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Community-Based 16S rDNA Fingerprinting Analysis of Geographically Distinct Marine Sediments of Unexplored Coastal Regions of Palk Bay and Gulf of Mannar

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Abstract

The present study aims to carefully delineate the bacterial community composition in marine sediments from different geographical coastal regions of Palk Bay and Gulf of Mannar that are known for human recreational activities. Bacterial richness in different marine sediments was assessed using 16S rRNA gene-based Denaturing Gradient Gel Electrophoresis (DGGE) which is a widely deployed fingerprinting technique. The DGGE profiles revealed that the bacterial community profiles of sediment from different coastal regions were complex and dynamic. The most dominant phylum present in the marine sediment samples were Proteobacteria followed by Cyanobacteria, Bacteriodetes, Firmicutes, Acidobacteria, and Actinobacteria. Cosmopolitan presence of Thioalkalivibrio sp. was observed in all the marine sediments. Sequencing of the abundant band reveals the presence of Vibrio spp. in all the marine sediments. Comparative illumina data analysis revealed the presence of 51 different Vibrio species in which Vibrio alginolyticus holds the highest abundance (67.2%) followed by V. harveyi (13.5%). This is the one of the very few reports that compared the complex microbial community composition of the marine sediments of different geographical regions of unexplored coastal region. Further in-depth analysis needs to be taken to understand the presence of complex microbial compositions and their functions through high-throughput whole metagenome sequencing and metaproteomic approaches.

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Acknowledgements

Financial support rendered to Mr. C. Aravindraja (File. No. 09/688(0027)/2014-EMR-I) in the form of Senior Research Fellowship by Council of Scientific & Industrial Research (CSIR), New Delhi is gratefully acknowledged. The authors sincerely acknowledge the computational and bioinformatics facility provided by the Alagappa University Bioinformatics Infrastructure Facility (funded by Department of Biotechnology (DBT), GOI; File No. BT/BI/25/012/2012, BIF). The authors thankfully acknowledge Department of Science & Technology (DST-FIST) (Grant No. SR-FST/LSI-087/2008), The University Grants Commission (UGC-SAP) (Grant No. F.3-28/2011 (SAP-II), and DST-PURSE [Grant No. SR/S9/Z-23/2010/42 (G)] for providing instrumentation facilities.

Funding

This study was supported by a Research grant from Department of Biotechnology (DBT), the Government of India (GOI) (Grant number BT/PR11994/NDB/52/134/2009).

Author information

Author notes

  1. Chairmandurai Aravindraja

    Present address: Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL, USA

  2. Dharmaprakash Viszwapriya

    Present address: Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA

Authors and Affiliations

  1. Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, 630 003, India

    Chairmandurai Aravindraja, Dharmaprakash Viszwapriya, Alaguvel Valliammai & Shunmugiah Karutha Pandian

Authors
  1. Chairmandurai Aravindraja
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  2. Dharmaprakash Viszwapriya
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  3. Alaguvel Valliammai
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  4. Shunmugiah Karutha Pandian
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Contributions

Conceived and designed the experiments: SKP, CA, & DV. Performed the experiments: CA & DV. Analyzed the data: CA, DV, & AV. Contributed reagents/materials/analysis tools: SKP. Wrote the paper: CA, DV, AV, & SKP.

Corresponding author

Correspondence to Shunmugiah Karutha Pandian.

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284_2021_2692_MOESM1_ESM.jpg

Fig. S1 Geographical map showing the location of samples collected. The small black boxes at the top image denote the three different geographical regions where the samples were collected. The enlarged view of the sample location along the coastal regions, namely, Karankadu and Thondi coastal region of Palk Bay and Keelakarai coastal region of Gulf of Mannar was represented in the bottom image. (JPG 2559 kb)

284_2021_2692_MOESM2_ESM.jpg

Fig. S2 Non-metric Multidimensional analysis of the bacterial diversity analysis of the marine sediments. The marine samples (S1 to S6) did not cluster together, which implied varied bacterial diversity in marine sediments. (JPG 90 kb)

284_2021_2692_MOESM3_ESM.jpg

Fig. S3 Heatmap analysis of the bacterial community at the Phylum level. Relative abundance at the phylum level were calculated and plotted based on the presence of eluted bands in the corresponding position in other samples. (TIFF 407 kb)

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Aravindraja, C., Viszwapriya, D., Valliammai, A. et al. Community-Based 16S rDNA Fingerprinting Analysis of Geographically Distinct Marine Sediments of Unexplored Coastal Regions of Palk Bay and Gulf of Mannar. Curr Microbiol 79, 60 (2022). https://doi.org/10.1007/s00284-021-02692-6

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  • DOI: https://doi.org/10.1007/s00284-021-02692-6