Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data Chandrashekar Mootapally 1,2 & Mayur S. Mahajan 3 & Neelam M. Nathani 2,4 Received: 26 July 2020 / Accepted: 24 August 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
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. Keywords Transposable genetic elements . Gulf of Kutch . Gulf of Khambat . Marine metagenomics
In a microbial community, plasmids are one of the most significant components of mobile genetic elements (MGEs) that are responsible for harboring and transmitting genes essential for survival and fitness [1]. They are extrachromosomal genetic elements and one of the most important “vehicles” among bacteria, archaea, and even eukarya, important Mootapally Chandrashekar and Mayur S. Mahajan contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00248-020-01587-6) contains supplementary material, which is available to authorized users. * Neelam M. Nathani [email protected] 1
Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364001, India
2
Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology, Government of Gujarat, Gandhinagar, Gujarat 382011, India
3
Gandhinagar, India
4
Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364001, India
specifically due to its ability to encode genetic traits in microbial communities, promoting rapid evolution and adaptation to the changing environmental conditions in a niche [2–5]. Increased anthropogenic activities demand an understanding of the environmental and genetic factors underlying plasmid mobility since
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