during developmental stages and pathogen infection. We concluded that ethylene treatments positively affected potato defensive genes expression levels against cyst nematode infection. The results emphasize the necessity of studying molecular signaling pathways controlling biotic stress responses. Understanding such mechanisms will be critical for the development of broad-spectrum and stress-tolerant crops in the future.

Improving crop drought resistance with plant growth regulators and rhizobacteria: Mechanisms, applications, and perspectives

Drought is one of the main abiotic stresses that cause crop yield loss. Improving crop yield under drought stress is a major goal of crop breeding, as it is critical to food security. The mechanism of plant drought resistance has been well studied, and diverse drought resistance genes have been identified in recent years, but transferring this knowledge from the laboratory to field production remains a significant challenge. Recently, some new strategies have become research frontiers owing to their advantages of low cost, convenience, strong field operability, and/or environmental friendliness. Exogenous plant growth regulator (PGR) treatment and microbe-based plant biotechnology have been used to effectively improve crop drought tolerance and preserve yield under drought stress. However, our understanding of the mechanisms by which PGRs regulate plant drought resistance and of plant-microbiome interactions under drought is still incomplete. In this review, we summarize these two strategies reported in recent studies, focusing on the mechanisms by which these exogenous treatments regulate crop drought resistance. Finally, future challenges and directions in crop drought resistance breeding are discussed.

Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity

Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host-microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy-molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant-pathogen interactions and in the enhancement of plant innate immunity.

Combination of Strobilurin and Triazole Chemicals for the Management of Blast Disease in Mushk Budji -Aromatic Rice

Rice blast is considered one of the most important fungal diseases of rice. Although diseases can be managed by using resistant cultivars, the blast pathogen has successfully overcome the single gene resistance in a short period and rendered several varieties susceptible to blast which were otherwise intended to be resistant. As such, chemical control is still the most efficient method of disease control for reducing the losses caused due to diseases. Field experiments were conducted over two successive years, 2018 and 2019, in temperate rice growing areas in northern India. All the fungicides effectively reduced leaf blast incidence and intensity, and neck blast incidence under field conditions. Tricyclazole proved most effective against rice blast and recorded a leaf blast incidence of only 8.41%. Among the combinations of fungicides, azoxystrobin + difenoconazole and azoxystrobin + tebuconazole were highly effective, recording a leaf blast incidence of 9.19 and 10.40%, respectively. The chemical combination mancozeb + carbendazim proved less effective in controlling the blast and it recorded a disease incidence of 27.61%. A similar trend was followed in neck blast incidence with tricyclazole, azoxystrobin + difenoconazole, and azoxystrobin + tebuconazole showing the highest levels of blast reductions. It is evident from the current study that the tested fungicide combinations can be used as alternatives to tricyclazole which is facing the challenges of fungicide resistance development and other environmental concerns and has been banned from use in India and other countries. The manuscript may provide a guideline of fungicide application to farmers cultivating susceptible varieties of rice.

Pharmacological properties of biogenically synthesized silver nanoparticles using endophyte Bacillus cereus extract of Berberis lyceum against oxidative stress and pathogenic multidrug-resistant bacteria

The emergence of multidrug resistance in pathogenic bacteria limits the utilization of available antibiotics. The development of alternate options to treat infectious diseases is the need of the day.The present study was aimed to synthesize, characterize and evaluate the bioactive properties of silver nanoparticles. Endophytic bacterium Bacillus cereus (MT193718) isolated from Berberis lycium was used to synthesize biocompatible silver nanoparticles. Antibacterial properties of AgNPs were evaluated against clinically isolated multidrug-resistant strains of Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae. AgNPs indicated significant antibacterial activity against S. aureus and K. pneumoniae fwith a zone of inhibition of 17 and 18 mm at a concentration of 1000 µg/ mL with minimum inhibitory concentration of 15.6 and 62.5 µg/mL respectively. Significant antioxidant activity with an IC50 value of 9.5 µg/mL was recorded. Biosynthesized AgNPs were found compatible with red blood cells at a concentration of 31.5 µg/ml with no clumping of erythrocytes. The study suggested that AgNPs synthesized by the endophytic bacterium Bacillus cereus are biologically active and can be used as antioxidant and antibacterial agents against drug-resistant bacteria.

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

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

Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer

Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO₃⁻/NH₄⁺ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.

Biological and biorational management of blast diseases in cereals caused by Magnaporthe oryzae

Blast diseases, caused by the fungal pathogen Magnaporthe oryzae, are among the most destructive diseases that occur on at least 50 species of grasses, including cultivated cereals wheat, and rice. Although fungicidal control of blast diseases has widely been researched, development of resistance of the pathogen against commercially available products makes this approach unreliable. Novel approaches such as the application of biopesticides against the blast fungus are needed for sustainable management of this economically important disease. Antagonistic microorganisms, such as fungi and probiotic bacteria from diverse taxonomic genera were found to suppress blast fungi both in vitro and in vivo. Various classes of secondary metabolites, such as alkaloids, phenolics, and terpenoids of plant and microbial origin significantly inhibit fungal growth and may also be effective in managing blast diseases. Common modes of action of microbial biocontrol agents include: antibiosis, production of lytic enzymes, induction of systemic resistance in host plant, and competition for nutrients or space. However, the precise mechanism of biocontrol of the blast fungus by antagonistic microorganisms and/or their bioactive secondary metabolites is not well understood. Commercial formulations of biocontrol agents and bioactive natural products could be cost-effective and sustainable but their availability at this time is extremely limited. This review updates our knowledge on the infection pathway of the wheat blast fungus, catalogs naturally occurring biocontrol agents that may be effective against blast diseases, and discusses their role in sustainable management of the disease.

Rice Blast Lesions: an Unexplored Phyllosphere Microhabitat for Novel Antagonistic Bacterial Species Against Magnaporthe oryzae

Dark brown necrotic lesions caused by Magnaporthe oryzae on rice foliage is a contrasting microhabitat for leaf-colonizing microbiome as compared with the surrounding healthy chlorophyll-rich tissues. We explored culturable bacterial communities of blast lesions by adopting microbiological tools for isolating effective biocontrol bacterial strains against M. oryzae. 16S rRNA gene sequencing-based molecular identification revealed a total of 17 bacterial species belonging to Achromobacter (2), Comamonas (1), Curtobacterium (1), Enterobacter (1), Leclercia (2), Microbacterium (1), Pantoea (3), Sphingobacterium (1), and Stenotrophomonas (5) found colonizing the lesion. Over 50% of the bacterial isolates were able to suppress the mycelial growth of M. oryzae either by secretory or volatile metabolites. Volatiles released by Achromobacter sp., Curtobacterium luteum, Microbacterium oleivorans, Pantoea ananatis, Stenotrophomonas maltophilia, and Stenotrophomonas sp., and were found to be fungicidal while others showed fungistatic action. In planta pathogen challenged evaluation trial revealed the biocontrol potential of Stenotrophomonas sp. and Microbacterium oleivorans that showed over 60% blast severity suppression on the rice leaf. The lesion-associated bacterial isolates were found to trigger expression of defense genes such as OsCEBiP, OsCERK1, OsEDS1, and OsPAD4 indicating their capability to elicit innate defense in rice against blast disease. The investigation culminated in the identification of potential biocontrol agents for the management of rice blast disease.

Rhizospheric bacterial community structure of Triticum and Aegilops revealed by pyrosequencing analysis of the 16S rRNA gene: dominance of the A genome over the B and D genomes

This study examined the relationship between host plant and rhizospheric bacterial community structure, including composition and diversity, in Triticum and Aegilops species (12 and two accessions, respectively) as well as three closely related species, barley, rye and oat (four accessions), to explore the possibility that wheat root and rhizosphere interaction can be utilized for wheat breeding and biotechnology in the future. For this purpose, DNA was isolated from rhizospheric soil samples and one control non-rhizospheric soil sample, and the 16S rRNA gene region was amplified and subjected to DNA pyrosequencing. A total of 132,888 amplicons were analyzed. Bacterial composition at the phylum level was similar among the 18 rhizospheric samples; however, the proportion of Acidobacteria was much lower in these samples than in the control non-rhizospheric soil sample, indicating that rhizospheres influenced the bacterial composition even at the higher taxonomic level. Across host plant genome types (three levels of ploidy and three major genomes, A, B and D), there was no detectable difference in phylum composition or species diversity. Estimated bacterial species diversity was higher in the control soil sample than in plant rhizospheric soils, implying that bacterial species diversity was reduced in rhizospheres. A PCoA plot and UPGMA dendrogram based on the bacterial species composition showed that control soil was distantly located from the plant rhizospheric samples and that Triticum, Aegilops and related species were well separated. PERMANOVA analysis detected statistically significant differentiation among these four groups. Clustering of Triticum species suggested that the A genome was dominant over the B and D genomes, with respect to the influence on rhizospheric bacterial species composition. Although the cause was not investigated in this study, these results clearly indicated that the genetic constitution of the plant host exerted a strong influence on rhizospheric bacterial community structure.

A Mixture of Piper Leaves Extracts and Rhizobacteria for Sustainable Plant Growth Promotion and Bio-Control of Blast Pathogen of Organic Bali Rice

Rice is a crop that is consumed as a staple food by the majority of the people in the world and therefore failure in rice crops, due to any reason, poses a severe threat of starvation. Rice blast, caused by a fungus Pyricularia oryzae, has been ranked among the most threatening plant diseases of rice and it is found wherever rice is grown. All of the rice blast disease management strategies employed so far have had limited success and rice blast has never been eliminated from rice fields. Hence, there is a need to look for the best remedy in terms of effectiveness, sustainability, and organic nature of the method. This study was aimed at determining the plant growth-promoting and fungicidal effects of a mixture of Piper caninum and Piper betle var. Nigra leaves extracts and rhizobacteria. Gas chromatography–mass spectrophotometry (GC-MS) analysis of a mixture of leaves extracts of these plants revealed the presence of new bioactive compounds such as alpha.-gurjunene, gamma.-terpinene, and ethyl 5-formyl 3-(2-ethoxycarbonyl) in a mixture of leaves extracts of P. caninum and P. betle var. Nigra. The mixture of these extracts reduced the intensity of blast disease, inhibited P. oryzae, and improved the growth, yield, and quality of Bali rice. All treatments comprising of different concentrations of a mixture of leaves extracts of P. caninum and P. betle var. Nigra plus rhizobacteria exhibited biocontrol and bioefficacy. However, a 2% concentration of a mixture of these leaves extracts with plant growth-promoting rhizobacteria (PGPR) exhibited potent inhibition of growth of P. oryzae, a significant reduction in the intensity of blast disease, and a maximum increase in growth, yield, and quality of Bali rice. In the 15th week, the intensity of blast disease decreased from 80.18% to 7.90%. The mixture of leaves extract + PGPR also improved the height of the plant, the number of tillers, number of leaves, number of grains per panicle, number of heads per panicle, and the full-grain weight per clump. Applications of various concentrations of a mixture of leaves extracts + PGPR resulted in improvement in the potential yield of rice, however, the application of 2% extracts + PGPR gave the highest potential yield of 5.61 tha−1 compared to the low yields in the control and other treatments. The high grain yield observed with the treatment was caused by the low intensity of blast disease. This treatment also strengthened the stem and prevented the drooping of the plant and improved the quality of rice grain.

Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

BACKGROUND

The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions.

FINDINGS

By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial "hubs" and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities.

CONCLUSION

We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

Population Structure and Genetic Diversity of Fungi Causing Rice Seedling Blight in Northeast China Based on Microsatellite Markers

Rice seedling blight, which is caused by diverse pathogenic microorganisms, occurs worldwide and is the most important seedling disease affecting rice production in Northeast China. To further characterize the population structure and genetic diversity of the fungi responsible for rice seedling blight in Northeast China, 225 fungal strains were isolated from diseased rice seedlings collected from various rice-producing areas. The isolated strains included Fusarium oxysporum (48.0%), F. verticillioides (11.6%), F. tricinctum (8.0%), F. redolens (6.7%), F. equiseti (6.2%), F. solani (6.2%), Rhizoctonia solani (6.7%), Alternaria alternata (4.0%), and Curvularia coatesiae (2.7%). F. oxysporum was the dominant fungal species causing rice seedling blight, with most isolates exhibiting moderate pathogenicity. Moreover, to our knowledge, this is the first study to identify A. alternata and C. coatesiae as causal agents of rice seedling blight in Northeast China. None of the F. oxysporum isolates were sensitive to 10 μg/ml of carbendazim, implying that carbendazim is ineffective for controlling rice seedling blight in Northeast China. The F. oxysporum isolates were divided into nine groups based on a simple sequence repeat analysis involving 14 primer pairs. In addition, an analysis of molecular variance revealed a significant correlation between the F. oxysporum population and geographical location, which had a significant effect on the differentiation of the dominant isolate population. The results of this study provide insights into the genetic diversity of F. oxysporum strains causing rice seedling blight and may be useful for selecting isolates to screen for disease-resistant rice varieties, evaluating fungicide efficacy, and developing effective disease management strategies.

Isolation and Characterization of Root-Associated Bacterial Endophytes and Their Biocontrol Potential against Major Fungal Phytopathogens of Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a major cereal food crop worldwide, and its growth and yield are affected by several fungal phytopathogens, including Magnaporthe oryzae, Fusarium graminearum, F. moniliforme, and Rhizoctonia solani. In the present study, we have isolated and characterized root-associated bacterial endophytes that have antifungal activities against rice fungal phytopathogens. A total of 122 root-associated bacterial endophytes, belonging to six genera (Bacillus, Fictibacillus, Lysinibacillus, Paenibacillus, Cupriavidus, and Microbacterium) and 22 species were isolated from three rice cultivars. Furthermore, the 16S rRNA sequence-based phylogeny results revealed that Bacillus was the most dominant bacterial genera, and that there were 15 different species among the isolates. Moreover, 71 root-associated endophytes showed antagonistic effects against four major fungal phytopathogens, including M. oryzae, F. graminearum,F. moniliforme, and R. solani. Additionally, the biochemical, physiological, and PCR amplification results of the antibiotic-related genes further supported the endophytes as potential biocontrolling agents against the rice fungal pathogens. Consequently, the findings in this study suggested that the isolated bacterial endophytes might have beneficial roles in rice defense responses, including several bioactive compound syntheses. The outcomes of this study advocate the use of natural endophytes as an alternative strategy towards the rice resistance response.

Green-Synthesization of Silver Nanoparticles Using Endophytic Bacteria Isolated from Garlic and Its Antifungal Activity against Wheat Fusarium Head Blight Pathogen Fusarium Graminearum

Nanoparticles are expected to play a vital role in the management of future plant diseases, and they are expected to provide an environmentally friendly alternative to traditional synthetic fungicides. In the present study, silver nanoparticles (AgNPs) were green synthesized through the mediation by using the endophytic bacterium Pseudomonas poae strain CO, which was isolated from garlic plants (Allium sativum). Following a confirmation analysis that used UV-Vis, we examined the in vitro antifungal activity of the biosynthesized AgNPs with the size of 19.8-44.9 nm, which showed strong inhibition in the mycelium growth, spore germination, the length of the germ tubes, and the mycotoxin production of the wheat Fusarium head blight pathogen Fusarium graminearum. Furthermore, the microscopic examination showed that the morphological of mycelia had deformities and collapsed when treated with AgNPs, causing DNA and proteins to leak outside cells. The biosynthesized AgNPs with strong antifungal activity were further characterized based on analyses of X-ray diffraction, transmission electron microscopy, scanning electron microscopy, EDS profiles, and Fourier transform infrared spectroscopy. Overall, the results from this study clearly indicate that the biosynthesized AgNPs may have a great potential in protecting wheat from fungal infection.

A Bioinformatics Guide to Plant Microbiome Analysis

Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

The antifungal action mode of the rice endophyte Streptomyces hygroscopicus OsiSh-2 as a potential biocontrol agent against the rice blast pathogen

Microbial antagonists and their bioactive metabolites provide one of the best alternatives to chemical pesticides to control crop disease for sustainable agriculture and global food security. The rice endophyte Streptomyces hygroscopicus OsiSh-2, with remarkable antagonistic activity towards the rice blast fungus Magnaporthe oryzae, was reported in our previous study. The present study deciphered the possible direct interaction mode of OsiSh-2 against M. oryzae. An in vitro antibiotic assay for OsiSh-2 culture filtrate revealed strong suppression of mycelial growth, conidial germination and appressorial formation of M. oryzae. Meanwhile, severe morphological and internal abnormalities in M. oryzae hyphae were observed under a scanning electron microscope and transmission electron microscope. Foliar treatment of rice seedlings by OsiSh-2 culture filtrate in the greenhouse and in the field showed 23.5% and 28.3% disease reduction, respectively. Correspondingly, OsiSh-2 culture filtrate could induce disorganized chitin deposition in the cell wall and lowered ergosterol content in the cell membrane of M. oryzae. Additionally, cell wall integrity pathway activation, large cell electrolytes release, reactive oxygen species accumulation and tricarboxylic acid cycle-related enzyme activity changes were found in M. oryzae. All these results suggested that the direct antagonistic activity of OsiSh-2 against M. oryzae may be attributed to damaging the integrity of the cell wall and membrane and disrupting mitochondrial function in the pathogen.

Screening of the High-Rhizosphere Competent Limoniastrum monopetalum' Culturable Endophyte Microbiota Allows the Recovery of Multifaceted and Versatile Biocontrol Agents

Halophyte Limoniastrum monopetalum, an evergreen shrub inhabiting the Mediterranean region, has well-documented phytoremediation potential for metal removal from polluted sites. It is also considered to be a medicinal halophyte with potent activity against plant pathogens. Therefore, L. monopetalum may be a suitable candidate for isolating endophytic microbiota members that provide plant growth promotion (PGP) and resistance to abiotic stresses. Selected for biocontrol abilities, these endophytes may represent multifaceted and versatile biocontrol agents, combining pathogen biocontrol in addition to PGP and plant protection against abiotic stresses. In this study 117 root culturable bacterial endophytes, including Gram-positive (Bacillus and Brevibacillus), Gram-negative (Proteus, Providencia, Serratia, Pantoea, Klebsiella, Enterobacter and Pectobacterium) and actinomycete Nocardiopsis genera have been recovered from L. monopetalum. The collection exhibited high levels of biocontrol abilities against bacterial (Agrobacterium tumefaciens MAT2 and Pectobacterium carotovorum MAT3) and fungal (Alternaria alternata XSZJY-1, Rhizoctonia bataticola MAT1 and Fusarium oxysporum f. sp. radicis lycopersici FORL) pathogens. Several bacteria also showed PGP capacity and resistance to antibiotics and metals. A highly promising candidate Bacillus licheniformis LMRE 36 with high PGP, biocontrol, metal and antibiotic, resistance was subsequently tested in planta (potato and olive trees) for biocontrol of a collection of 14 highly damaging Fusarium species. LMRE 36 proved very effective against the collection in both species and against an emerging Fusarium sp. threatening olive trees culture in nurseries. These findings provide a demonstration of our pyramiding strategy. Our strategy was effective in combining desirable traits in biocontrol agents towards broad-spectrum resistance against pathogens and protection of crops from abiotic stresses. Stacking multiple desirable traits into a single biocontrol agent is achieved by first, careful selection of a host for endophytic microbiota recovery; second, stringent in vitro selection of candidates from the collection; and third, application of the selected biocontrol agents in planta experiments. That pyramiding strategy could be successfully used to mitigate effects of diverse biotic and abiotic stresses on plant growth and productivity. It is anticipated that the strategy will provide a new generation of biocontrol agents by targeting the microbiota of plants in hostile environments.

Drought tolerance improvement in plants: an endophytic bacterial approach

Climate change is a crucial issue among the serious emerging problems which got a global attention in the last few decades. With the climate change, worldwide crop production has been seriously affected by drought stress. In this regard, various technologies including traditional breeding and genetic engineering are used to cope with drought stress. However, the interactions between plants and endophytic bacteria emerged as an interesting era of knowledge that can be used for novel agriculture practices. Endophytic bacteria which survive within plant tissues are among the most appropriate technologies improving plant growth and yield under drought conditions. These endophytic bacteria live within plant tissues and release various phytochemicals that assist plant to withstand in harsh environmental conditions, i.e., drought stress. Their plant growth-promoting characteristics include nitrogen fixation, phosphate solubilization, mineral uptake, and the production of siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various phytohormones. These plant growth promoting characteristics of endophytic bacteria improve root length and density, which lead to the enhance drought tolerance. In addition, plant-endophytic bacteria assist plant to withstand against drought stress by producing drought-tolerant substances, for instance, abscisic acid, indole-3-acetic acid, ACC deaminase, and various volatile compounds. Indirectly, endophytic bacteria also improve osmotic adjustment, relative water content, and antioxidant activity of inoculated plants. Altogether, these bacterial-mediated drought tolerance and plant growth-promoting processes continue even under severe drought conditions which lead to enhanced plant growth promotion and yield. The present review highlights a natural and environment-friendly strategy in the form of drought-tolerant and plant growth-promoting endophytic bacteria to improve drought tolerance in plants.

Pseudomonas Cyclic Lipopeptides Suppress the Rice Blast Fungus Magnaporthe oryzae by Induced Resistance and Direct Antagonism

Beneficial Pseudomonas spp. produce an array of antimicrobial secondary metabolites such as cyclic lipopeptides (CLPs). We investigated the capacity of CLP-producing Pseudomonas strains and their crude CLP extracts to control rice blast caused by Magnaporthe oryzae, both in a direct manner and via induced systemic resistance (ISR). In planta biocontrol assays showed that lokisin-, white line inducing principle (WLIP)-, entolysin- and N3-producing strains successfully induced resistance to M. oryzae VT5M1. Furthermore, crude extracts of lokisin, WLIP and entolysin gave similar ISR results when tested in planta. In contrast, a xantholysin-producing strain and crude extracts of N3, xantholysin and orfamide did not induce resistance against the rice blast disease. The role of WLIP in triggering ISR was further confirmed by using WLIP-deficient mutants. The severity of rice blast disease was significantly reduced when M. oryzae spores were pre-treated with crude extracts of N3, lokisin, WLIP, entolysin or orfamide prior to inoculation. In vitro microscopic assays further revealed the capacity of crude N3, lokisin, WLIP, entolysin, xantholysin and orfamide to significantly inhibit appressoria formation by M. oryzae. In addition, the lokisin and WLIP biosynthetic gene clusters in the producing strains are described. In short, our study demonstrates the biological activity of structurally diverse CLPs in the control of the rice blast disease caused by M. oryzae. Furthermore, we provide insight into the non-ribosomal peptide synthetase genes encoding the WLIP and lokisin biosynthetic machineries.

The Control of Rice Blast Disease by the Novel Biofungicide Formulations

The study aims to develop novel biofungicide formulations against rice blast disease. A total of 300 rhizobacteria strains were isolated from rice field soil and were examined for the inhibition of Magnaporthe oryzae growth in a vitro test. Among them, only six rhizobacteria showed inhibition against M. oryzae. The three strains that showed the highest inhibition were Bacillus subtilis 5, B. cereus 3S5, and Pseudomonas fluorecens 10S2. A rice hull mixture and liquid medium were mixed with the above-mentioned bacterial suspensions into three bacterial formulas and tested separately on the rice cultivar UPLRi-5 after infection by M. oryzae under a controlled condition. The three novel biofungicide formulas significantly inhibited rice blast disease intensity with a mean disease control rate being approximately 31% higher than the control. The formulas proved to be effective and should be considered as promising novel treatments for rice blast disease.

Biogenic Cyanide Production Promotes Dissolution of Gold Nanoparticles in Soil

Gold nanoparticles (Au NPs) are often used to study the physiochemical behavior and distribution of nanomaterials in natural systems because they are assumed to be inert under environmental conditions, even though Au can be oxidized and dissolved by a common environmental compound: cyanide. We used the cyanogenic soil bacterium, Chromobacterium violaceum, to demonstrate that quorum-sensing-regulated cyanide production could lead to a high rate of oxidative dissolution of Au NPs in soil. After 7 days of incubation in a pH 7.0 soil inoculated with C. violaceum, labile Au concentration increased from 0 to 15%. There was no observable dissolution when Au NPs were incubated in abiotic soil. In the same soil adjusted to pH 7.5, labile Au concentration increased up to 29% over the same time frame. Furthermore, we demonstrated that Au dissolution required quorum-sensing-regulated cyanide production in soil by inoculating the soil with different cell densities and using a quorum-sensing-deficient mutant of C. violaceum, CV026. Au NP dissolution experiments in liquid media coupled with mass spectrometry analysis confirmed that biogenic cyanide oxidized Au NPs to soluble Au(CN)₂^-. These results demonstrate under which conditions biologically enhanced metal dissolution can contribute to the overall geochemical transformation kinetics of nanoparticle in soils, even though the materials may be inert in abiotic environments.

Trichoderma erinaceum Bio-Priming Modulates the WRKYs Defense Programming in Tomato Against the Fusarium oxysporum f. sp. lycopersici (Fol) Challenged Condition

The beneficial association and interaction of rhizocompetent microorganisms are widely used for plant biofertilization and amelioration of stress-induced damage in plants. To explore the regulatory mechanism involved in plant defense while associating with beneficial microbial species, and their interplay when co-inoculated with pathogens, we evaluated the response of tomato defense-related WRKY gene transcripts. The present study was carried out to examine the qRT-PCR-based relative quantification of differentially expressed defense-related genes in tomato (Solanum lycopersicum L.; variety S-22) primed with Trichoderma erinaceum against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). The tissue-specific and time-bound expression profile changes under the four different treatments "(unprimed, Fol challenged, T. erinaceum primed and Fol+ T. erinaceum)" revealed that the highest upregulation was observed in the transcript profile of SlWRKY31 (root) and SlWRKY37 (leaf) in T. erinaceum bioprimed treated plants at 24 h with 16.51- and 14.07-fold increase, respectively. In contrast, SlWRKY4 showed downregulation with the highest repression in T. erinaceum bioprimed root (24 h) and leaf (48 h) tissue samples with 0.03 and 0.08 fold decrease, respectively. Qualitative expression of PR proteins (chitinases and glucanases) was found elicited in T. erinaceum primed plants. However, the antioxidative activity of tomato superoxide dismutase and catalase increased with the highest upregulation of SOD and SlGPX1 in Fol + T. erinaceum treatments. We observed that these expression changes were accompanied by 32.06% lesser H₂O₂ production in T. erinaceum bioprimed samples. The aggravated defense response in all the treated conditions was also reflected by an increased lignified stem tissues. Overall, we conclude that T. erinaceum bio-priming modulated the defense transcriptome of tomato after the Fol challenged conditions, and were accompanied by enhanced accumulation of defense-related WRKY transcripts, increased antioxidative enzyme activities, and the reinforcements through a higher number of lignified cell layers.

The impact of microbes in the orchestration of plants' resistance to biotic stress: a disease management approach

The struggle for survival is a natural and a continuous process. Microbes are struggling to survive by depending on plants for their nutrition while plants on the other hand are resisting the attack of microbes in order to survive. This interaction is a tug of war and the knowledge of microbe-plant relationship will enable farmers/agriculturists improve crop health, yield, sustain regular food supply, and minimize the use of agrochemicals such as fungicides and pesticides in the fight against plant pathogens. Although, these chemicals are capable of inhibiting pathogens, they also constitute an environmental hazard. However, certain microbes known as plant growth-promoting microbes (PGPM) aid in the sensitization and priming of the plant immune defense arsenal for it to conquer invading pathogens. PGPM perform this function by the production of elicitors such as volatile organic compounds, antimicrobials, and/or through competition. These elicitors are capable of inducing the expression of pathogenesis-related genes in plants through induced systemic resistance or acquired systemic resistance channels. This review discusses the current findings on the influence and participation of microbes in plants' resistance to biotic stress and to suggest integrative approach as a better practice in disease management and control for the achievement of sustainable environment, agriculture, and increasing food production.