DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance.

DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.

Unearthing the power of microbes as plant microbiome for sustainable agriculture.

In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.

Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion.

Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and ß-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.

Bioactive antifungal metabolites produced by Streptomyces amritsarensis V31 help to control diverse phytopathogenic fungi.

Actinomycetes due to their unique repertoire of antimicrobial secondary metabolites can be an eco-friendly and sustainable alternative to agrochemicals to control plant pathogens. In the present study, antifungal activity of twenty different actinomycetes was evaluated via dual culture plate assay against six different phytopathogens, viz., Alternaria alternata, Aspergillus flavus, Fusarium oxysporum f. sp. lycopersici, Sarocladium oryzae, Sclerotinia sclerotiorum, and Rhizoctonia solani. Two potential isolates, Streptomyces amritsarensis V31 and Kribella karoonensis MSCA185 showing high antifungal activity against all six fungal pathogens, were further evaluated after extraction of bioactive metabolites in different solvents. Metabolite extracted from S. amritsarensis V31 in different solvents inhibited Rhizoctonia solani (7.5-65%), Alternaria alternata (5.5-52.7%), Aspergillus flavus (8-30.7%), Fusarium oxysporum f. sp. lycopersici (25-44%), Sarocladium oryzae (11-55.5%), and Sclerotinia sclerotiorum (29.7-40.5%); 1000 D diluted methanolic extract of S. amritsarensis V31 showed growth inhibition against R. solani (23.3%), A. flavus (7.7%), F. oxysporum (22.2%), S. oryzae (16.7%), and S. sclerotiorum (19.0%). Metabolite extracts of S. amritsarensis V31 significantly reduced the incidence of rice sheath blight both as preventive and curative sprays. Chemical profiling of the metabolites in DMSO extract of S. amritsarensis V31 revealed 6-amino-5-nitrosopyrimidine-2,4-diol as the predominant compound present. It was evident from the LC-MS analyses that S. amritsarensis V31 produced a mixture of potential antifungal compounds which inhibited the growth of different phytopathogenic fungi. The results of this study indicated that metabolite extracts of S. amritsarensis V31 can be exploited as a bio-fungicide to control phytopathogenic fungi.

A novel function of N-signaling in plants with special reference to Trichoderma interaction influencing plant growth, nitrogen use efficiency, and cross talk with plant hormones.

Trichoderma spp. is considered as a plant growth promoter and biocontrol fungal agents. They colonize on the surface of root in most of the agriculture crops. They secrete different secondary metabolites and enzymes which promote different physiological processes as well as protect plants from various environmental stresses. This is part of their vital functions. They are widely exploited as a biocontrol agent and plant growth promoter in agricultural fields. Colonization of Trichoderma with roots can enhance nutrient acquisition from surrounding soil to root and can substantially increase nitrogen use efficiency (NUE) in crops and linked with activation of plant signaling cascade. Among Trichoderma species, only some Trichoderma species were well characterized which help in the uptake of nitrogen-containing compound (especially nitrate form) and induced nitric oxide (NO) in plants. Both nitrate and NO are known as a signaling agent, involved in plant growth and development and disease resistance. Activation of these signaling molecules may crosstalk with other signaling molecule (Ca2+) and phytohormone (auxin, gibberellins, cytokinin and ethylene). This ability of Trichoderma is important to agriculture not only for increased plant growth but also to control plant diseases. Recently, Trichoderma strains have been shown to encompass the ability to regulate transcripts level of high-affinity nitrate transporters and probably it was positively regulated by NO. This review aims to focus the usage of Trichoderma strains on crops by their abilities to regulate transcript levels, probably through activation of plant N signaling transduction that improve plant health.

Trichoderma asperellum T42 induces local defense against Xanthomonas oryzae pv. oryzae under nitrate and ammonium nutrients in tobacco.

Trichoderma has been explored and found to play a vital role in the defense mechanism of plants. However, its effects on host disease management in the presence of N nutrients remains elusive. The present study aimed to assess the latent effects of Trichoderma asperellum T42 on oxidative burst-mediated defense mechanisms against Xanthomonas oryzae pv. oryzae (Xoo) in tobacco plants fed 10 mM NO3 - and 3 mM NH4 + nutrients. The nitrate-fed tobacco plants displayed an increased HR when Xoo infected, which was enhanced in the Trichoderma-treated plants. This mechanism was enhanced by the involvement of Trichoderma, which elicited NO production and enhanced the expression pattern of NO-modulating genes (NR, NOA and ARC). The real-time NO fluorescence intensity was alleviated in the NH4 +-fed tobacco plants compared to that fed NO3 - nutrient, suggesting the significant role of Trichoderma-elicited NO. The nitrite content and NR activity demonstration further confirmed that nitrate metabolism led to NO generation. The production of ROS (H2O2) in the plant leaves well-corroborated that the disease resistance was mediated through the oxidative burst mechanism. Nitrate application resulted in greater ROS production compared to NH4 + nutrient after Xoo infection at 12 h post-infection (hpi). Additionally, the mechanism of enhanced plant defense under NO3 - and NH4 + nutrients mediated by Trichoderma involved NO, ROS production and induction of PR1a MEK3 and antioxidant enzyme transcription level. Moreover, the use of sodium nitroprusside (100 µM) with Xoo suspension in the leaves matched the disease resistance mediated via NO burst. Altogether, this study provides novel insights into the fundamental mechanism behind the role of Trichoderma in the activation of plant defense against non-host pathogens under N nutrients.