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Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India

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Abstract

Upwelling and mud banks are two prominent oceanographic features in the coastal waters along the south west coast of India during the southwest monsoon (MON) season. The present study investigates the microbial diversity in the coastal environments of Alappuzha, India, where upwelling and mud banks co-exist. Water samples were collected from three stations, M1, M2, and M3, on a weekly basis to estimate the physico-chemical parameters and microbial abundance (MA). Presence of cold waters (< 26 °C) with high nitrate (6–8 µM) and low dissolved oxygen (5 µM) in the sub surface waters during monsoon (M) confirmed the presence of upwelling at all the three stations. Simultaneously, presence of unusually calm waters was seen at M2 alone during M indicating the formation of mud banks. The microbial diversity was determined from three stations, with distinct oceanographic conditions (M1: coastal reference station with only upwelling, M2: mud banks + upwelling, and M3: offshore reference station with only upwelling). The water samples were collected during two seasons, pre-monsoon (April) and M (July) and analysed using 16S rRNA-based Illumina high-throughput metagenomic sequencing. Proteobacteria was the most dominant phyla, followed by Bacteroidetes, Firmicutes, Cyanobacteria, Actinobacteria, and Verrucomicrobia in order, with variations in their relative abundance spatially and seasonally. Though the MA increased during M at all the stations, the relative abundance of most of the bacterial phyla except Proteobacteria decreased during M season. Interestingly, most of the sequences at M2 during mud banks were unclassified at the class level indicating the presence of unique microbial populations in this station. Prediction of metabolic activity revealed ammonia oxidation, nitrite reduction, sulphate reduction, xylan degradation, dehalogenation, chitin degradation, etc. as important functions. The metabolic activity throws light on the role of microbes in this environment thereby providing a system-scale perspective of microbial community interactions.

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Abbreviations

CTD:

Conductivity temperature depth

DO:

Dissolved oxygen

CH4 :

Methane

BA:

Bacterial abundance

TVC:

Total viable counts

PRM:

Pre-monsoon

M:

Monsoon

EtBr:

Ethidium bromide

PCoA:

Principal coordinate analysis

OTUs:

Operational taxonomic units

UPMA:

Unweighted pair group method with arithmetic averages

DOC:

Dissolved organic carbon

AOA:

Ammonia-oxidizing Archaea

AOB:

Ammonia-oxidizing Bacteria

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Acknowledgements

The authors are grateful to the Director, NIO, Goa and Scientist-in-charge, CSIR-NIO (RC), Kochi for their support and advice. JV and AS is grateful to Council of Scientific and Industrial Research (CSIR), New Delhi, for the Senior Research Fellowship Grant. AVK is grateful to AcSIR, CSIR and DST for the DST-INSPIRE Fellowship. NVK is grateful to SERB, India for the National Postdoctoral Fellowship. This is NIO Contribution Number 6371.

Funding

Funding was provided by National Institute of Oceanography, India (Grany No. OLP1709).

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Authors and Affiliations

  1. Regional Centre, CSIR-National Institute of Oceanography, Dr. Salim Ali Road, Post Box No. 1913, Kochi, Kerala, 682 018, India

    A. Parvathi, Vijayan Jasna, Vijaya Krishna Aswathy, Vinod Kumar Nathan, Sreekumar Aparna & K. K. Balachandran

  2. Space Application Centre, Jodhpur Tekra, Ahmadabad, Gujarat, 380015, India

    Vijaya Krishna Aswathy

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  1. A. Parvathi
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Parvathi, A., Jasna, V., Aswathy, V.K. et al. Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India. Mol Biol Rep 46, 3113–3127 (2019). https://doi.org/10.1007/s11033-019-04766-y

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