Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Basak P

PROVIDER: S-EPMC4778633 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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

Basak Pijush P Pramanik Arnab A Sengupta Sohan S Nag Sudip S Bhattacharyya Anish A Roy Debojyoti D Pattanayak Rudradip R Ghosh Abhrajyoti A Chattopadhyay Dhrubajyoti D Bhattacharyya Maitree M

Genomics data 20151201

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 Biopro ...[more]

PMID: 26981367

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Project description:Two consortia (Consortium A and Consortium B) that can use 1,4-dioxane (a groundwater contaminant of emerging concern) as the sole carbon source were enriched from Rice University (Houston, TX, USA) campus soil. Phylogenetic analysis by 16S rRNA sequencing revealed the dominant genus in both of the consortia is Mycobacterium (56% in Consortium A and 49% in Consortium B). The predominance of Mycobacterium spp, in these consortia support the notion that this is an important and commonly encountered genus of dioxane degraders. Among other genera present that make at least 2% of these consortia, only Afipia encompasses a strain (i.e., Afipia sp. D1) that was reported to degrade dioxane as sole carbon and energy source. A nested PCR analysis using two degenerate primers to target the hydroxylase alpha subunit of groups 3 to 6 SDIMOs was performed to gain insights into which enzymes were responsible for dioxane degradation by these consortia. The purified products obtained from the second PCR run were sequenced and compared to genes databases (NCBI) encompassing all of the currently reported SDIMOs. The dominant SDIMO genes in Consortium A corresponded to a group-6 putative propane monooxygenase-like SDIMO (98.8%); while in Consortium B, SDIMO genes from both groups 5 (47.3%) and 6 (51.9%) were observed. In both consortia, the relative abundance of thmA/dxmA gene was negligible (0.03%), which is consistent with the negative amplification of these genes as verified in qPCR. Overall, the high relative abundance of group-6 putative propane monooxygenases in our two consortia suggests the novel finding that group 6-SDIMOs could also play an important role in dioxane degradation. This underscores the need for further research on genes and enzymes involved in dioxane biodegradation to develop novel biomarkers that can be useful for forensic analysis and performance assessment of bioremediation and natural attenuation at dioxane-impacted sites. DNA was extracted from bacteria biomass harvested in exponential growth phase, when half or more of the added dioxane (100 mg/L) was consumed. Total DNA extractions were performed using the UltraClean® Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s protocol. The V4 region of the 16S rRNA gene was amplified by PCR using the forward 515F and reverse 806R primers. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) by Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against the RDPII (http://rdp.cme.msu.edu) and NCBI (www.ncbi.nlm.nih.gov) databases.Previously designed degenerate primers NVC57, NVC58, NVC65 and NVC66 to target conserved regions in the soluble di-iron monooxygenases (SDIMO) alpha subunit gene (groups 3 to 6) were used to examine the presence and diversity of SDIMO genes in these two consortia. A nested PCR strategy was used to increase the PCR product yield. In the first run, the PCR mixture contained 1 µL of NVC65 and NVC58 primer mixture (10 µM), 20 ng of the extracted genomic DNA, 12.5 µL of KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems, Wilmington, MA, USA), and nuclease-free water to yield a total volume of 25 µL. PCR was performed in a Bio-Rad Thermal Cycler (Bio-Rad, Hercules, CA, USA) with the following temperature profile: initial denaturation (94°C, 5 min), then 29 amplification cycles (94°C for 30 s, 55°C for 30 s, 72°C for 1 min per kb) and a final extension (72°C for 5 min). The length of the PCR products in the first run was checked by 1% agarose gel and DNA bands of the correct size (1100 bp) were excised and purified. 20 ng of the purified PCR product was used as the DNA template in the second run, with the second set of primers (NVC57 and NVC66). The purified product (420 bp) from the second PCR was sent to MR DNA (www.mrdnalab.com, Shallowater, TX, USA) for Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). A database including all of the currently reported SDIMO genes on NCBI was created and used to taxonomically classify the final OTUs.

Dataset Information

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

Publications

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

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