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In the present study, we explored four different geothermal spots of the Deulajhari spring cluster at a proximity of 10–20 meters with temperatures of 43 to 65°C to unravel their genesis, bacterial diversity and CAZyme potential. However, minor variations in physicochemical properties; TOC, sodium, chloride, zinc and nitrate were observed, including the pH of the spring openings. Illumina based amplicon sequencing revealed Firmicutes, Proteobacteria and Chloroflexi as the major bacterial phylum with higher abundance in the DJ04 sample. The alpha diversity of all the springs was almost same, whereas beta diversity revealed variations in the degree of uniqueness of OTUs at different temperatures. Statistical analysis established a positive correlation between sulfur content with Heliobacterium, Thermodesulfovibrio, Thermodesulfobacterium and Herpetosipho as well as TOC and HCO3 with Thermoanaerobacter, Desulfovibrio, Candidatus solibacter and Dehalogenimona. The major hydrocarbon family genes and Carbohydrate Active Enzyme pathways were predicted to be highest in DJ04 with elevated concentrations of HCO3 and TOC. Higher homogeneity in geo-physicochemical and microbial features direct the possibility of the common origin of these springs through plumbing systems. However, the minor variations in diversity and functionality were due to variations in temperature in spring openings through the mixing of subsurface water contaminated with carbohydrates from leaf biomass litter. Functional characterization of the thermophilic bacteria of this spring provides essential scope for further industrial applications. The biogeochemical reasons hypothesized for the genesis of unique multiple openings in the cluster are also of interest to conservation scientists for taking measures toward necessary laws and regulations to protect and preserve these springs.

Objectives The emergence and outbreak of colistin-resistant CRKP (carbapenem-resistant Klebsiella pneumoniae) have been the major global public threat in recent years. Present study emphasized the genome-wide distribution, characterization of drug resistance virulence genes in an extremely drug-resistant (XDR) Klebsiella pneumoniae strain isolated from a patient with drug-induced hepatitis, hospitalized in a tertiary care facility in India. Methods The total genomic DNA was sequenced using the Illumina Hiseq platform. De novo assembly of reads was done using CLC genomics workbench. Genome annotation was performed using PROKKA. Sequence typing (ST), virulence-related genes and antimicrobial resistance genes were predicted from genome sequences. Phenotypic evaluation of efflux pump function was done in presence of colistin and efflux pump inhibitor (EPI). Result Antibiogram analysis confirmed the isolate to be XDR. The number of contigs in assembly file was found to be 867 with a total of 6,060,836 bases and a total of 5547 coding sequences. The isolate exhibited high resistance to colistin due to mutations in two-component systems and predicted to be efflux mediated. The sequence typing of Klebsiella pneumoniae SDL79 is assigned to ST147. Conclusion This is the first whole genome analysis of XDR Klebsiella pneumoniae ST147 from a hospital conferring co-resistance to last resort drugs. However, the detailed molecular mechanism behind the drug resistance will be carried out in our future endeavors.

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.

Enzymes of microbial origin are of immense importance for organic material decomposition leading to bioremediation of organic waste, bioenergy generation, large-scale industrial bioprocesses, etc. The market demand for microbial cellulase enzyme is growing more rapidly which ultimately becomes the driving force towards research on this biocatalyst, widely used in various industrial activities. The use of novel cellulase genes obtained from various thermophiles through metagenomics and genetic engineering as well as following metabolic engineering pathways would be able to enhance the production of thermophilic cellulase at industrial scale. The present review is mainly focused on thermophilic cellulolytic bacteria, discoveries on cellulase gene, genetically modified cellulase, metabolic engineering, and their various industrial applications. A lot of lacunae are yet to overcome for thermophiles such as metagenome analysis, metabolic pathway modification study, search of heterologous hosts in gene expression system, and improved recombinant strain for better cellulase yield as well as value-added product formation.

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.

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.

Background & objectives: The prevalence of multidrug-resistant (MDR) Escherichia coli isolates producing β-lactamase enzyme is a growing problem across the globe. Strain typing is an epidemiologically important tool not only for detecting the cross transmission of nosocomial pathogens but also for determining the source of infection. The present study was conducted to understand the clonal relationship among various β-lactamase-producing MDR E. coli isolates using enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR). Methods: A total of 41 MDR E. coli isolates were randomly collected from various clinical samples and processed. Isolated organisms were tested for antibiotics resistance pattern. Phenotypic detection of metallo β-lactamases (MBL) was carried out by the imipenem-ethylenediaminetetraacetic acid disc diffusion/double-disc synergy test. AmpC enzyme production was tested by a modified three-dimensional extract test. Results: Almost all isolates were found sensitive to colistin. A high percentage of drug resistance was observed in these isolates against ceftazidime (100%), cefotaxime (100%), cefepime (100%), ofloxacin (97.56%), amoxicillin/clavulanic acid (97.56%) and norfloxacin (85.36%). Of the 41 isolates, ESBL producers were found to be predominant, i.e., 22 (53.65%), followed by AmpC (6, 14.63%) and MBL (5, 12.19%). Interpretation & conclusions: At 60 per cent similarity cut-off value, the dendrogram analysis showed that there were a total of 14 unique clusters of ERIC (CL-1 - CL-14) within the 41 E. coli isolates, which revealed the genetic diversity existing between them.

Microbial cellulases, a major group of industrial enzymes, have a wide range of applications as far as biotechnological, environmental issues, industrial products, and processes are concerned. Thermophilic bacteria act as a good source for industrial cellulase because of its compatibility during industrial harsh processes, for example, deinking of paper, softening of fabric material, pulp and paper, biostoning and biopolishing of fabric materials, juice, and animal feed, etc. Genome mediated application of thermophilic bacteria in various fields has become a rising fantasy among biotechnologists in the current scenario. The genetic manipulation of thermophilic bacteria may lead to enhanced cellulase production through recombinant technology, an emerging technology towards cellulase gene isolation of thermophilic bacteria and their expression in suitable hosts for enhanced cellulase production. Cellulase gene isolation from various thermophilic bacteria could be done through various approaches, such as a classical approach, whole genome isolation, whole metagenome isolation, and bioinformatics. In this chapter, various methods toward the isolation of cellulase genes from thermophilic bacteria are described which may lead to novel cellulase gene discovery as well as enhanced cellulase enzyme production.

Cyanobacteria are the most ancient lineages of the domain Bacteria and have been playing a crucial role in shaping our planet through their highly proliferating nature in harsh environmental conditions because of their adaptability to grow along with other photosynthetic and heterotrophic microbial community with varied ranges of salinity, pH, temperature, radiation, and water potential. Rise in temperature is reported to be the deciding factor in bringing down the microbial community diversity of hot springs. In the present study, for the first time, we reported the current status of the variability in community structure and predicted metabolic activity among cyanobacteria population of two sulfur hot springs, Atri at 48 °C and Taptapani at 58 °C, from the state of Odisha, Eastern India, using metagenomic approach. We further tried to establish the relationship between the differential occurrences of cyanobacteria clades with those of coexisting non-cyanobacteria clades chloroflexi from our previously published findings of hot spring microbial diversity analysis.

Arsenic is a gray-appearing metalloid which occurs naturally and is the 20th most prolific element in the earth’s crust. It is an integral part of more than 200 minerals. These are mostly ores containing sulfides, along with copper, nickel, lead, and other metals. In the environment, arsenic and its compounds are very mobile. Although in its organic form arsenic is nontoxic, it is highly toxic in its inorganic form (arsenite, a free form of arsenic) with arsine gas being the most fatal. The World Health Organization recommends a concentration below 20 mg/l for an individual to be considered free of arsenic poisoning. Accumulation of arsenic in the body beyond this level could adversely affect human health. An individual suffering from chronic arsenic poisoning via contaminated water could suffer from severe skin-related ailments like melanosis (pigmentation of the skin), keratosis (associated with the formation of rough, dry, and popular skin lesions), and leucomelanosis (also known as spotted melanosis) ultimately leading to arsenicosis in the long term. Other than that arsenic poisoning also may lead to other manifestations like neurological disorders, diabetes mellitus, high blood pressure, obstetric problems, disorders of the respiratory system, and cancer in the lung, skin, and bladder. The Indian subcontinent is very rich in arsenic, and countries like India and Bangladesh are a disaster waiting to happen. West Bengal, India, is a state severely affected by arsenic-contaminated water, and a case study showed an astounding 16 sites from one single village with very high concentrations of arsenic. As such, it is the need of the hour for governments to be ready with an immediate action plan to tackle such large-scale disasters. Existing solutions to this problem include phytoremediation via hyperaccumulation with plants like Pteris vittata and grasses like A. delicatula and use of phosphate-based fertilizers. However, a long-term use of phosphate-based fertilizers may ultimately lead to an algal bloom in water bodies, and phytoremediation is a time-consuming process. Planktons, however, have the potential to be a game changer in tackling arsenic-contaminated water bodies by virtue of accumulation and bioremediation. Spirulina platensis, a typical plankton, produces an enzyme called arsenite S-adenosylmethionine methyltransferase which has the ability to methylate arsenic making it nontoxic. This enzyme confers Spirulina platensis the unique ability to convert the toxic trivalent arsenic to its nontoxic pentavalent form. Spirulina platensis produces this enzyme by the virtue of arsenite S-adenosylmethionine methyltransferase (SpArsM) gene.

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.

Infectious diseases caused by ESBL producing Enterobacteriaceae are an emerging problem worldwide which increases the empirical treatment failure, hospital cost, rate of morbidity and mortality. This also leads to the Hospital infection outbreak. Present study was undertaken to determine the frequency of blaTEM, blaCTX-M and blaSHV genes among Enterobacteriaceae. A total of 751 non-repeated clinical isolates of Enterobacteriaceae family were included in this study. Antibiotic susceptibility test was done and minimal inhibitory concentration (MIC) against four antibiotics was carried out. Five hundred fifteen multi drug resistant isolates were tested for ESBL by CLSI confirmatory method. Isolates showing ESBL positive by phenotypic method were screened for blaTEM, blaCTX-M and blaSHV genes by monoplex PCR. Two blaTEM and two blaCTX-M amplified products were selected randomly for sequencing. Sequencing data was submitted to NCBI data base. Of the 515 MDR isolates, 140 showed ESBL production by phenotypic method. All the ESBL producing isolates showed resistant to ceftazidime (100%). IMP, TGC and CL drugs could be preferred for the treatment of ESBL producers as these drugs showed a lower rate of resistance. blaTEM gene was the predominant (96.42%) followed by blaCTX-M (75%) and blaSHV (17.85%). All the three bla genes were occurred in 22 (17.14%) isolates. All the phenotypically confirmed ESBL producers were found contain any one of the three bla genes. It is concluded from the study that the blaTEM was predominantly found in Enterobacteriaceae and blaCTX-M gene also seemed to emerging.

Deciphering the microbial diversity of the Deulajhari thermal springs is the major goal of our study. In our study the taxonomic description of the bacterial community structure was deduced from the 1.52 Gb metagenomics sequence size from the Deulajhari hot spring located in the Angul district of Odisha. Covered with the dense foliage, it has a high temperature, i.e. 69°C and alkaline pH i.e. 8.09. Various physiochemical parameter analysis of the sediment like; electro conductivity (0.025dSm−1), total organic carbon content (0.356%), nitrogen (125 kg/ha), phosphorus (7.88 kg/ha) and potassium (169.34 kg/ha) were done. Sediment sample of the Deulajhari hot spring was further processed for the 16S rRNA V3-V4 region by the amplicon metagenome sequencing from community DNA. Approximately 88.12% of the total microbial diversity was represented by the Proteobacteria followed by Bacteroidetes 10.76%, Firmicutes 0.35%, Spirochetes 0.18%, Thermi 0.13% and chloroflexi 0.11% at the phylum level. Thus through the metagenomics sequencing of the Deulajhari hot spring using IIllumina platform, we represent the complete microbial community structure present there in respective of their allocation, profusion and diverse coexisting microbiota.

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.

Deulajhari hot spring is located in the Angul district of Odisha. The significance of this hot spring is the presence of the hot spring cluster adjacent to the cold spring which attracts the attention of microbiologists to understand the role of physio-chemical factors of these springs on bacterial community structure. Next-generation sequencing technology helps us to depict the pioneering microflora of any ecological niche based on metagenomic approach. Our study represents the first Illumina based metagenomic study of Deulajhari hot spring DH1, and DH2 of the cluster with temperature 65 °C to 55 °C respectively establishing a difference of 10 °C. Comprehensive study of microbiota of these two hot springs was done using the metagenomic sequencing of 16S rRNA of V3‐V4 region extracting metagenomic DNA from the two hot spring sediments. Sequencing community DNA reported about 28 phyla in spring DH1 of which the majority were Chloroflexi (22.98%), Proteobacteria (15.51%), Acidobacteria (14.51%), Chlorobi (9.52%), Nitrospirae (8.54%), and Armatimonadetes (7.07%), at the existing physiochemical conditions like; temperature 65 °C, pH 8.06, electro conductivity 0.020 dSm−1, and total organic carbon (TOC) 3.76%. About 40 phyla were detected in cluster DH2 at the existing physiochemical parameters like temperature 55 °C, pH 8.10, electro conductivity 0.019 dSm−1, and total organic carbon (TOC) 0.58% predominated with Chloroflexi (41.98%), Proteobacteria (10.74%), Nitrospirae (10.01%), Chlorobi (8.73%), Acidobacteria (6.73%) and Planctomycetes (3.73%). Approximately 68 class, 107 order, 171 genus and 184 species were reported in cluster DH1 but 102 class, 180 order, 375 genus and 411 species in cluster DH2. The comparative metagenomics study of the Deulajhari hot spring clusters DH1, and DH2 depicts the differential profile of the microbiota.Metagenome sequences of these two hot spring clusters are deposited to the SRA database and are available in NCBI with accession no. SRX1459734 for DH1 and SRX1459735 for DH2. Keywords: Deulajhari, 16S rRNA, Next-generation sequencing, Metagenomics