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The parA Region of Broad-Host-Range PromA Plasmids Is a Carrier of Mobile Genes

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Abstract

The ecological competences in microbiomes are driven by the adaptive capabilities present within microbiome members. Horizontal gene transfer (HGT) promoted by plasmids provides a rapid adaptive strategy to microbiomes, an interesting feature considering the constantly changing conditions in most environments. This study examined the parA locus, found in the highly promiscuous PromA class of plasmids, as the insertion site for incoming genes. A novel PCR system was designed that enabled examining insertions into this locus. Microbiomes of mangrove sediments, salt marsh, mycosphere, and bulk soil revealed habitat-specific sets of insertions in this plasmid region. Furthermore, such habitats could be differentiated based on patterns of parA-inserted genes, and the genes carried by these plasmids. Thus, a suite of dioxygenase-related genes and transposase elements were found in oil-affected mangroves, whereas genes involved in nitrogen and carbon cycling were detected in salt marsh and soils. All genes detected could be associated with capabilities of members of the microbiome to adapt to and survive in each habitat. The methodology developed in this work was effective, sensitive, and practical, allowing detection of mobilized genes between microorganisms.

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Acknowledgements

We acknowledge Jolanda Brons and Deborah Leite for their technical support during the experiments and Francisco Dini Andreote for help in the figure preparation. We also thank FAPESP for their financial support for this study (process 2015/01290-8) and CNPq (Universal Project—443815/2014-3). SRC received a grant from CAPES.

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Authors and Affiliations

  1. Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil

    Armando Cavalcante Franco Dias, Simone Raposo Cotta & Fernando Dini Andreote

  2. Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands

    Armando Cavalcante Franco Dias, Simone Raposo Cotta & Jan Dirk van Elsas

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  1. Armando Cavalcante Franco Dias
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  2. Simone Raposo Cotta
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  3. Fernando Dini Andreote
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  4. Jan Dirk van Elsas
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Correspondence to Armando Cavalcante Franco Dias.

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Dias, A.C.F., Cotta, S.R., Andreote, F.D. et al. The parA Region of Broad-Host-Range PromA Plasmids Is a Carrier of Mobile Genes. Microb Ecol 75, 479–486 (2018). https://doi.org/10.1007/s00248-017-1059-y

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  • DOI: https://doi.org/10.1007/s00248-017-1059-y

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