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Prokaryotic Diversity in Oxygen Depleted Waters of the Bay of Bengal Inferred Using Culture-Dependent and -Independent Methods

  • Genevieve L. Fernandes
  • Belle D. Shenoy
  • Larissa D. Menezes
  • Ram M. Meena
  • Samir R. DamareEmail author
Original Research Article

Abstract

There are regions in the world oceans where oxygen saturation is at its lowest, evident at depths between shelf to upper bathyal zone. These regions are known as Oxygen Minimum Zones (OMZs), which reportedly support phylogenetically diverse microbes. In this study, we aimed to characterize prokaryotic diversity in the water samples collected from 43, 200 and 1000 m depth of the Bay of Bengal Time Series location (BoBTS—18.0027°N, 89.0174°E) in the OMZ region. Illumina sequencing generated 3,921,854 reads of 16S rRNA gene amplicons, which corresponded to 5778 operational taxonomic units. The distribution of bacteria at class level varied with depth and oxygen concentration. α-Proteobacteria was found in abundance in 43 m and 1000 m depth water samples. γ-Proteobacteria was prominently detected in oxygen-depleted depths of 200 m and 1000 m. AB16 (Marine Group A, originally SAR406) was restricted at dissolved oxygen concentration of 1.5 μM at 200 m. Archaeal members were observed in low abundance (2%), with a high occurrence of phylum Euryarchaeota at 43 m, while Crenarchaeota was detected only at 200 m depth. Select bacterial cultures were screened for their ability to reduce nitrate in vitro, to obtain insights into their possible role in the nitrogen cycle. A total of 156 bacterial isolates clustered majorly with Alcanivorax, Bacillus, Erythrobacter, Halomonas, Idiomarina and Marinobacter. Among them, 11 bacterial genera showed positive nitrate reduction in the Griess test. A large percentage (63.55%) of 16S rRNA gene amplicons corresponded to unidentified OTUs at genus or higher taxonomic levels, suggesting a greater undiscovered prokaryotic diversity in this oxygen depleted region.

Keywords

Bacteria High throughput sequencing Nitrate reducers North Indian Ocean 

Notes

Acknowledgements

The authors are thankful to Director, CSIR-NIO, and Head, Biological Oceanography Division for all the infrastructure and facilities. We are grateful to the Chief Scientists, Captains and Crew of the cruises SSD005 and SSD020. We thank Dr Damodar M. Shenoy from the Chemical Oceanography Division and anonymous reviewers for their valuable suggestions to improve the manuscript. The cruises were part of the SIBER program (GAP2425) funded by the Ministry of Earth Sciences (MoES), Government of India. CSIR India is acknowledged for funding the research through the PSC0108 (INDIAS IDEA) project. This publication has CSIR-NIO contribution number 6351.

Author Contributions

SD and BDS planned the work and was executed by GF and LM. GF was involved in sampling. RM has carried out the sequencing of the cultured isolates using in-house DNA sequencer. The results were analysed by SD, BDS, GF and LM. The manuscript was written and reviewed by SD, BDS, GF and LM.

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest.

Supplementary material

12088_2019_786_MOESM1_ESM.doc (496 kb)
Supplementary material 1 (DOC 496 kb)

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Copyright information

© Association of Microbiologists of India 2019

Authors and Affiliations

  1. 1.Biological Oceanography DivisionCSIR-National Institute of OceanographyDona PaulaIndia
  2. 2.Department of MicrobiologyGoa UniversityTaleigao PlateauIndia
  3. 3.CSIR-National Institute of Oceanography Regional CentreVisakhapatnamIndia

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