Zero budget natural farming components Jeevamrit and Beejamrit augment Spinacia oleracea L. (spinach) growth by ameliorating the negative impacts of the salt and drought stress.

The growth of crop plants, particularly spinach (Spinacia oleracea L.), can be significantly impeded by salinity and drought. However, pre-treating spinach plants with traditional biofertilizers like Jeevamrit and Beejamrit (JB) substantially reverses the salinity and drought-induced inhibitory effects. Hence, this study aims to elucidate the underlying mechanisms that govern the efficacy of traditional fertilizers. The present work employed comprehensive biochemical, physiological, and molecular approaches to investigate the processes by which JB alleviates abiotic stress. The JB treatment effectively boosts spinach growth by increasing nutrient uptake and antioxidant enzyme activity, which mitigates the detrimental effects of drought and salinity-induced stress. Under salt and drought stress conditions, the application of JB resulted in an impressive rise in germination percentages of 80 and 60%, respectively. In addition, the application of JB treatment resulted in a 50% decrease in electrolyte leakage and a 75% rise in the relative water content of the spinach plants. Furthermore, the significant reduction in proline and glycine betaine levels in plants treated with JB provides additional evidence of the treatment's ability to prevent cell death caused by environmental stressors. Following JB treatment, the spinach plants exhibited substantially higher total chlorophyll content was also observed. Additionally, using 16S rRNA sequencing, we discovered and characterized five plant-beneficial bacteria from the JB bio-inoculants. These bacterial isolates comprise a number of traits that contribute to growth augmentation in plants. These evidences suggest that the presence of the aforesaid microorganisms (along with additional ones) is accountable for the JB-mediated stimulation of plant growth and development.

Bacillus subtilis ER-08, a multifunctional plant growth-promoting rhizobacterium, promotes the growth of fenugreek (Trigonella foenum-graecum L.) plants under salt and drought stress.

Introduction: Sustainable agriculture and meeting the world's food needs face considerable obstacles from abiotic stresses such as soil salinity and drought. This critical issue was addressed by our current study, which sought to uncover multi-trait bioinoculants from hostile ecosystems that could help mitigate salinity and drought stresses at the same time. Methods: The Bacillus subtilis ER-08 (BST) strain was isolated from the halotolerant plant Fagonia cretica which was collected from the Little Rann of Kachchh, India. Various biochemical and molecular approaches were applied for the detailed characterization of the BST isolate. Results and discussion: The BST isolate demonstrated notable plant growth-promoting qualities. Fenugreek seed biopriming was performed using the BST isolate. The effect of BST seed treatment on fenugreek developmental indices as well as abiotic alleviation was examined under greenhouse conditions. The BST produced 83.7 g ml-1 gibberellins (GA3) and 176.1 g ml-1 indole-3 acetic acid. Moreover, hydrogen cyanide, siderophore, exopolysaccharides (EPS), ammonia, cellulase, protease, pectinase, and chitinase were also produced by the BST strain. Interestingly, 52% of Fusarium oxysporum mycelial growth was suppressed by the BST isolate under in vitro conditions. Furthermore, BST isolates functioned well under several abiotic stress conditions, for instance, salinity (4 and 6 ds m-1), pH (5, 7, and 9), drought (PEG6000 at 10%, 20%, and 30%), and temperature (25°C, 35°C, 37°C, and 55°C). This study indicates that the BST strain might serve as an effective bio-inoculant for minimizing the detrimental effects of abiotic stresses.

Evaluation of the growth-inducing efficacy of various Bacillus species on the salt-stressed tomato (Lycopersicon esculentum Mill.).

Plants are affected by salt stress in a variety of ways, including water deficiency, ion toxicity, nutrient imbalance, and oxidative stress, all of which can cause cellular damage or plant death. Halotolerant plant growth-promoting rhizobacteria (PGPR) could be a viable alternative for tomato plants growing in arid and semi-arid environments. The aim of this research was to isolate halotolerant plant growth promoting Bacillus sp. to promote tomato (Lycopersicon esculentum Mill.) growth and salt stress resistance. 107 PGPR strains were isolated from the rhizospheres of 'Kesudo' (Butea monosperma Lam.), 'Kawaria' (Cassia tora L.), and 'Arjun' (Terminalia arjuna Roxb.) plants to test their plant growth promoting abilities, including indole-3-acetic acid, phosphate solubilization, siderophore production, and ACC deaminase activity. Five bacterial strains (Bacillus pumilus (NCT4), Bacillus firmus (NCT1), Bacillus licheniformis (LCT4), Bacillus cereus (LAT3), and Bacillus safensis (LBM4)) were chosen for 16S rRNA on the basis of PGPR traits. Compared to PGPR untreated plants, tomato plants developed from PGPR-treated seeds had considerably increased germination percentage, seedling growth, plant height, dry weight, and leaf area. As comparison to PGPR non-inoculated plants, salt-stressed tomato plants treated with PGPR strains had higher levels of total soluble sugar, proline, and chlorophyll as well as higher levels of SOD, CAT, APX, and GR activity. PGPR-inoculated salt-stressed tomato plants had lower MDA, sodium, and chloride levels than non-inoculated plants. In addition, magnesium, calcium, potassium, phosphorus, and iron levels were higher in PGPR treated plants when subjected to salt stress. These results indicate that halotolerant PGPR strains can increase tomato productivity and tolerance to salt stress by removing salt stress's negative effects on plant growth.

Repurposing of the herbal formulations: molecular docking and molecular dynamics simulation studies to validate the efficacy of phytocompounds against SARS-CoV-2 proteins.

Herbal formulations mentioned in traditional medicinal texts were investigated for in silico effect against SARS-COV-2 proteins involved in various functions of a virus such as attachment, entry, replication, transcription, etc. To repurpose and validate polyherbal formulations, molecular docking was performed to study the interactions of more than 150 compounds from various formulations against the SARS-CoV-2 proteins. Molecular dynamics (MD) simulation was performed to evaluate the interaction of top scored ligands with the various receptor proteins. The docking results showed that Liquiritic acid, Liquorice acid, Terchebulin, Glabrolide, Casuarinin, Corilagin, Chebulagic acid, Neochebulinic acid, Daturataturin A, and Taraxerol were effective against SARS-COV-2 proteins with higher binding affinities with different proteins. Results of MD simulations validated the stability of ligands from potent formulations with various receptors of SARS-CoV-2. Binding free energy analysis suggested the favourable interactions of phytocompounds with the recpetors. Besides, in silico comparison of the various formulations determined that Pathyadi kwath, Sanjeevani vati, Yashtimadhu, Tribhuvan Keeratiras, and Septillin were more effective than Samshamni vati, AYUSH-64, and Trikatu. Polyherbal formulations having anti-COVID-19 potential can be used for the treatment with adequate monitoring. New formulations may also be developed for systematic trials based on ranking from these studies.Communicated by Ramaswamy H. Sarma.

Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology.

Humanity has seen numerous pandemics during its course of evolution. The list includes several incidents from the past, such as measles, Ebola, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS), etc. The latest edition to this is coronavirus disease 2019 (COVID-19), caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of August 18, 2020, COVID-19 has affected over 21 million people from 180 + countries with 0.7 million deaths across the globe. Genomic technologies have enabled us to understand the genomic constitution of pathogens, their virulence, evolution, and rate of mutation, etc. To date, more than 83,000 viral genomes have been deposited in public repositories, such as GISAID and NCBI. While we are writing this, India is the third most affected country by COVID-19, with 2.7 million cases and > 53,000 deaths. Gujarat is the 11th highest affected state with a 3.48% death rate compared to the national average of 1.91%. In this study, a total of 502 SARS-CoV-2 genomes from Gujarat were sequenced and analyzed to understand its phylogenetic distribution and variants against global and national sequences. Further variants were analyzed from diseased and recovered patients from Gujarat and the world to understand its role in pathogenesis. Among the missense mutations present in the Gujarat SARS-CoV-2 genomes, C28854T (Ser194Leu) had an allele frequency of 47.62 and 7.25% in deceased patients from the Gujarat and global datasets, respectively. In contrast, the allele frequency of 35.16 and 3.20% was observed in recovered patients from the Gujarat and global datasets, respectively. It is a deleterious mutation present in the nucleocapsid (N) gene and is significantly associated with mortality in Gujarat patients with a p-value of 0.067 and in the global dataset with a p-value of 0.000924. The other deleterious variant identified in deceased patients from Gujarat (p-value of 0.355) and the world (p-value of 2.43E-06) is G25563T, which is located in Orf3a and plays a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct clusters under the GH clade of GISAID. This study will shed light on the viral haplotype in SARS-CoV-2 samples from Gujarat, India.

Molecular survey of basidiomycetes and divergence time estimation: An Indian perspective.

This study outlines the biodiversity of mushrooms of India. It reveals the molecular biodiversity and divergence time estimation of basidiomycetes from Gujarat, India. A total of 267 mushrooms were collected from 10 locations across the state. 225 ITS sequences were generated belonging to 105 species, 59 genera and 29 families. Phylogenetic analysis of Agaricaceae reveals monophyletic clade of Podaxis differentiating it from Coprinus. Further, the ancient nature of Podaxis supports the hypothesis that gasteroid forms evolved from secotioid forms. Members of Polyporaceae appeared polyphyletic. Further, our results of a close phylogenetic relationship between Trametes and Lenziteslead us to propose that the genera Trametes may by enlarged to include Lenzites. The tricholomatoid clade shows a clear demarcation for Entolomataceae. However, Lyophyllaceae and Tricholomataceae could not be distinguished clearly. Distribution studies of the mushrooms showed omnipresence of Ganoderma and Schizophyllum. Further, divergence time estimation shows that Dacrymycetes evolved in the Neoproterozoic Era and Hymenochaetales diverged from Agaricomycetes during the Silurian period.

Development of PR genes panel for screening aphid-tolerant cultivars in Brassica juncea.

The exorbitant yield loss incurred by Indian farmers every year (10-90%) in rapeseed-mustard (Brassica juncea) is chiefly attributed to the progressive infestation of mustard fields by Lipaphis erysimi (Kalt.), a major insect pest belonging to the family of Homoptera. Currently there are no successful tolerant cultivars developed by conventional means in Brassica juncea with systemic plant responses in the form of direct or indirect defenses against aphid attack. Lack of specific methods for screening large numbers of genotypes required in breeding for selection of tolerant cultivars in mustard is one of the main causes of slow progress in developing resistant varieties of Brassica juncea. Traditional phenotype-based breeding has to be augmented with recent molecular approaches for potential genotype selection and cultivar development in Brassica juncea. In current study a pathogen-responsive gene panel was developed which could be used for expression-assisted breeding program in mustard for selection of tolerant types against aphid infestation, minimizing the huge crop losses suffered by farmers every year.

A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World.

Here we present the first report on the taxonomic diversity of the microbial communities of the saline desert of the Great Rann of Kutch, Gujarat, India, using a metagenomic approach. Seven samples, differing in salinity levels and covering different seasons, were analysed to investigate the dynamics of microbial communities in relation to salinity and season. Metagenomic data generated using whole metagenome sequencing revealed that despite its very high salinity (4.11-30.79 %), the saline desert's microbiota had a rich microbial diversity that included all major phyla. Notably, 67 archaeal genera, representing more than 60 % of all known archaeal genera, were present in this ecosystem. A strong positive correlation (0.85) was observed between the presence of the extremely halophilic bacterium Salinibacter and salinity level. Taxonomic and functional comparisons of the saline desert metagenome with those of other publicly available metagenomes (i.e. sea, hypersaline lagoon, solar saltern, brine, hot desert) was carried out. The microbial community of the Kutch was found to be unique yet more similar to the sea biomes followed by hypersaline lagoon.

Tobacco habituated and non-habituated subjects exhibit different mutational spectrums in head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common non-skin cancer in the world. Tobacco chewing is implicated with most of the cases of HNSCC but this type of cancer is increasing in non-tobacco chewers as well. This study was instigated to provide comprehensive variant and gene-level data in HNSCC subjects of the Indian population and fill the gap in the literature on comparative assessment of gene mutations in cancer subjects with a habit of tobacco and those without any habit using targeted amplicon sequencing. We performed targeted Amplicon sequencing of 409 tumor suppressor genes and oncogenes, frequently mutated across many cancer types, including head and neck. DNA from primary tumor tissues and matched blood was analyzed for HNSCC patients with a habit of tobacco and those without any habit. PDE4DIP, SYNE1, and NOTCH1 emerged as the highly mutated genes in HNSCC. A total of 39 candidate causal variants in 22 unique cancer driver genes were identified in non-habitual (WoH) and habitual (WH) subjects. Comparison of genes from both the subjects, showed seven unique cancer driver genes (KIT, ATM, RNF213, GATA2, DST, RET, CYP2C19) in WoH, while WH showed five (IL7R, PKHD1, MLL3, PTPRD, MAPK8) and 10 genes (SETD2, ATR, CDKN2A, NCOA4, TP53, SYNE1, KAT6B, THBS1, PTPRT, and FGFR3) were common to both subjects. In addition to this NOTCH1, NOTCH2, and NOTCH4 gene were found to be mutated only in habitual subjects. These findings strongly support a causal role for tobacco, acting via PI3K and MAPK pathway inhibition and stimulation of various genes leading to oncogenic transformations in case of tobacco chewers. In case of non-tobacco chewers it appears that mutations in the pathway affecting the squamous epithelial lineage and DNA repair genes lead to HNSCC. Somatic mutation in CYP2C19 gene in the non-habitual subjects suggests that this gene may have a tobacco independent role in development and progression of HNSCC. In addition to sharing high mutation rate, NOTCH gene family was found to be mutated only in habitual sample. Further, presence of mutated genes not earlier reported to be involved in HNSCC, suggest that the Indian sub-continent may have different sets of genes, as compared to other parts of the world, involved in the development and progression of HNSCC.

Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy.

Present study attempts in revealing taxonomic and functional diversity of microorganism from petroleum muck using metagenomics approach. Using Ion Torrent Personal Genome Machine, total of 249 Mb raw data were obtained which was analysed using MG-RAST platform. The taxonomic analysis revealed predominance of Proteobacteria with Gammaproteobacteria as major class and Pseudomonas stutzeri as most abundant organism. Several enzymes involved in aliphatic and aromatic hydrocarbon degradation through both aerobic and anaerobic routes and proteins related to stress response were also present. Comparison of our metagenome with the existing metagenomes from oil-contaminated sites and wastewater treatment plant indicated uniqueness of this metagenome taxonomically and functionally. Based on these results a hypothetical community model showing survival and syntrophy of microorganisms in hydrocarbon-rich environment is proposed. Validation of the metagenome data was done in three tiers by validating major OTUs by isolating oil-degrading microbes, confirmation of key genes responsible for hydrocarbon degradation by Sanger sequencing and studying functional dynamics for degradation of the hydrocarbons by the muck meta-community using GC-MS.

Complete mitogenome of Asiatic lion resolves phylogenetic status within Panthera.

BACKGROUND: The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. RESULTS: The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. CONCLUSION: This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.