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Variations in the bacterial and fungal community structure along the hypoxic gradient of the Arabian Sea oxygen-depleted environment based on eDNA metabarcoding analysis

  • Vilas Bhagwat Phartade

    Dr. Vilas Bhagwat Phartade is a researcher in the Biological Oceanography Division at CSIR-National Institute of Oceanography, Goa, India. He recently completed his Ph.D. in Biotechnology, where he investigated the beneficial properties of coral mucus and its associated microbial communities, focusing on their roles in coral health under diverse environmental conditions. Following this, he expanded his research to include the characterization of microbial communities across various marine habitats.

     ORCID logo     , Ashutosh Shankar Parab

    Dr. Ashutosh Shankar Parab, senior project associate, is a marine microbiologist specializing in microbial ecology and biogeochemical cycling within marine ecosystems including oxygen minimum zones. His research mainly integrates metagenomics, and functional profiling through molecular tools to explore microbial diversity and carbon dynamics across marine environments.

     ORCID logo     , Cathrine Sumathi Manohar

    Dr. Cathrine Sumathi Manohar is a senior principal scientist with 20 years of research experience in various aspects of Marine Sciences especially in Microbiology, Molecular Biology, Biotechnology and Biological Oceanography. Research work mainly deals with understanding microbial diversity using molecular techniques. She has studied the biotechnological potential of mangrove, seaweed and coral-associated microbes. She has successfully led and been a team member in over 10 research projects, funded by various ministries from the Government of India.

     ORCID logo EMAIL logo     , Pravin Kumar

    Dr. Pravin Kumar is a research fellow under the supervision of Dr. S. Krishnamurthi at MTCC, CSIR-IMTECH, Chandigarh, India. His work focuses on exploring the biopotentials of marine prokaryotes, particularly their interactions with algae, corals, and sponges.

     ORCID logo     and Srinivasan Krishnamurthi

    Dr. Srinivasan Krishnamurthi is a principal scientist at the Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India. His research group focuses on exploring the diversity of extremophiles, rare or difficult-to-cultivate prokaryotic communities, and host-associated microbes, with an emphasis on their ecological significance and bioprospecting potential.

     ORCID logo
Published/Copyright: May 1, 2025
Botanica Marina
From the journal Botanica Marina Volume 68 Issue 4

Abstract

The Arabian Sea hosts one of the major perennial, oceanic oxygen-depleted environments (ODE) in the water column, influencing the seabed beneath it. These regions harbor a vast diversity of microbial communities, which play a significant role in the global budgets of key biogenic elements like carbon, nitrogen and oxygen. This study assessed the relative importance of bacterial and fungal communities in the Arabian Sea ODE using eDNA metabarcoding tools. Sediment samples from four stations at ∼200–1,200 m depths were analyzed across a hypoxic gradient, with 5–35 μM dissolved oxygen levels. Species diversity and richness indices revealed that bacterial and fungal communities were the highest at an oxygen threshold of 10–20 μM, with variations in their community composition along the hypoxic gradient. The bacterial phylum Proteobacteria was dominant in the sediment of all stations. However, the relative abundances of phyla such as Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes and Actinobacteria varied across the stations. The phyla Ascomycota and Basidiomycota dominated the fungal communities at all the stations. However, Mucoromycota was present only at stations with 20–35 μM oxygen levels. These results enhance our understanding of microbial community distribution in the Arabian Sea ODE.

Keywords: amplicon sequencing; hypoxic regions; Indian Ocean; microbial diversity; sediment
Corresponding author: Cathrine Sumathi Manohar, Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, India; and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India, E-mail:
Vilas Bhagwat Phartade and Ashutosh Shankar Parab contributed equally to this work.

Funding source: National Institute of Oceanography, India

Award Identifier / Grant number: PSC0108

About the authors

Vilas Bhagwat Phartade

Dr. Vilas Bhagwat Phartade is a researcher in the Biological Oceanography Division at CSIR-National Institute of Oceanography, Goa, India. He recently completed his Ph.D. in Biotechnology, where he investigated the beneficial properties of coral mucus and its associated microbial communities, focusing on their roles in coral health under diverse environmental conditions. Following this, he expanded his research to include the characterization of microbial communities across various marine habitats.

Ashutosh Shankar Parab

Dr. Ashutosh Shankar Parab, senior project associate, is a marine microbiologist specializing in microbial ecology and biogeochemical cycling within marine ecosystems including oxygen minimum zones. His research mainly integrates metagenomics, and functional profiling through molecular tools to explore microbial diversity and carbon dynamics across marine environments.

Cathrine Sumathi Manohar

Dr. Cathrine Sumathi Manohar is a senior principal scientist with 20 years of research experience in various aspects of Marine Sciences especially in Microbiology, Molecular Biology, Biotechnology and Biological Oceanography. Research work mainly deals with understanding microbial diversity using molecular techniques. She has studied the biotechnological potential of mangrove, seaweed and coral-associated microbes. She has successfully led and been a team member in over 10 research projects, funded by various ministries from the Government of India.

Pravin Kumar

Dr. Pravin Kumar is a research fellow under the supervision of Dr. S. Krishnamurthi at MTCC, CSIR-IMTECH, Chandigarh, India. His work focuses on exploring the biopotentials of marine prokaryotes, particularly their interactions with algae, corals, and sponges.

Srinivasan Krishnamurthi

Dr. Srinivasan Krishnamurthi is a principal scientist at the Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India. His research group focuses on exploring the diversity of extremophiles, rare or difficult-to-cultivate prokaryotic communities, and host-associated microbes, with an emphasis on their ecological significance and bioprospecting potential.

Acknowledgments

The authors are thankful to the captain, crew, ship cell staff and colleagues on board RV Sindhu Sankalp for all their support during cruise no. SSK046. They are also thankful for Research Grant no. PSC0108 from the Council of Scientific and Industrial Research, India. This is NIO manuscript contribution no. 7409.

  1. Research ethics: This article contains no animal studies and meets the ethical guidelines.

  2. Informed consent: Not applicable.

  3. Author contributions: Phartade Vilas Bhagwat and Ashutosh Shankar Parab was responsible for the data curation, writing and editing of the manuscript. Cathrine Sumathi Manohar was responsible for the conceptualisation, fund acquisition, data curation, provided supervision, manuscript preparation, review and editing. Pravin Kumar contributed in the data analysis, validation and preparation of the manuscript. Srinivasan Krishnamurthi contributed to the data analysis, review and editing. The authors have accepted responsibility for the entire content of this manuscript and approved its submission.

  4. Use of Large Language Models, AI and Machine Learning Tools: None declared.

  5. Conflict of interest: The authors state no conflict of interest.

  6. Research funding: This study was supported by the research project INDIAS IDEA: Indian Aquatic Ecosystems: Impact of Deoxygenation, Eutrophication and Acidification (Grant no. PSC0108) from Council of Scientific and Industrial Research, India.

  7. Data availability: Metagenomic data used for this manuscript is deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under the bio project identifier PRJNA1060920.

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Received: 2024-07-03
Accepted: 2025-04-02
Published Online: 2025-05-01
Published in Print: 2025-08-26

© 2025 Walter de Gruyter GmbH, Berlin/Boston

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https://doi.org/10.1515/bot-2024-0054
Keywords for this article
amplicon sequencing; hypoxic regions; Indian Ocean; microbial diversity; sediment

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