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Thermal springs have been the most resourceful ecological niches to understand the intricacies of the microbial community structure building. In the present study, the microbial community structure...

In this investigation, sixty morphologically different ginger rhizomes, collected from an active germplasm conservatory of High Altitude Research Station, Odisha, India, were characterized using morphological traits and molecular markers. Larger variations in morphological characters were observed among the 45 ginger accessions out of 60 accessions. Out of 22 markers, 9 ISSR and 13 SSR markers used for analysis generated 42 and 160 polymorphic bands accounting to 55% and 63.29% of the total polymorphic bands, respectively; this depicts that SSR markers have better efficiency over ISSR markers. A high degree of variation is detected in multivariate analysis (PCA and UPGMA) of both morphological traits and combined molecular markers, in which the ginger accessions clustered into five and four distinct groups. This explains the existence of large variation in morphological traits despite markers used. Genetic distance between the accessions determined from Nei’s dissimilarity matrix was used to find out the potential duplicates within the accessions collected. Twenty-nine accessions having mean genetic distance (MGD) less than threshold MGD (average MGD) value 0.174 were considered as ‘potential duplicate’ accessions and were reduced to one group, and the rest 31 were considered distinct genotype out of 60 accessions. From this analysis, 48.3% of the collection were considered as potential duplicates and deemed to be redundant. However, careful elimination of redundant through molecular analysis supported with passport data will help to eradicate existing synonyms used by farmers and improve management practices of the ginger germplasm conservatory.

Worldwide concern about the energy security and search for alternate energy source as fuel has created attention because of increased demand and fast depleting nonrenewable resources of fuel. In order to meet the increasing energy demand, we need to approach the sustainable, cost-effective alternates which should be able to cater unlimited resource utilization potential. Among the next-generation biofuels, butanol is the one which shows the ability to meet both the current and upcoming future energy crisis over the existing biofuels, for its distinguished merits; high energy density, high air-fuel ratio and lower hygroscopicity which make butanol superior over the other. In this review, we summarized all the methods attempted to screen out a high-stress tolerant strain through the various approach like; variation in sampling methods, media optimization, manipulation in physiochemical parameters etc. and then adapting them to high butanol environment. Secondly, the possible techniques involved in the identification of butanol tolerant gene and its overexpression in heterologous host or butanol tolerant microbes through genetic engineering, manipulating the metabolic pathway through engineering synergistically integrated with other disciplines such as synthetic biology as well as systems biology, has been discussed in detail. Apart from this, the present review also highlights the various bottlenecks, achievements and prospects for the commercialization of the butanol as the next generation of biofuel.

Biofilm formation is a major threat to the society, as it adds to the severity of bacterial infection making antimicrobial agents ineffective. In the present study, the antibacterial and antibiofil...

The emergence of colistin-carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) in bloodstream infection results in high mortality, and virulence factor contributes further to the difficulty of treatment. A total of 158 carbapenem-resistant K. pneumoniae (CRKP) isolates causing bloodstream infection were collected from three Indian tertiary care hospitals during the 9-month study period, of which 27 isolates exhibited resistance to both colistin and carbapenem antibiotics. In this study, all the strains were characterized for antimicrobial resistance, virulence factors and capsular serotypes that facilitate the development of colistin and carbapenem-resistant K.pneumoniae (CCR-Kp) in bloodstream infection. Fourteen isolates displayed extremely drug resistance (XDR), susceptible only to tigecycline, and the remaining 13 isolates displayed multidrug resistance (MDR). The gene prevalence analysis for CCR-Kp isolates showed the predominance of bla(KPC) (81.48%) followed by bla(NDM) (62.96%), bla(VIM) (37.03%) and bla(IMP) (18.51%) genes. The distribution of virulence genes was found to be fimH (81.48%), wabG (59.25%), mrkD (55.56%), entB (48.15%), irp1 (33.33%), and rmpA (18.52%). The capsular serotypes K1, K2, K5 and K54 have been identified in 16 isolates. The absence of plasmid-mediated colistin resistance (mcr) genes implies the involvement of other mechanisms. The ERIC and (GTG)(5) molecular typing methods detected 18 and 22 distinct clustering patterns among the CCR-Kp isolates, respectively. A strong correlation between ERIC and (GTG)5 genotyping method was established with antimicrobial resistance patterns and virulence determinants at P

Lipase based formulations has been a rising interest to laundry detergent industry for their ecofriendly property over phosphate-based counterparts and compatibility with chemical detergents ingredients. A thermo-stable Anoxybacillus sp. ARS-1 isolated from Taptapani Hotspring, India was characterized for optimum lipase production employing statistical model central composite design (CCD) under four independent variables (temperature, pH, % moisture and bio-surfactant) by solid substrate fermentation (SSF) using mustard cake. The output was utilized to find the effect of parameters and their interaction employing response surface methodology (RSM). A quadratic regression with R2¼0.955 established the model to be statically best fitting and a predicted highest lipase production of 29.4IU/g at an optimum temperature of 57.5oC, pH 8.31, moisture 50% and 1.2mg of bio-surfactant. Experimental production of 30.3IU/g lipase at above conditions validated the fitness of model. Anoxybacillus sp. ARS-1 produced lipase was found to resist almost all chemical detergents as well as common laundry detergent, proving it to be a prospective additive for incorporation.

An efficient and reproducible protocol for in vitro plant regeneration was developed for Lawsonia inermis L. using cotyledonary node explant derived from axenic seedlings. Highest shoot proliferation frequency (ca 96.6%) was achieved on Murashige and Skoog’s, 1962 (MS) basal medium supplemented with 8.88 μM 6-Benzyladenine (BA) + 2.68 μM Napthalene acetic acid (NAA). Up-scaling of shoots was carried out using in vitro nodes on MS medium supplemented with 4.44 μM BA. So overall, an average of 238 shoots was produced at 75 days. Of the four different forms of cotyledonary node explants evaluated, highest shoot multiplication was observed in cotyledonary node explant with two whole cotyledons. In vitro regenerated shoots were best rooted (ca 34.3 roots / shoot) on ½ MS medium devoid of any growth regulator. The plantlets were successfully acclimated in sand:soil:: 1:1and established in the garden soil. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis revealed a homogeneous amplification profile for all micropropagated plants validating the genetic fidelity of the in vitro-regenerated plants and supporting the regeneration protocol for economic commercial exploitation.

The emergence of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has been increasing rapidly across the world. The presence of virulence factors in ESBL producers further adds to the pathogenicity and severity of infection, which often complicate empirical therapy and sometimes result in treatment failures. In the present study, 227 non-repeated clinical isolates of K. pneumoniae obtained from different clinical specimens from a tertiary care hospital in India were analyzed to detect the genes responsible for ESBL production (blaTEM, blaCTX-M, and blaSHV), virulence (fimH-1, mrkD, entB, irp-1), and capsule production (K1-K2). Phenotypically identified 72 ESBL producing K. pneumoniae isolates were further subjected to PCR based genotypic analysis but only 20 were found to have at least one of the ESBL producing genes. blaTEM was the most predominant gene (100%), followed by blaSHV (90%), and blaCTX-M (85%). Similarly, the most common virulence genes were fimH-1 (70%), entB (65%), markD (55%), irp-1 (25%), K1 (25%), and K2 (20%). REP-PCR profile separated them into five major clusters (I-V), indicating the existing heterogeneity among the isolates. The resistance profile data obtained from the present study can serve as the information base to understand the infection pattern prevailing in the hospital and for physicians to recommend suitable antibiotics for the patients.

The emergence of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has been increasing rapidly across the world. The presence of virulence factors in ESBL producers further adds to the pathogenicity and severity of infection, which often complicate empirical therapy and sometimes result in treatment failures. In the present study, 227 non-repeated clinical isolates of K. pneumoniae obtained from different clinical specimens from a tertiary care hospital in India were analyzed to detect the genes responsible for ESBL production (blaTEM, blaCTX-M, and blaSHV), virulence (fimH-1, mrkD, entB, irp-1), and capsule production (K1-K2). Phenotypically identified 72 ESBL producing K. pneumoniae isolates were further subjected to PCR based genotypic analysis but only 20 were found to have at least one of the ESBL producing genes. blaTEM was the most predominant gene (100%), followed by blaSHV (90%), and blaCTX-M (85%). Similarly, the most common virulence genes were fimH-1 (70%), entB (65%), markD (55%), irp-1 (25%), K1 (25%), and K2 (20%). REP-PCR profile separated them into five major clusters (I-V), indicating the existing heterogeneity among the isolates. The resistance profile data obtained from the present study can serve as the information base to understand the infection pattern prevailing in the hospital and for physicians to recommend suitable antibiotics for the patients.

Oral biofilm formation is the defense mechanism exhibited by oral pathogens against antimicrobial agents responsible for causing several oral infections. Lipase mediated catalytic degradation of biofilm formed in-vitro by oral pathogens Enterococcus faecalis and Streptococcus mutans is attempted in the present approach. Lipase was produced from sesame oil cake biomass using thermophilic Pseudomonas formosensis TB5 isolated from sediment of Tarabalo hot spring, Odisha. The experiment was designed by using Design-Expert (v.6.0.7). The statistical method central composite design and response surface methodology was carried out to study the interaction between various parameters (pH, temperature, moisture and biosurfactant) on lipase production in a solid-state fermentation process. A quadratic regression model with (R2 = 0.8642), was found to be best fitting and predicted maximum lipase production to be 47.2IU/g at an optimum pH (8.34), temperature (51.63 °C), moisture (52.51%) and biosurfactant (1.36 mg) using sesame oil cake. Experimentally, lipase was produced at a concentration of 50.78IU/g at above predicted optimum conditions which validated the fitness of model, the value being very close to the predicted one. Lipase from P. formosensis was found to degrade biofilm of oral pathogens, proving to be scope of its use a prospective biological agent for dental biofilm treatment after undertaking further analysis.

An efficient, reliable and reproducible plant regeneration protocol was developed for Lawsonia inermis L. using mature nodal explants. Shoot proliferation (81.6 %) with 7.8 shoots/explant was achieved on Murashige and Skoog’s (MS) medium supplemented with 1.0 mg l−1 6-benzyladenine. Shoot numbers were up-scaled by inducing multiple shoots from axenic nodal segments derived from the primary shoots on the shoot regeneration medium. Thus the authors could achieve ca. 129–134 shoots from single nodal explant. Ninety-three percent rooting of in vitro regenerated shoots was achieved on growth regulator free half-strength MS medium. Regenerated plantlets were successfully transferred to soil with 85 % survival rate. Genetic stability analyses of the in vitro regenerated plants using random amplified polymorphic DNA and inter simple sequence repeat markers revealed a homogeneous amplification profile for all micropropagated plants. This is the first report that evaluates the use of molecular markers to establish genetic fidelity of micropropagated L. inermis for the rapid clonal multiplication and true-to-type production of plant for attaining the ever increasing demand in pharmaceutical industries.

Ginger (Zingiber officinale Rosc.) rhizome has great demand in food and pharmaceutical industry. Odisha is the second largest ginger-cultivating state, and considered as best suitable after Kerala, in India. Forty-eight germplasm from 10 agro-climatic zones of Odisha were genetically characterized and potential duplicates were identified employing 25 polymorphic markers (RAPD, ISSR, SSR). These markers together amplified 170 polymorphic, 136 monomorphic, and 2 unique bands. SSR markers were the most efficient in generating highest primer resolving power (44.85), primer index (10.28), and number of polymorphic bands (67). Genotype–environment interaction was clearly demonstrated from UPGMA dendrogram based on Jaccard’s similarity coefficients and SAHN clustering which divided 48 samples into 8 sub-clusters (showing 80 % congruence with their places of geographical origin). H (0.211), I (0.38), and Gst (0.239) indices revealed genetic diversity within and genetic differentiation among 10 populations. AMOVA showed higher genetic variability among populations (64 %) than within populations (36 %). Ginger accessions having a mean genetic distance less than 0.21 (threshold average genetic distance) were considered redundant. Forty-eight samples could be reduced to 11 genetically diverse groups (each group contains duplicates but is different from each other) which confirmed 77 % of the collection to be redundant. Identification of duplicates can be useful to eliminate confusion regarding synonyms among farmers, help selection of suitable ginger seed material, and facilitate judicious management of germplasm in conservatory. Genetic diversity analysis unraveled the scope of genetic improvement and breeding program. Clustering analysis showed grouping of majority of samples to respective agro-climatic zones and established the possible interaction between genotype and environment.

Extreme environments are the main source of industrially suitable biocatalysts. The non-cultivable approach of searching enzymes is known to provide ample scope to accomplish novelty for their industrial applications. Lip479 clone out of seven lipase-producing clones obtained from Taptapani hot spring was found to be optimally active at pH 8.0 and temperature 65 °C. The recombinant Lip479 was highly stable in organic solvents, methanol, DMF, DMSO, acetone, and dichloromethane. Lip479 lipase activity was enhanced in the presence of K+, Mn2+, Na+, Zn2+, and Ca2+ except for Fe3+. The ability of Lip479 lipase to act on long carbon chain of 4-nitrophenyl myristate suggests it might be a true lipase. Lip479 clone was found to have ORF of 1251 bp encoding 416 amino acid residues of 42.57 KDa size (theoretically calculated). The presence of conserved motif Ala-His-Ser-Gln-Gly and Zn2+-binding consensus sequence (GAAHAAKH) of the clone assigns the protein to lipase family 1.5. Phylogenetic lineage of the protein sequence of Lip479 was traced to family 1.5 as it was clubbed up with those of reported lipases of the same family. The above biochemical features indicated that Lip479 lipase can be a potential biocatalyst for its use in various industries.

The rapid lifestyle of industrialization and increasing demand of fossil oil that are going to be scarce in future date have led to think the alternative source of renewable energy as fuels to meet our energy demands. Fossil fuel is challenged with increasing price and a decreasing quantity, and burning of the fuels is putting the environment into threat toward pollution and global warming. Various steps toward cultivating oil crops such as Jatropha, corn, coconut, soybean, and oil palm have been encouraged, but productivity of oil has been very less, i.e., 5% of total biomass, and it needs vast acres of cultivated land. Therefore, to overcome the problem, today’s world is moving toward microalgae cultivation, which in comparison can grow faster in wastelands/uncultivated lands and can produce up to 80% of the dry weight of algae biomass. Microalgae are phototrophic and are able to transform carbon dioxide into biofuels, valuable bioactive compounds, foods, and feeds. In spite of all positivity, microalgae biofuel is still not common man’s fuel due to various hurdles. Overhead harvesting cost is 20–30% higher to the cultivation cost of algae; it can reduce the nonrenewable resources (nitrogen, phosphorus) for which still date it cannot reach to common man. However, limited supply of these renewable oils and high cost stop it to be a potential challenger in the face of other petroleum-based fuels. Overall, economic feasibility and environmental suitability cannot be forgotten when venturing into scaling up for future commercialization.

Ginger (Zingiber officinale Rosc.) is an important herb of the family Zingiberaceae. It is accepted as a universal cure for a multitude of diseases in Indian systems of medicine and its rhizomes are equally popular as a spice ingredient throughout Asia. SNPs, the definitive genetic markers, representing the finest resolution of a DNA sequence, are abundantly found in populations having a lower rate of mutation and are used for genomic analysis. The public ESTs sequences mostly lack quality files, making high quality SNPs detection more difficult since it is exclusively based on sequence comparisons. In the present study, current dbESTs of NCBI was mined and 38115 ginger ESTs sequences were obtained and assembled into contigs using CAP3 program. In this analysis, recent software tool QualitySNP was used to detect 11523 potential SNPs sites, 8810 high quality SNPs and 1008 indels polymorphisms with a frequency of 1.61 SNPs / 10 kbp. Of ESTs libraries generated from three ginger tissues together, rhizomes had a frequency of 0.32 SNPs and 0.03 indels per 10 kbp whereas the leaves had a frequency of 2.51 SNPs and 0.23 indels per 10 kbp and root is showing relative frequency of 0.76/10 kbp SNPs and 0.02/10 kbp indels. The present analysis provides additional information about the tissue wise presence of haplotypes (222), distribution of high quality exonic (2355) and intronic (6455) SNPs and information about singletons (7538) in addition to contigs transitions and transversions ratio (0.57). Among all tissue detected SNPs, transversions number is higher in comparison to the number of transitions. Quality SNPs detected in this work can be used as markers for further ginger genetic experiments.

Odisha (East India) is home to several hot springs, of which Atri and Taptapani are the two with variation in temperature and located in the Mahanadi geothermal province having altitude 120 and 1800 ft., respectively, above sea level. Average temperature of Atri hot spring is as higher as 58 ± 5°C as compared to 48 ± 5°C of Taptapani. In-depth analysis of the microbial diversity of these hot springs through 16S rRNA deep sequencing analysis, targeting V3 region was performed using Illumina bar-coded sequencing platform. Existence of higher microbial diversity in Atri hot spring (1662 OTUs; 2708 species) as compared to Taptapani (1561 Operational Taxonomic Units [OTUs]; 2045 species) is supported by higher value of diversity indices for Atri (6.24, Shannon; 0.95, Simpson) than Taptapani (4.03, Shannon; 0.79, Simpson), probably due to favorable influence of environmental parameters around it. Irrespective of the four databases (GREENGENE, M5RNA, Ribosomal Database Project [RDP], and Small Subunit [SSU] databases) used for understanding community structure, the dominant phyla in the Atri hot spring were different from the predominant populations in the Taptapani in terms of percentage representation in different databases. From Principal Coordinates Analysis [PCoA] analysis, Atri and Taptapani metagenome, on comparison with other three metagenomes, were found to be matching with the community structure of hot springs of Gujarat, India, but differed from that of saline desert. Furthermore, predicted functional analysis in both the hot springs were found to be affiliated with carbohydrate, amino acids, energy, vitamins and cofactor, nucleotide, membrane transport metabolic pathways, and the genes involved in them, although their intensity of occurrence was varying as analyzed through PICRUSt and Tax4Fun probably due to physicochemical parameters prevailing around each hot spring. The present study for the first time has revealed the differential microbial community structure and predicted functional diversity of Atri and Taptapani hot springs of Odisha in such a great detail.

Ginger (Zingiber officinale Rosc.), a well-known member of family Zingiberaceae, is bestowed with number of medicinal properties which is because of the secondary metabolites, essential oil and oleoresin, it contains in its rhizome. The drug yielding potential is known to depend on agro-climatic conditions prevailing at the place cultivation. Present study deals with comparative transcriptome analysis of two sample of elite ginger variety Suprabha collected from two different agro-climatic zones of Odisha. Transcriptome assembly for both the samples was done using next generation sequencing methodology. The raw data of size 10.8 and 11.8GB obtained from analysis of two rhizomes S1Z4 and S2Z5 collected from Bhubaneswar and Koraput and are available in NCBI accession number SAMN03761169 and SAMN03761176 respectively. We identified 60,452 and 54,748 transcripts using trinity tool respectively from ginger rhizome of S1Z4 and S2Z5. The transcript length varied from 300bp to 15,213bp and 8988bp and N50 value of 1415bp and 1334bp respectively for S1Z4 and S2Z5. To the best of our knowledge, this is the first comparative transcriptome analysis of elite ginger cultivars Suprabha from two different agro-climatic conditions of Odisha, India which will help to understand the effect of agro-climatic conditions on differential expression of secondary metabolites.

Zingiber officinale Rosc., known as ginger, is an Asian crop, popularly used in every household kitchen and commercially used in bakery, beverage, food and pharmaceutical industries. The present study deals with de novo transcriptome assembly of an elite ginger cultivar Suruchi by next generation sequencing methodology. From the analysis 10.9GB raw data was obtained which can be available in NCBI accession number SAMN03761185. We identified 41,969 transcripts using Trinity RNA-Seq from ginger rhizome of Suruchi variety from Odisha. The transcript length varied from 300bp to 8404bp with a total length of 3,96,40,526bp and N50 of 1251bp. To the best of our knowledge, this is the first transcriptome data of an elite ginger cultivar Suruchi released for Odisha state of India which will help molecular biologists to develop genetic markers for identification of cultivars.