Research Article by Enketeswara Subudhi
Ginger (Zingiber officinale Rosc.) is an important herb of the family Zingiberaceae. It is accept... more 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.
Molecular techniques play a critical role in studies of phylogeny and, thus, have been applied to... more Molecular techniques play a critical role in studies of phylogeny and, thus, have been applied to understand the distribution and extent of genetic variation within and between species. In the present study, a genetic analysis was undertaken using molecular markers (9 ISSR and 13 SSR) on 60 ginger cultivars from different regions of the eastern coast of India (Odisha). The data obtained with 22 polymorphic markers revealed moderate to high diversity in the collection. Both ISSR and SSR markers were efficient in distinguishing all the 60 ginger cultivars. A total of 42 and 160 polymorphic bands were observed with ISSR and SSR markers, respectively. However, SSR markers were observed to be better at displaying average polymorphism (63.29%) than ISSR markers (55%). Analysis of molecular variance results showed that 52 and 66% of the variation occurred among different ginger populations, whereas 48 and 34% of the variation was found within populations, respectively, using ISSR and SSR markers, indicating that ginger cultivars display significant genetic diversity at the population level. Principal coordinates analysis and the dendrogram constructed out of combined data of both markers showed grouping of ginger accessions to their respective area of collection, indicating geographical closeness due to genetic similarity irrespective of the relationship that exists at the morphological level.
Ginger (Zingiber officinale Rosc.), a well-known member of family Zingiberaceae, is bestowed with... more 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 rhi-zome. 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 11.8 GB 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 300 bp to 15,213 bp and 8988 bp and N50 value of 1415 bp and 1334 bp 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.
Deulajhari hot spring is located in the Angul district of Odisha. The significance of this hot sp... more 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.
Zingiber officinale Rosc., known as ginger, is an Asian crop, popularly used in every household k... more 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 10.9 GB 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 300 bp to 8404 bp with a total length of 3,96,40,526 bp and N50 of 1251 bp. 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.
Conference Presentations by Enketeswara Subudhi
Deciphering the microbial diversity of the Deulajhari thermal springs is the major goal of our st... more 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 Bacteroidetes10.76%, 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.
Papers by Enketeswara Subudhi
The Role of Microalgae in Wastewater Treatment, 2018
The ever-increasing need of energy both in the domestic and industrial front has augmented the co... more The ever-increasing need of energy both in the domestic and industrial front has augmented the consumption of fossil fuel; consequently, complexity arises owing to exhausting fuel supplies and due to their contribution to climate change by the emission of large quantities of greenhouse gases. The renewable, economic, and carbon-neutral biofuel from algae has made it a promising feedstock that can curtail global dependency on rapidly depleting fossil fuel-based petro diesel. Moreover, higher biomass and cellular lipid accumulation competence and economic sustainability even in large-scale production make algae a better choice than other existing oil crops. There are quite a few studies reporting number of green microalgae as a potential feedstock for biofuel production. Accumulation of lipid in microalgae is species dependent, and in potential strains it ranges from 25% to 60% of dry cell weight, in modified growth conditions; however, some microalgae are reported to accumulate more than 60% of cellular lipid content. The present chapter is specifically aimed to review freshwater green microalga Scenedesmus abundans as a prospective feedstock for high-quality biofuel production.
Industrial Crops and Products, Aug 1, 2023
Industrial Crops and Products
New and Future Developments in Microbial Biotechnology and Bioengineering
Abstract Investigation of microbial community structure and biology has been progressing with the... more Abstract Investigation of microbial community structure and biology has been progressing with the help of high-throughput functional genomics which have proven to be irreplaceable for studying diverse microbial communities. In this chapter, we discuss emerging strategies for microbial community analysis through metagenomic profiling and beyond. These are complemented and expanded by innovative DNA sequencing approaches for identifying (below species) strain-level variations and sequential community dynamics; assessing RNA, cDNA, and proteins to capture community functional activity in a more effective way, such as metatranscriptomics and metaproteomics, by mapping DNA or RNA reads directly to databases of gene sequences. Such databases include: COGs (Clusters of Orthologous Groups) KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, Pfam, NOGs (Nonsupervised Orthologous Groups), and UniRef (UniProt Reference) Clusters. In this chapter, we describe the skills, current technological advances, and unresolved challenges involved in the functional analysis of microbial communities.
Antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARG) have been regard... more Antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARG) have been regarded as emerging environmental pollutants in the entire world as these are known to cause public health hazards. The untreated biomedical wastes from healthcare units as well as the water from domestic and municipal wastes, are the sink for these pollutants and are disseminated into the river. The contaminated river's surface water with these pollutants poses a risk to public health due to the possibility of human exposure via bathing, drinking, and mobility in the food chain. In addition, heavy metals, the other major anthropogenic pollutant of river water, are known to drive bacterial resistance to antibiotics. Water of any urban city has been accepted as the index of determination of antimicrobial resistance (AMR) pollution load of any Urban city. No critical ethical issues are involved in conducting routine molecular surveillance and are considered safe to deal with. Therefore, und...
The Role of Microalgae in Wastewater Treatment, 2018
Arsenic is a gray-appearing metalloid which occurs naturally and is the 20th most prolific elemen... more 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...
Cyanobacteria are the most ancient lineages of the domain Bacteria and have been playing a crucia... more 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 chloroflex...
Biocatalysis and Agricultural Biotechnology, 2021
Abstract Oral biofilm formation is the defense mechanism exhibited by oral pathogens against anti... more Abstract 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 oC), 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.
The Role of Microalgae in Wastewater Treatment, 2018
The rapid lifestyle of industrialization and increasing demand of fossil oil that are going to be... more 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 al...
Thermal springs have been the most resourceful ecological niches to understand the intricacies of... more 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 was investigated in five ecologically different hot springs. The highest number of OTUs was observed at low temperatures (42 °C) whereas an increasing number of unclassified bacteria was observed with a temperature rise. The statistical correlation predicted that temperature, total dissolved solids and ions were the primary environmental factors in controlling the community composition and diversity. The relative abundance of Proteobacteria, Cyanobacteria showed a positive correlation with moderate temperature whereas growth of Chloroflexi and Nitrospira was unstable at 65 °C. The observed LCBD was negatively correlated to the bacteria richness. A high relative abundance of Planctomycetes was restricted to Odisha hot springs (AT, TP, and DJ). We further hypothesize that abundance of most ...
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Research Article by Enketeswara Subudhi
Conference Presentations by Enketeswara Subudhi
Papers by Enketeswara Subudhi