Pijush Basak

Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans

Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions.

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

Bacterial diversity assessment of pristine mangrove microbial community from Dhulibhashani, Sundarbans using 16S rRNA gene tag sequencing

The global knowledge of microbial diversity and function in Sundarbans ecosystem is still scarce, despite global advancement in understanding the microbial diversity. In the present study, we have analyzed the diversity and distribution of bacteria in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. Metagenome is comprised of 1,53,926 sequences with 108.8 Mbp data and with 55 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA245459. Bacterial community metagenome sequences were analyzed by MG-RAST software representing the presence of 56,547 species belonging to 44 different phyla. The taxonomic analysis revealed the dominance of phyla Proteobacteria within our dataset. Further taxonomic analysis revealed abundance of Bacteroidetes, Acidobactreia, Firmicutes, Actinobacteria, Nitrospirae, Cyanobacteria, Planctomycetes and Fusobacteria group as the predominant bacterial assemblages in this largely pristine mangrove habitat. The distribution of different community datasets obtained from four sediment samples originated from one sampling station at two different depths providing better understanding of the sediment bacterial diversity and its relationship to the ecosystem dynamics of this pristine mangrove sediment of Dhulibhashani in, Sundarbans.

Changing bacterial profile of Sundarbans, the world heritage mangrove: Impact of anthropogenic interventions

Abstract Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

Interaction of KRAS G-quadruplex with natural polyphenols: A spectroscopic analysis with molecular modeling.

Researchers are endeavoring to find out new therapeutics for curing cancer and G-quadruplex DNA has already been identified as a prospective one in this venture. Stabilizing G-quadruplex structures of telomere has emerged to be an important strategy in this context. Mutation in KRAS is mostly responsible for pancreatic, lung and colon cancer. In this present study we explored binding and conformational behaviour of G-quadruplex with different ligands by utilizing several biophysical techniques. Natural polyphenols like Curcumin and Ellagic acid were observed to bind with the G-quadruplex and enhance the melting temperature significantly indicating higher stability. UV-vis spectroscopy confirms formation of G quadruplex-ligand complex for both the compounds with specific binding affinity. Fluorimetric studies revealed that Ellagic acid had stronger binding affinity, 1.10×10(5)M(-1) compared to Curcumin, 1.6×10(4)M(-1) towards G-quadruplex. Interestingly, Curcumin provides greater stability by stacking on the top of the quadruplex structure with the help of the loops compared to Ellagic acid as is evident by docking studies. The keto form of curcumin showed stronger affinity than the enol form. We have developed a general model to estimate the influence of the ligands towards stabilizing the G-quadruplex subsequently characterizing the binding profile to enlighten prospective therapeutics.

Cataloguing the bacterial diversity of the Sundarbans mangrove, India in the light of metagenomics.

In this present study we report the profile of bacterial community at variable depth of soil sediment in the worlds largest tropical mangrove sediments of Sundarbans, India using 16S rRNA gene amplicon sequencing. Metagenome of three samples consisted of 61301 sequences with 32.0 Mbp and 55.6% G + C content. Metagenome data of this study are available at NCBI under the Biosample data base accession no. SRX883521. The taxonomic analysis of 2746 species belonged to 33 different phyla revealing the dominance of Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Acidobacteria, Nitrospirae and Actinobacteria respectively. Remarkably less than 5.0% sequences belong to a poorly characterized group. Our pyrosequencing data report unfolds the bacterial community profile at different depth of soil sediment indicating the changing community pattern, in the light of specific chronology.

Pyrosequencing based profiling of the bacterial community in the Chilika Lake, the largest lagoon of India.

Brackish water lake is the most extraordinary reservoir for bacterial community with an adaptability of tolerance to saline stress. In the present study, metagenomic approach was implemented utilising 454-pyrosequencing platform to gain deeper insights into the bacterial diversity profile of the soil sediment of Chilika Lake, Odisha, India. Metagenome contained 68,150 sequences with 31,896,430 bp and 56.79% G + C content. Metagenome sequences data are now available at NCBI under the Sequence Read Archive (SRA) database with accession no. SRX753382. Bacterial community metagenome sequences were analysed by MG-RAST server representing the presence of 16,212 species belonging to 45 different phyla. The dominating phyla were Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Bacteroidetes and Planctomycetes. The analysis of bacterial community datasets obtained from two different saline soil sediments revealed significant differences in bacterial community composition and diversity value providing better understanding of the ecosystem dynamics of Chilika Lake.

Transition Metal Induced Conformational Change of Heme Proteins

Binding interaction of transition metals copper, cadmium, and mercury with heme proteins were explored using isothermal calorimetry. Consequent conformational changes of the native proteins analyzed by circular dichroic spectroscopy revealed differential structural alteration of heme proteins. But, significant distortion in myoglobin structure was noted due to bioconjugation with mercury whose greater ionic radius may be responsible for this preferential behavior.

Metagenomic exploration of the bacterial community structure at Paradip Port, Odisha, India

This is a pioneering report on the metagenomic exploration of the bacterial diversity from a busy sea port in Paradip, Odisha, India. In our study, high-throughput sequencing of community 16S rRNA gene amplicon was performed using 454 GS Junior platform. Metagenome contain 34,121 sequences with 16,677,333 bp and 56.3% G + C content. Metagenome sequences data are now available at NCBI under the Sequence Read Archive (SRA) database with accession no. SRX897055. Community metagenome sequence revealed the presence of 11,705 species belonging to 40 different phyla. Bacteroidetes (23%), Firmicutes (19%), Proteobacteria (17%), Spirochaetes (10%), Nitrospirae (8%), Actinobacteria (7%) and Acidobacteria (3%) are the predominant bacterial phyla in this port soil. Analysis of metagenomic sequences unfolded the interesting distribution of several phyla which pointed to the significant anthropogenic intervention influencing the bacterial community character of this port.

Denaturation properties and folding transition states of leghemoglobin and other heme proteins

This work reports unfolding transitions of monomeric heme proteins leghemoglobin (Lb), myoglobin (Mb), and cytochrome c (Cyt c) utilizing UV-Vis spectra, steady-state and time-resolved fluorescence methods. Conformational stabilities of the native “folded” state of the proteins and their “unfolded” states were investigated in the light of a two-state transition model. Two-state transition values for ΔGD (298K) were obtained by denaturation with the chaotropic agents urea and guanidium hydrochloride (GdnHCl). The free energy value of Lb is the lowest compared to Cyt c and Mb along the denaturation pathway. The m value is also the lowest for Lb compared to Cyt c and Mb. The m value (a measure of dependence of ΔGD on denaturant concentration) for Cyt c and Mb is lower when it is denatured with urea compared to GdnHCl. The UV-Vis absorbance maximum and steady state fluorescence emission maximum were drastically red shifted in the presence of a certain denaturant concentration both in cases of Mb and Lb, but the scenario is different for Cyt c. The results are analyzed using a two-state transition model. The lifetime data clearly indicate the presence of an intermediate state during denaturation. The unfolding transition can modulate the conformation, stability, and surface exposure of these biologically important proteins.