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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data

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Abstract

Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.

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Data Availability

All the raw reads used to classify the plasmid content in the data are submitted to EBI under bioproject IDs PRJEB26614 and PRJEB26615 [7, 10]. All data generated or analyzed during this study are included in this article (and its supplementary information files).

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Acknowledgments

We thank the boat crew and Dr. Paresh Poriya, Dr. Imtiyaz Belim, and Dr. Jignesh Dabhi for on board support during the sampling from the gulfs. We are extremely grateful to Maharaja Krishnakumarsinhji Bhavnagar University for providing the administrative platform for execution of the projects.

Funding

The work was part of the projects funded by the Science and Engineering Research Board, Government of India, in the form of Early Career Research Award as National Post-Doctoral Fellowship to MCS and NMN under Grant No. PDF/2016/001239 and Grant No. PDF/2016/000190, respectively.

Author information

Author notes

  1. Mootapally Chandrashekar and Mayur S. Mahajan contributed equally to this work.

Authors and Affiliations

  1. Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364001, India

    Chandrashekar Mootapally

  2. Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology, Government of Gujarat, Gandhinagar, Gujarat, 382011, India

    Chandrashekar Mootapally & Neelam M. Nathani

  3. Gandhinagar, India

    Mayur S. Mahajan

  4. Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364001, India

    Neelam M. Nathani

Authors
  1. Chandrashekar Mootapally
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  2. Mayur S. Mahajan
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  3. Neelam M. Nathani
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Contributions

N.M.N.: planned the study, extracted DNA, and wrote the manuscript. M.S.M.: analyzed the data and helped in manuscript drafting. C.M.: planned the study, organized the sampling, collected the samples, extracted DNA, analyzed and interpreted the data.

Corresponding author

Correspondence to Neelam M. Nathani.

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Conflict of Interest

The authors declare that they have no conflict of interests.

Electronic supplementary material

Online Resource 1

Percentage reads classified as plasmid sequences in the studied 9 metagenomics samples (PNG 517 kb)

High Resolution (TIF 1908 kb)

Online Resource 2

The assembles sequences of samples GOCS1–4, GOKS1–4 and A used in the study as fasta file in a zipped folder (FASTA 2924 kb)

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Online Resource 3

KEGG Ontology (KO) based hits in the studied samples (raw hits, data is not normalized in this figure) (XLSX 11 kb)

Online Resource 4

Hits for KO level2 classification in the studied samples (XLSX 19 kb)

Online Resource 5

Hits for KO level3 classification for the studied samples (XLSX 19 kb)

Online Resource 6

Heatmap describing the SEED subsystem based hits in the studied samples (raw hits, data is not normalized in this figure) (PNG 484 kb)

High Resolution (TIF 2052 kb)

Online Resource 7

Hits for Subsystem level2 classification in the studied samples (XLSX 63 kb)

Online Resource 8

Hits for Subsystem level3 classification for the studied samples (PNG 1911 kb)

High Resolution (TIF 17763 kb)

Online Resource 9

Functional level hits for KO significantly (p < 0.05) varying between the studied groups (based on the regions) (PNG 1566 kb)

High Resolution (TIF 14370 kb)

Online Resource 10

Functional level hits for SEED significantly (p < 0.05) varying between the studied groups (based on the regions) (XLSX 43 kb)

Online Resource 11

ARG hits for all the samples based on CARD database. The hits above the 40% coverage (indicated above the red highlight) were considered for discussion (XLSX 21 kb)

Online Resource 12

ARG hits for all the samples based on ARG-ANNOT database. The hits above the 40% coverage (indicated above the red highlight) were considered for discussion (XLSX 109 kb)

Online Resource 13

Hits for virulence factor encoding sequences for all the samples based on VFDB. The hits above the 40% coverage (indicated above the red highlight) were considered for discussion (XLSX 109 kb)

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Mootapally, C., Mahajan, M.S. & Nathani, N.M. Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data. Microb Ecol 81, 540–548 (2021). https://doi.org/10.1007/s00248-020-01587-6

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  • DOI: https://doi.org/10.1007/s00248-020-01587-6

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