Molecular Biology Reports

, Volume 46, Issue 3, pp 3113–3127 | Cite as

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

  • A. ParvathiEmail author
  • Vijayan Jasna
  • Vijaya Krishna Aswathy
  • Vinod Kumar Nathan
  • Sreekumar Aparna
  • K. K. Balachandran
Original Article


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.


Upwelling Bacterial metagenome Mud banks Upwelling Archaea 



Conductivity temperature depth


Dissolved oxygen




Bacterial abundance


Total viable counts






Ethidium bromide


Principal coordinate analysis


Operational taxonomic units


Unweighted pair group method with arithmetic averages


Dissolved organic carbon


Ammonia-oxidizing Archaea


Ammonia-oxidizing Bacteria



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

Compliance with ethical standards

Conflict of interest

The authors declares that they have no competing interests.

Supplementary material

11033_2019_4766_MOESM1_ESM.pdf (192 kb)
Supplementary material 1 (PDF 191 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Regional CentreCSIR-National Institute of OceanographyKochiIndia
  2. 2.Space Application CentreAhmadabadIndia

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