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The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India

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Abstract

An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3ʺ)-Ib, and APH (6)-Id that provide resistance by encoding resistance–nodulation–cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.

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Data availability

All nucleotide sequences assembled in this study have been deposited in the DDBJ/ENA/GenBank: Stutzerimonas frequens CAM01 assembly (accession code JAQBSX000000000) under the BioProject PRJNA916631.

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Acknowledgements

The authors would like to acknowledge the Department of Biotechnology (DBT), New Delhi, India for the research grant and Forest Department for providing permission to carry this research at Palk Bay (Ref. No. WL (A)/16437/2014).

Funding

The authors would like to thank Department of Biotechnology, Department of Science and Technology (GOI) for the research grant for the project BT/PR40420/NDB/39/741/2020 under Marine Bioresource and Biotechnology Programme.

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Authors and Affiliations

  1. Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India

    Afreen Hussain, S. Hari Krishna Kumar, R. Prathiviraj, Ashish Ashwin Kumar, Kalyani Renjith & Joseph Selvin

  2. Department of Food Science and Technology, School of Life Sciences, Pondicherry University, Puducherry, India

    G. Seghal Kiran

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  1. Afreen Hussain
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  2. S. Hari Krishna Kumar
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  3. R. Prathiviraj
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  4. Ashish Ashwin Kumar
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  5. Kalyani Renjith
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  6. G. Seghal Kiran
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  7. Joseph Selvin
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Contributions

AH, SHK Kumar, and RP—writing, review and editing; AH, SHK, GSK, and JS—study conceptualization; AH, AAK, and KR—experimental design; AH and AAK—field sampling; SHK Kumar and RP—bioinformatic analysis; JS—project investigation and funding procurement. All authors contributed to the article and approved the submitted version.

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Correspondence to Joseph Selvin.

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Communicated by Wen-Jun Li.

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Hussain, A., Kumar, S.H.K., Prathiviraj, R. et al. The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India. Arch Microbiol 205, 319 (2023). https://doi.org/10.1007/s00203-023-03656-z

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