First report of leaf spot of maize caused by Curvularia verruculosa in India.

Curvularia leaf spot affects maize plants worldwide and is commonly caused by Curvularia lunata, C. geniculata, and C. pallescens (Manzar et al. 2022; Manzar et al. 2021; Choudhary et al. 2011). In February 2017, leaf spot symptoms were observed in a Deogaon, (25.74 N, 82.99 E) in Uttar Pradesh, India, with disease incidence of less than 10% of the plants in maize fields. On the leaves and sheaths, variously shaped yellow spots were developed. The spots were 2.5 mm in diameter and frequently grew larger, reaching a diameter of 1 cm. They were encircled by a chlorotic halo with dark borders. The symptomatic tissue showing leaf spots of 10 plants was taken and cut into pieces (4 mm2) then surface sterilized with 1% sodium hypochlorite for 1 min, and rinsed three times with distilled water. The cut leaf tissue was placed on the Petri plate containing potato dextrose agar medium amended with streptomycin sulfate (125 ppm). Then incubated at 25±2°C with a 12-h light and dark period, after 5 days of incubation, five pure cultures were obtained using the hyphal tip technique. The pure culture was incubated at 26±2°C for 10 days. The upper surface of the colony was dark grayish black with fluffy mycelia, and the reverse colony was dark brown. The conidia have three septa, are light brown to dark brown in color, straight to curved, ellipsoidal to fusiform, and have two bigger, darker central cells than terminal cells. On average, conidia are between 27.22 to 31.21 mm long and 10.61 to 12.62 mm wide (n=30). The morphological description is similar to the Curvularia verruculosa morphological traits described by Tandon & Bilgrami (Ellis 1966). Molecular identification was done in addition to supporting morphological identification. The nucleopore GDNA Fungus Kit (Genetix Brand, India) was used to extract the genomic DNA of the E40 isolate. The ITS rDNA region (White et al. 1990) and the glyceraldehyde-3-phosphate dehydrogenase (gpd) gene (Berbee et al. 1999) were amplified through PCR(Manzar et al., 2022).The amplicons were bidirectional sequenced through the Sanger sequencing method. The similarity percentage of E40 isolate matched 100% with MH859788 (CBS444.70 ) of Curvularia verruculosa strain for ITS, and 100% with LT715824 (CBS150.63) of Curvularia verruculosa strain for gpd after Blastn analysis. The gene sequences were deposited to GenBank and accession no. OR262893 for ITS, and LC773704 for gpd were assigned. As a result, C. verruculosa was determined to be the presumed pathogen by both morphology and molecular characteristics. The pathogenicity of E40 isolate was performed twice by spraying (106 conidia/ml in sterile water) onto the leaves of 25 days old maize plant cv. Kanchan (n = 10). Uninoculated healthy maize plants (n=5) were sprayed only with autoclaved water. All pots are kept in a glass house at 25°C±2°C with 90% relative humidity. After 15 days of pathogen inoculation the foliar spots with chlorotic halo, enlarger upto 1cm, and from these spots the identical fungus was reisolated. The reisolated fungus showed similar morphological characteristics to C. verruculosa. Control plants showed no symptoms. C. verruculosa has been previously reported as a causative agent of leaf spot disease in Common beans (Wei et al., 2022), Cotton (Shirsath et al., 2018). To our knowledge, this is the first report of leaf blight caused by C. verruculosa on maize in India.

Multifarious Plant Growth-Promoting Rhizobacterium Enterobacter sp. CM94-Mediated Systemic Tolerance and Growth Promotion of Chickpea (Cicer arietinum L.) under Salinity Stress.

BACKGROUND: Chickpea is one of the most important leguminous crops and its productivity is significantly affected by salinity stress. The use of ecofriendly, salt-tolerant, plant growth-promoting rhizobacteria (PGPR) as a bioinoculant can be very effective in mitigating salinity stress in crop plants. In the present study, we explored, characterized, and evaluated a potential PGPR isolate for improving chickpea growth under salt stress. METHODS: A potential PGPR was isolated from rhizospheric soils of chickpea plants grown in the salt-affected area of eastern Uttar Pradesh, India. The isolate was screened for salt tolerance and characterized for its metabolic potential and different plant growth-promoting attributes. Further, the potential of the isolate to promote chickpea growth under different salt concentrations was determined by a greenhouse experiment. RESULTS: A rhizobacteria isolate, CM94, which could tolerate a NaCl concentration of up to 8% was selected for this study. Based on the BIOLOG carbon source utilization, isolate CM94 was metabolically versatile and able to produce multiple plant growth-promoting attributes, such as indole acetic acid, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophore, hydrogen cyanide (HCN), and ammonia as well as solubilized phosphate. A polyphasic approach involving the analysis of fatty acid methyl ester (FAME) and 16S rRNA gene sequencing confirmed the identity of the isolate as Enterobacter sp. The results of greenhouse experiments revealed that isolate CM94 inoculation significantly enhanced the shoot length, root length, and fresh and dry weight of chickpea plants, under variable salinity stress. In addition, inoculation improved the chlorophyll, proline, sugar, and protein content in the tissues of the plant, while lowering lipid peroxidation. Furthermore, isolate CM94 reduced oxidative stress by enhancing the enzymatic activities of superoxide dismutase, catalase, and peroxidase compared to in the respective uninoculated plants. CONCLUSIONS: Overall, the results suggested that using Enterobacter sp. CM94 could significantly mitigate salinity stress and enhance chickpea growth under saline conditions. Such studies will be helpful in identifying efficient microorganisms to alleviate salinity stress, which in turn will help, to devise ecofriendly microbial technologies.

Quinoa germ-enriched pasta: Technological, nutritional, textural, and morphological properties.

Germ is the most significant component of quinoa having good nutritional value. Quinoa germ (QG), with balanced amino acid profile and unsaturated fatty acid, is a unique ingredient for human nutrition. In present study, pasta supplemented with QG was characterized for physical, nutritional, morphological, and textural properties. Dough rheology showed increased farinograph water absorption and decreased dough stability with the addition of QG. Addition of QG up to 30% significantly improved the pasta protein content from 13.55% to 20.55%. The substitution of QG to pasta showed decrease in whiteness index and increase in optimum cooking time, swelling index, cooked weight, and cooking loss. It is reported that 20% QG supplement pasta was found to be acceptable; beyond, this level the pasta quality was inferior. Firmness value of pasta significantly increased up to 20% supplementation of QG from 157 to 178 g. The micrographs of pasta with the addition of QG observed increased protein matrix around the starch granules. The results inferred that the QG can serve as a potential functional ingredient for the development of nutritionally enhanced pasta for food industry. PRACTICAL APPLICATION: Quinoa germ (QG) is concentrated source of nutrient with unique nutrition and alternative source of protein. Pasta is the one the popular and fast-growing food in world and explored for enhancement of its nutritional composition to target a larger population with specific nutrient demand. Hence, pasta becomes important vehicle for the supplementation. Developed QG-enriched high-protein pasta will help industry to produce nutritious products at large scale.

Effect of heat treatments on quinoa germ quality and its storage study.

Quinoa is a potential crop to address the situation as it offers a plethora of benefits as it is nutritionally rich and can adapt to extreme climatic and salt conditions. Quinoa germ consists of almost 25-30% of whole grain. Quinoa germ obtained using roller milling has remarkable nutritional properties with high protein, fat and mineral content. Presence higher fat content limits shelf-life of quinoa germ. The objective of the present investigation is to study the effect of different treatment on stabilization of quinoa germ and its storge study. Quinoa germ was subjected to microwave and infrared treatment for shelf-life extension. Colour properties of the germ has not changed drastically by both treatments. Sorption behavior of quinoa germ stored at different RH was studied and results showed typical sigmoid curve for all samples. Sorption studies revealed that treated quinoa germ were stable at 64% RH. The storage study was carried out at accelerated conditions using PET/PE packaging material. Based on the results of the study, it can be inferred that the quinoa germ can be kept up to three months at accelerated conditions. Study demonstrated that microwave treatments of quinoa germ showed highest shelf life of three months at accelerated conditions.

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties.

Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

Salinity Alleviation and Reduction in Oxidative Stress by Endophytic and Rhizospheric Microbes in Two Rice Cultivars.

Increased soil salinity poses serious limitations in crop yield and quality; thus, an attempt was made to explore microbial agents to mitigate the ill effects of salinity in rice. The hypothesis was mapping of microbial induction of stress tolerance in rice. Since the rhizosphere and endosphere are two different functional niches directly affected by salinity, it could be very crucial to evaluate them for salinity alleviation. In this experiment, endophytic and rhizospheric microbes were tested for differences in salinity stress alleviation traits in two rice cultivars, CO51 and PB1. Two endophytic bacteria, Bacillus haynesii 2P2 and Bacillus safensis BTL5, were tested with two rhizospheric bacteria, Brevibacterium frigoritolerans W19 and Pseudomonas fluorescens 1001, under elevated salinity (200 mM NaCl) along with Trichoderma viride as an inoculated check. The pot study indicated towards the presence of variable salinity mitigation mechanisms among these strains. Improvement in the photosynthetic machinery was also recorded. These inoculants were evaluated for the induction of antioxidant enzymes viz. CAT, SOD, PO, PPO, APX, and PAL activity along with the effect on proline levels. Modulation of the expression of salt stress responsive genes OsPIP1, MnSOD1, cAPXa, CATa, SERF, and DHN was assessed. Root architecture parameters viz. cumulative length of total root, projection area, average diameter, surface area, root volume, fractal dimension, number of tips, and forks were studied. Confocal scanning laser microscopy indicated accumulation of Na+ in leaves using cell impermeant Sodium Green™, Tetra (Tetramethylammonium) Salt. It was found that each of these parameters were induced differentially by endophytic bacteria, rhizospheric bacteria, and fungus, indicating different paths to complement one ultimate plant function. The biomass accumulation and number of effective tillers were highest in T4 (Bacillus haynesii 2P2) plants in both cultivars and showed the possibility of cultivar specific consortium. These strains and their mechanisms could form the basis for further evaluating microbial strains for climate-resilient agriculture.

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.

Bacterial chitinases: genetics, engineering and applications.

Chitinases are a group of enzymes that catalyze chitin hydrolysis and are present in all domains of life. Chitinases belong to different glycosyl hydrolase families with great diversity in their sequences. Microorganisms such as bacteria and fungi produce chitinases for nutrition, and energy, and to parasitize the chitinous hosts. But chitinases from bacteria are of special interest due to their ubiquitous nature and ability to perform under extreme conditions. Chitinases produced by bacteria have been explored for their use in agriculture and industry. In agriculture, their main role is to control chitin-containing insect pests, fungal pathogens, and nematodes. In the seafood industry, they found their role in the management of processing wastes which are mainly chitinous substances. Chitinases are also used to synthesize low molecular weight chitooligomers which are proven bioactive compounds with activities such as anti-tumour, antimicrobial, and immunity modulation. Considering their importance in ecology and biotechnological applications, several bacterial chitinases have been studied in the last two decades. Despite their potential, bacterial chitinases have a few limitations such as low production and lack of secretion systems which make the wild-type enzymes unfit for their applications in industries and other allied sectors. This review is an attempt to collate significant works in bacterial chitinases and their application in various industries and the employment of various tools and techniques for improvement to meet industrial requirements.

Colorimetric loop-mediated isothermal amplification assay for detection and ecological monitoring of Sarocladium oryzae, an important seed-borne pathogen of rice.

Accurate and timely disease detection plays a critical role in achieving sustainable crop protection. Globally, rice has been a staple crop for centuries plagued by the diseases that greatly hamper its productivity. Sheath rot, an emerging disease of rice caused by the seed-borne pathogen Sarocladium oryzae, has reportedly caused heavy losses to agricultural produce in recent years. Our study has led to the development and validation of a LAMP assay for early detection of S. oryzae, the causal agent of sheath rot from the live-infected tissues, seeds, weeds, and environmental samples. The assay could detect as low as 1.6 fg/µl of the pathogen in 15 min. The assay was implemented to bio-surveil the presence of this pathogen by testing it on three weed species (Echinochloa colona, Echinochloa crus-galli, and Cyperus teneriffae) growing around the rice fields. The results showed the presence of the pathogen in two of the weed species viz. E. colona and E. crus-galli. The assay was used to test 13 different rice varieties for the presence of S. oryzae in seeds. In total, three of the varieties did not show the presence of S. oryzae in their seeds while the rest were found to harbor the pathogen. The developed assay can effectively be used to detect and screen the presence of S. oryzae in live samples including seeds and field soil.

Bio-priming with a consortium of Streptomyces araujoniae strains modulates defense response in chickpea against Fusarium wilt.

Wilt caused by Fusarium oxysporum f. sp. ciceris (Foc) is one of the major diseases of chickpea affecting the potential yield significantly. Productivity and biotic stress resilience are both improved by the association and interaction of Streptomyces spp. with crop plants. In the present study, we evaluated two Streptomyces araujoniae strains (TN11 and TN19) for controlling the wilt of chickpea individually and as a consortium. The response of Foc challenged chickpea to inoculation with S. araujoniae TN11 and TN19 individually and as a consortium was recorded in terms of changes in physio-biochemical and expression of genes coding superoxide dismutase (SOD), peroxidase, and catalase. Priming with a consortium of TN11 and TN19 reduced the disease severity by 50-58% when challenged with Foc. Consortium primed-challenged plants recorded lower shoot dry weight to fresh weight ratio and root dry weight to fresh weight ratio as compared to challenged non-primed plants. The pathogen-challenged consortium primed plants recorded the highest accumulation of proline and electrolyte leakage. Similarly, total chlorophyll and carotenoids were recorded highest in the consortium treatment. Expression of genes coding SOD, peroxidase, and catalase was up-regulated which corroborated with higher activities of SOD, peroxidase, and catalase in consortium primed-challenged plants as compared to the challenged non-primed plants. Ethyl acetate extracts of TN11 and TN19 inhibited the growth of fungal pathogens viz., Fusarium oxysporum f. sp. ciceris. Macrophomina phaseolina, F. udum, and Sclerotinia sclerotiarum by 54-73%. LC-MS analyses of the extracts showed the presence of a variety of antifungal compounds like erucamide and valinomycin in TN11 and valinomycin and dinactin in TN19. These findings suggest that the consortium of two strains of S. araujoniae (TN11 and TN19) can modulate defense response in chickpea against wilt and can be explored as a biocontrol strategy.

Multi-Gene Phylogenetic Approach for Identification and Diversity Analysis of Bipolaris maydis and Curvularia lunata Isolates Causing Foliar Blight of Zea mays.

Bipolaris species are known to be important plant pathogens that commonly cause leaf spot, root rot, and seedling blight in a wide range of hosts worldwide. In 2017, complex symptomatic cases of maydis leaf blight (caused by Bipolaris maydis) and maize leaf spot (caused by Curvularia lunata) have become increasingly significant in the main maize-growing regions of India. A total of 186 samples of maydis leaf blight and 129 maize leaf spot samples were collected, in 2017, from 20 sampling sites in the main maize-growing regions of India to explore the diversity and identity of this pathogenic causal agent. A total of 77 Bipolaris maydis isolates and 74 Curvularia lunata isolates were screened based on morphological and molecular characterization and phylogenetic analysis based on ribosomal markers-nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) region, 28S nuclear ribosomal large subunit rRNA gene (LSU), D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA), and protein-coding gene-glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Due to a dearth of molecular data from ex-type cultures, the use of few gene regions for species resolution, and overlapping morphological features, species recognition in Bipolaris has proven difficult. The present study used the multi-gene phylogenetic approach for proper identification and diversity of geographically distributed B. maydis and C. lunata isolates in Indian settings and provides useful insight into and explanation of its quantitative findings.

Transcriptome Analysis to Understand Salt Stress Regulation Mechanism of Chromohalobacter salexigens ANJ207.

Soil salinity is one of the major global issues affecting soil quality and agricultural productivity. The plant growth-promoting halophilic bacteria that can thrive in regions of high salt (NaCl) concentration have the ability to promote the growth of plants in salty environments. In this study, attempts have been made to understand the salinity adaptation of plant growth-promoting moderately halophilic bacteria Chromohalobacter salexigens ANJ207 at the genetic level through transcriptome analysis. In order to identify the stress-responsive genes, the transcriptome sequencing of C. salexigens ANJ207 under different salt concentrations was carried out. Among the 8,936 transcripts obtained, 93 were upregulated while 1,149 were downregulated when the NaCl concentration was increased from 5 to 10%. At 10% NaCl concentration, genes coding for lactate dehydrogenase, catalase, and OsmC-like protein were upregulated. On the other hand, when salinity was increased from 10 to 25%, 1,954 genes were upregulated, while 1,287 were downregulated. At 25% NaCl, genes coding for PNPase, potassium transporter, aconitase, excinuclease subunit ABC, and transposase were found to be upregulated. The quantitative real-time PCR analysis showed an increase in the transcript of genes related to the biosynthesis of glycine betaine coline genes (gbcA, gbcB, and L-pro) and in the transcript of genes related to the uptake of glycine betaine (OpuAC, OpuAA, and OpuAB). The transcription of the genes involved in the biosynthesis of L-hydroxyproline (proD and proS) and one stress response proteolysis gene for periplasmic membrane stress sensing (serP) were also found to be increased. The presence of genes for various compatible solutes and their increase in expression at the high salt concentration indicated that a coordinated contribution by various compatible solutes might be responsible for salinity adaptation in ANJ207. The investigation provides new insights into the functional roles of various genes involved in salt stress tolerance and oxidative stress tolerance produced by high salt concentration in ANJ207 and further support the notion regarding the utilization of bacterium and their gene(s) in ameliorating salinity problem in agriculture.

Efficacy and Safety of Ayurveda interventions in the management of conjunctivitis: A systematic review and meta-analysis.

BACKGROUND: Conjunctivitis is the inflammation of the conjunctiva. Although data on clinical efficacy and safety of various ayurvedic treatments in conjunctivitis is published, systematic review is not done. This systematic review and meta-analysis aims to evaluate the efficacy and safety of ayurvedic treatments in conjunctivitis. METHODS: A literature search of the Cochrane Library (Cochrane central register of controlled trials: issue 6 of 12, June 2018), Pub Med, AYUSH research portal (Govt. of India), DHARA portal, Google scholar and online clinical trials registers was done. Randomized controlled trials (RCTs), quasi-randomized controlled trials (QRCTs), controlled clinical trials (CCTs) and multiple arms clinical trials were identified in which Ayurveda treatments with any dose, type, schedule, drug, dosage form, and advised Pathayapathya (lifestyle changes) were selected. RESULTS: We identified 13 eligible RCTs, five CCTs and two multiple arms clinical trials which includes a total of 816 participants. Meta analysis of data from five trials showed that ayurvedic treatments benefitted more compared with non-ayurveda interventions in symptoms like itching (SMD = -0.98, 95% CI (-1.30,-0.65) p < 0.00001, I2 = 38%), pain (SMD = -0.57, 95% CI (-0.87, -0.29, P = 0.0001, I2 = 0%), ropy discharge (SMD = -1.02, 95% CI(-1.45, -0.59), P < 0.00001, I2 = 0%), conjunctival congestion (SMD = -0.67, 95% CI (-0.91, -0.43), p < 0.00001, I2 = 0%), foreign body sensation (SMD = -0.68, 95% CI(-1.06, -0.29), p = 0.0006, I2 = 46%, Fig. 8) and lid heaviness (SMD = -0.66, 95% CI(- 0.98, -0.33), p < 0.0001, I2 = 0%). CONCLUSIONS: Although some findings confirm the benefit of ayurveda as opposed to non ayurveda for the treatment of conjunctivitis, since the studies have high risk of bias and are of lower quality, the findings could not be generalized. There is a need for high quality studies in ayurveda in this regard. PROSPERO REGISTRATION: CRD42019129436.

Effect of Silymarin and Quercetin in a Miniaturized Scaffold in Wistar Rats against Non-alcoholic Fatty Liver Disease.

Silymarin and quercetin (SQ) are known antioxidants with substantial free radical scavenging activities. The efficacy of SQ activity is restricted due to poor absorption and availability. This study aims to increase the hepatoprotective activity of SQ by a newer delivery technique. We have optimized a technique, miniaturized scaffold (MS), for the delivery of active compounds of SQ. SQ molecules were embedded in MS and characterized by morphology, particle size, miniaturization efficiency, and functional group. Further, the hepatoprotective effects of MSQ were investigated through in vitro and in vivo methods. Hepatotoxicity was induced in rats by carbon tetrachloride (CCl4), and subsequently, hepatotoxic rats were treated with the miniaturized scaffold of SQ (MSQ) for 8 weeks. The body weight were significantly high in groups fed with MSQ. A substantial decrease in triglyceride, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase activities were observed in rats treated with MSQ. Similarly, rats treated with MSQ exhibited lower lipid accumulation in the hepatocytes. The experiments clearly demonstrated the efficacy of MSQ as a superior hepatoprotective agent against non-alcoholic fatty liver disease simulated through toxicity induced by CCl4.

Analysis of Biosynthetic Gene Clusters, Secretory, and Antimicrobial Peptides Reveals Environmental Suitability of Exiguobacterium profundum PHM11.

Halotolerant bacteria produce a wide range of bioactive compounds with important applications in agriculture for abiotic stress amelioration and plant growth promotion. In the present study, 17 biosynthetic gene clusters (BGCs) were identified in Exiguobacterium profundum PHM11 belonging to saccharides, desmotamide, pseudaminic acid, dipeptide aldehydes, and terpene biosynthetic pathways representing approximately one-sixth of genomes. The terpene biosynthetic pathway was conserved in Exiguobacterium spp. while the E. profundum PHM11 genome confirms the presence of the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway for the isopentenyl diphosphate (IPP) synthesis. Further, 2,877 signal peptides (SPs) were identified using the PrediSi server, out of which 592 proteins were prophesied for the secretion having a transmembrane helix (TMH). In addition, antimicrobial peptides (AMPs) were also identified using BAGEL4. The transcriptome analysis of PHM11 under salt stress reveals the differential expression of putative secretion and transporter genes having SPs and TMH. Priming of the rice, wheat and maize seeds with PHM11 under salt stress led to improvement in the root length, root diameters, surface area, number of links and forks, and shoot length. The study shows that the presence of BGCs, SPs, and secretion proteins constituting TMH and AMPs provides superior competitiveness in the environment and make E. profundum PHM11 a suitable candidate for plant growth promotion under salt stress.

A rapid colorimetric LAMP assay for detection of Rhizoctonia solani AG-1 IA causing sheath blight of rice.

Rhizoctonia solani is one of the most devastating pathogens. R. solani AG-1 IA causes sheath blight in rice, maize, and other Gramineous plants. Accurate identification is essential for the effective management of this pathogen. In the present study, a set of four primers were designed viz. RSPG1, RSPG2, RSPG4, and RSPG5 for polygalacturonase (PG) gene, an important virulence factor in phytopathogenic fungi. All four primer sets showed specific amplification of 300 bp (RSPG1F/R), 375 bp (RSPG2F/R), 500 bp (RSPG4F/R) and 336 bp (RSPG5F/R) amplicons. q-PCR detection using each primer sets could detect up to 10 pg of DNA. We also designed six primers (RS_pg_F3_1/RS_pg_B3_1, RS_pg_FIP_1.1/RS-pg_BIP_1.1, and RS_pg_LF_1/RS_pg_LB_1) for PG gene. Further, a colorimetric LAMP assay developed yielded visual confirmation of the pathogen within 45 min of sample collection when coupled with rapid high throughput template preparation method (rHTTP) from infected samples. The sensitivity of the LAMP assay was as low as 1.65 fg/µl of template DNA and could effectively detect R. solani AG-1 IA from diseased plant tissues and soil samples. The LAMP assay was highly specific for R. solani as it did not show any amplification with other AG groups of R. solani and closely related fungal and bacterial outgroups. This study will help in designing an effective point of care diagnostic method for early monitoring of R. solani and thereby planning timely preventive measures against the pathogen.

Pan-genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11.

The stint of the bacterial species is convoluting, but the new algorithms to calculate genome-to-genome distance (GGD) and DNA-DNA hybridization (DDH) for comparative genome analysis have rejuvenated the exploration of species and sub-species characterization. The present study reports the first whole genome sequence of Exiguobacterium profundum PHM11. PHM11 genome consist of ~ 2.92 Mb comprising 48 contigs, 47.93% G + C content. Functional annotations revealed a total of 3033 protein coding genes and 33 non-protein coding genes. Out of these, only 2316 could be characterized and others reported as hypothetical proteins. The comparative analysis of predicted proteome of PHM11 with five other Exiguobacterium sp. identified 3806 clusters, out of which the PHM11 shared a total of 2723 clusters having 1664 common clusters, 131 singletons and 928 distributed between five species. The pan-genome analysis of 70 different genomic sequences of Exigubacterium strains devoid of a species taxon was done on the basis of GGD and the DDH which identified eight genomes analogous to the PHM11 at species level and may be characterized as E. profundum. The ANI value and phylogenetic tree analysis also support the same. The results regarding pan-genome analysis provide a convincing insight for delineation of these eight strains to species.

Bacterial endophyte mediated plant tolerance to salinity: growth responses and mechanisms of action.

Salinity stress is one of the key constraints for sustainable crop production. It has gained immense importance in the backdrop of climate change induced imbalanced terrestrial water budgets. The traditional agronomic approaches and breeding salt-tolerant genotypes have often proved insufficient to alleviate salinity stress. Newer approaches like the use of bacterial endophytes associated with agricultural crops have occupied center place recently, owing to their advantageous role in improving crop growth, health and yield. Research evidences have revealed that bacterial endophytes can promote plant growth by accelerating availability of mineral nutrients, helping in production of phytohormones, siderophores, and enzymes, and also by activating systemic resistance against insect pest and pathogens in plants. These research developments have opened an innovative boulevard in agriculture for capitalizing bacterial endophytes, single species or consortium, to enhance plant salt tolerance capabilities, and ultimately lead to translational refinement of crop-production business under salty environments. This article reviews the latest research progress on the identification and functional characterization of salt tolerant endophytic bacteria and illustrates various mechanisms triggered by them for plant growth promotion under saline environment.