Molecular Characterization Reveals Biodiversity and Biopotential of Rhizobacterial Isolates of Bacillus Spp.

Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 µg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 µM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27-34%), root length (20-50%), shoot length (20-40%), vigor index (50-75%), carotenoid content (0.543-1.733), and lycopene content (2.333-2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.

Adhatoda vasica and Tinospora cordifolia extracts ameliorate clinical and molecular markers in mild COVID-19 patients: a randomized open-label three-armed study.

BACKGROUND: SARS-CoV-2 infections caused mild-to-moderate illness. However, a sizable portion of infected people experience a rapid progression of hyper-inflammatory and hypoxic respiratory illness that necessitates an effective and safer remedy to combat COVID-19. METHODS: A total of 150 COVID-19-positive patients with no to mild symptoms, between the age groups 19-65 years were enrolled in this randomized, open-labeled three-armed clinical trial. Among them, 136 patients completed the study with RT-PCR negative reports. The patients received herbal drugs orally (Group A (Adhatoda vasica; AV; 500 mg; n = 50); Group B (Tinospora cordifolia; TC; 500 mg; n = 43), and Group C (AV + TC; 250 mg each; n = 43)) for 14 days. Clinical symptoms, vital parameters, and viral clearance were taken as primary outcomes, and biochemical, hematological parameters, cytokines, and biomarkers were evaluated at three time points as secondary outcomes. RESULTS: We found that the mean viral clearance time was 13.92 days (95% confidence interval [CI] 12.85-14.99) in Group A, 13.44 days (95% confidence interval [CI] 12.14-14.74) in Group B, and 11.86 days (95% confidence interval [CI] 10.62-13.11) days in Group C. Over a period of 14 days, the mean temperature in Groups A, and B significantly decreased linearly. In Group A, during the trial period, eosinophils, and PT/INR increased significantly, while monocytes, SGOT, globulin, serum ferritin, and HIF-1α, a marker of hypoxia reduced significantly. On the other hand, in Group B hsCRP decreased at mid-treatment. Eosinophil levels increased in Group C during the treatment, while MCP-3 levels were significantly reduced. CONCLUSIONS: All the patients of the three-armed interventions recovered from COVID-19 and none of them reported any adverse effects from the drugs. Group C patients (AV + TC) resulted in a quicker viral clearance as compared to the other two groups. We provide the first clinical report of AV herbal extract acting as a modifier of HIF-1α in COVID-19 patients along with a reduction in levels of ferritin, VEGF, and PT/INR as the markers of hypoxia, inflammation, and thrombosis highlighting the potential use in progression stages, whereas the TC group showed immunomodulatory effects. Trial registration Clinical Trials Database -India (ICMR-NIMS), CTRI/2020/09/028043. Registered 24th September 2020, https://www.ctri.nic.in/Clinicaltrials/pdf_generate.php?trialid=47443&EncHid=&modid=&compid=%27,%2747443det%27.

Withdrawal notice to "Structural and functional characterization for interaction of silver nanoparticles with ergostrol in Trichoderma harzianum" [Microb. Pathog. 125 (2018) 318-324].

This article has been withdrawn at the request of the editor and publisher. The publisher regrets that an error occurred which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error. The full Elsevier Policy on Article Withdrawal can be found at (https://www.elsevier.com/about/policies/article-withdrawal).

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture.

MAIN CONCLUSION: This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere.

Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like ß-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.

AYURAKSHA, a prophylactic Ayurvedic immunity boosting kit reducing positivity percentage of IgG COVID-19 among frontline Indian Delhi police personnel: A non-randomized controlled intervention trial.

Objective: The world continues to face the COVID-19 crisis, and efforts are underway to integrate traditional medicine interventions for its effective management. The study aimed to determine the efficacy of the "AYURAKSHA" kit in terms of post-interventional percentage of COVID-19 IgG positivity, immunity levels, and quality of life (QoL) against COVID-19. Method: This was a non-randomized controlled, prospective intervention trial, done after the distribution of 80,000 AYURAKSHA kits (constituent of Sanshamani Vati, AYUSH Kadha, and Anu Taila) among Delhi police participants in India. Among 47,827 participants, the trial group (n = 101) was evaluated with the positivity percentage of IgG COVID-19 and Immune Status Questionnaire (ISQ) scores as a primary outcome and the WHO Quality of Life Brief Version (QOL BREF) scores along with hematological parameters as a secondary outcome in comparison to the control group (n = 71). Results: The data showed that the percentage of COVID-19 IgG positivity was significantly lower in the trial group (17.5 %) as compared to the control group (39.4 %, p = 0.003), indicating the lower risk (55.6%) of COVID-19 infection in the trial group. The decreased incidence (5.05%) and reduced mortality percentage (0.44%) of COVID-19 among Delhi police officers during peak times of the pandemic also corroborate our findings. The ISQ score and WHO-QOL BREF tool analysis showed the improved scores in the trial group when compared with the controls. Furthermore, no dysregulated blood profile and no increase in inflammation markers like C-reactive protein, erythrocyte sedimentation rate, Interleukin-6 (IL-6) were observed in the trial group. However, significantly enhanced (p = 0.027) IL-6 levels and random blood sugar levels were found in the control group (p = 0.032), compared to a trial group (p = 0.165) post-intervention. Importantly, the control group showed more significant (p = 0.0001) decline in lymphocyte subsets CD3+ (% change = 21.04), CD4+ (% change = 20.34) and CD8+ (% change = 21.54) levels than in trial group, confirming more severity of COVID-19 infection in the control group. Conclusion: The AYURAKSHA kit is associated with reduced COVID-19 positivity and with a better quality of life among the trial group. Hence, the study encourages in-depth research and future integration of traditional medicines for the prevention of the COVID-19 pandemic. Clinical trial registration: http://ctri.nic.in/, identifier: CTRI/2020/05/025171.

Sugarcane Root Transcriptome Analysis Revealed the Role of Plant Hormones in the Colonization of an Endophytic Diazotroph.

Some sugarcane germplasms can absorb higher amounts of nitrogen via atmospheric nitrogen fixation through the bacterial diazotrophs. Most endophytic diazotrophs usually penetrate through the root, colonize inside the plant, and fix the nitrogen. To assess the plant's bacterial association during root colonization, strain GXS16 was tagged with a plasmid-bear green fluorescent protein (GFP) gene. The results demonstrated that the strain can colonize roots all the way to the maturation zone. The strain GXS16 showed maximum nitrogenase enzyme activity at pH 8 and 30°C, and nitrogenase activity is less affected by different carbon sources. Further, strain GXS16 colonization response was investigated through plant hormones analysis and RNAseq. The results showed that the bacterial colonization gradually increased with time, and the H2O2 and malondialdehyde (MDA) content significantly increased at 1 day after inoculation. There were no substantial changes noticed in proline content, and the ethylene content was detected initially, but it decreased with time. The abscisic acid (ABA) content showed significant increases of 91.9, 43.9, and 18.7%, but conversely, the gibberellin (GA3) content decreased by 12.9, 28.5, and 45.2% at 1, 3, and 5 days after inoculation, respectively. The GXS16 inoculation significantly increased the activities of catalase (CAT), superoxide dismutase (SOD), polyphenol oxidase (PPO), ascorbate peroxidase (APX), and glutathione reductase (GR) at different timepoint. In contrast, the peroxisome (POD) activity had no changes detected during the treatment. In the case of RNAseq analysis, 2437, 6678, and 4568 differentially expressed genes (DEGs) were identified from 1, 3, and 5 days inoculated root samples, and 601 DEGs were shared in all samples. The number or the expression diversity of DEGs related to ethylene was much higher than that of ABA or GA, which indicated the critical role of ethylene in regulating the sugarcane roots response to GXS16 inoculation.

Does eugenol affect the microtensile bond strength of self-adhering composite? - An in vitro study.

Objectives: The objective of the study is to evaluate the effect of eugenol-based temporary on microtensile bond strength of self-adhering composite at 1 day and 7-day time intervals. Materials and Methods: Occlusal enamel of 24 human molars was removed. Zinc oxide eugenol (ZnOE) and noneugenol temporary cement (ZnONE) were placed on the dentin surfaces and left for different times (1 day, 7 days). After removal of temporary cement, teeth were randomly divided into eight subgroups: subgroup GE1S (n = 3): ZnOE cement + Self-adhering composite (SAC), subgroup GE1N (n = 3): ZnOE cement + adhesive system (one coat 7 universal) + nanohybrid composite, subgroup GE7S (n = 3): ZnOE cement + SAC, subgroup GE7N (n = 3): ZnOE cement + adhesive system + nanohybrid composite, subgroup GNE1S (n = 3): ZnONE cement + SAC, subgroup GNE1N (n = 3): ZnONE cement + adhesive system + nanohybrid composite, subgroup GNE7S (n = 3): ZnONE cement + SAC, subgroup GNE7N (n = 3): ZnONE cement + adhesive system + nanohybrid composite. Four sticks per tooth were obtained, resulting in 12 sticks per group with a cross-sectional area of 0.5 mm 2. The µTBS test was performed with a crosshead speed of 0.5 mm/min. Statistical Analysis: Kruskal-Wallis and Mann-Whitney U-test were used for analysis. Results: Highest and lowest mean value of microtensile bond strength was observed in GNE7N (12.75MPa) and GE1S (1.42MPa), respectively. Conclusion: The presence of eugenol at early stage, i.e. 1 day, has a negative influence on microtensile bond strength of SAC. At 7 days, the negative effect of eugenol on microtensile bond strength gets nullified. Thus, a waiting period of 1 week is sufficient to overcome negative influence of eugenol-based temporaries on polymerization of SAC.

Structural and functional characterization for interaction of silver nanoparticles with ergostrol in Trichoderma harzianum.

Silver ions, because of its recognised antimicrobial activity are reported in several regions for the very long time while ergosterol, apart from its role as a secondary metabolite, structural component of the fungal cell membranes, also turns out to be activating defence response in plants. Silver ions biosynthesized by terpene ergosterol producing Trichoderma harzianum could be used against other plant pathogenic fungi. In this work, possible interaction of the silver ions with ergosterol enzyme has been investigated using a computational approach. Protein model construction via prior knowledge of sequences and molecular ligand docking experiments as well as structural and sequence comparisons were executed to identify potential active-site in ergosterol enzyme. Moldock score of -48.5747 with the reranking score of -40.0228 has been reported by Molegro Virtual Docker(MVD) at ergosterol enzyme's active site positions for silver ion. Apart from the core of the active site, four other positions have been occupied by silver ion. The interacting site surrounded by Cys339, Arg343, Lue365, Leu336 and Trp371 formed hydrophobic bonds with silver. The anti-microbial activity against phytopathogens is believed to increase synergistically when combined with ergosterol enzyme. Thus the computational analysis of silver ion in conjugation with ergosterol enzyme provided additional strategies to improve the ability of the Trichoderma strains in biocontrol of pathogenic fungi. In the present study, silver ion based formulations which are produced by strong bio-control fungi as shown were estimated in response to different plant pathogen in further studies.

Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere.

The use of Trichoderma isolates with efficient antagonistic activity represents a potentially effective and alternative disease management strategy to replace health hazardous chemical control. In this context, twenty isolates were obtained from tomato rhizosphere and evaluated by their antagonistic activity against four fungal pathogens (Fusarium oxysporum f. sp. lycopersici, Alternaria alternata, Colletotrichum gloeosporoides and Rhizoctonia solani). The production of extracellular cell wall degrading enzymes of tested isolates was also measured. All the isolates significantly reduced the mycelial growth of tested pathogens but the amount of growth reduction varied significantly as well. There was a positive correlation between the antagonistic capacity of Trichoderma isolates towards fungal pathogens and their lytic enzyme production. The Trichoderma isolates were initially sorted according to morphology and based on the translation elongation factor 1-α gene sequence similarity, the isolates were designated as Trichoderma harzianum, T. koningii, T. asperellum, T. virens and T. viride. PCA analysis explained 31.53, 61.95, 62.22 and 60.25% genetic variation among Trichoderma isolates based on RAPD, REP-, ERIC- and BOX element analysis, respectively. ERG-1 gene, encoding a squalene epoxidase has been used for the first time for diversity analysis of antagonistic Trichoderma from tomato rhizosphere. Phylogenetic analysis of ERG-1 gene sequences revealed close relatedness of ERG-1sequences with earlier reported sequences of Hypocrea lixii, T. arundinaceum and T. reesei. However, ERG-1 gene also showed heterogeneity among some antagonistic isolates and indicated the possibility of occurrence of squalene epoxidase driven triterpene biosynthesis as an alternative biocontrol mechanism in Trichoderma species.

Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment.

Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2%) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates.

A review on role of psychological factors in the etiopathogenesis of Pandu Roga with reference to iron deficiency anemia.

"Pandu" Roga is a disease entity described in Ayurveda which has clinical features similar to that of various types of anemia, in which there develops a pale-yellow discoloration on the skin. Besides the various etiological factors, Acharya Charaka has specially described some psychological causative factors among which Chinta (excessive worry), Bhaya (fear) and Shoka (grief) are three main factors, which play an important role in the pathogenesis of Pandu Roga. This paper aims to explore the scientific explanations for the above stated factors in the causation of Pandu Roga (anemia). Hence, a thorough search was made on the internet using the keywords anemia, psychological stress, anger, fear and some scientific studies were found on the concerned topic. It reveal that these factors disturb the process of iron distribution within the body and affects the process of erythropoiesis causing iron deficiency anemia.

Mating type genes and genetic markers to decipher intraspecific variability among Fusarium udum isolates from pigeonpea.

To ascertain the variability in Fusarium udum (Fu) isolates associated with pigeonpea wilt is a difficult task, if based solely on morphological and cultural characters. In this respect, the robustness of five different genetic marker viz., random amplified polymorphic DNA (RAPD), enterobacterial repetitive intergenic consensus (ERIC), BOX elements, mating type locus, and microsatellite markers were employed to decipher intra-specific variability in Fu isolates. All techniques yielded intra-specific polymorphism, but different levels of discrimination were obtained. RAPD-PCR was more discriminatory, enabling the detection of thirteen variants among twenty Fu isolates. By microsatellite, ERIC- and BOX-PCR fingerprinting, the isolates were categorized in seven, five, and two clusters, respectively. Cluster analysis of the combined data also showed that the Fu isolates were grouped into ten clusters, sharing 50-100% similarity. The occurrence of both mating types in Fu isolates is reported for the first time in this study. All examined isolates harbored one of the two mating-type idiomorphs, but never both, which suggests a heterothallic mating system of sexual reproduction among them. Information obtained from comparing results of different molecular marker systems should be useful to organize the genetic variability and ideally, will improve disease management practices by identifying sources of inoculum and isolate characteristics.

Using the information value method in a geographic information system and remote sensing for malaria mapping: a case study from India.

BACKGROUND: This paper explores the scope of malaria-susceptibility modelling to predict malaria occurrence in an area. OBJECTIVE: An attempt has been made in Varanasi district, India, to evaluate the status of malaria disease and to develop a model by which malaria-prone zones could be predicted using five classes of relative malaria susceptibility, i.e.very low, low, moderate, high and very high categories. The information value (Info Val) method was used to assess malaria occurrence and various time-were used as the independent variables. A geographical information system (GIS) is employed to investigate associations between such variables and distribution of different mosquitoes responsible for malaria transmission. Accurate prediction of risk depends on a number of variables, such as land use, NDVI, climatic factors, population, distance to health centres, ponds, streams and roads etc., all of which have an influence on malaria transmission or reporting. Climatic factors, particularly rainfall, temperature and relative humidity, are known to have a major influence on the biology of mosquitoes. To produce a malaria-susceptibility map using this method, weightings are calculated for various classes in each group. The groups are then superimposed to prepare a Malaria Susceptibility Index (MSI) map. RESULTS: We found that 3.87% of the malaria cases were found in areas with a low malaria-susceptibility level predicted from the model, whereas 39.86% and 26.29% of malaria cases were found in predicted high and very high susceptibility level areas, respectively. CONCLUSIONS: Malaria susceptibility modelled using a GIS may have a role in predicting the risks of malaria and enable public health interventions to be better targeted.