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Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome

Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laisa Corrêa Braga Marques, Nathalie Fortin, View ORCID ProfileB. Jesse Shapiro
doi: https://doi.org/10.1101/2020.11.17.386995
Olga M. Pérez-Carrascal
1Département de Sciences Biologiques, Université́ de Montréal, Montréal, Québec, Canada
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  • For correspondence: jesse.shapiro@mcgill.ca olga.maria.perez-carrascal@umontreal.ca nicolas.tromas@umontreal.ca
Nicolas Tromas
1Département de Sciences Biologiques, Université́ de Montréal, Montréal, Québec, Canada
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  • For correspondence: jesse.shapiro@mcgill.ca olga.maria.perez-carrascal@umontreal.ca nicolas.tromas@umontreal.ca
Yves Terrat
1Département de Sciences Biologiques, Université́ de Montréal, Montréal, Québec, Canada
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Elisa Moreno
1Département de Sciences Biologiques, Université́ de Montréal, Montréal, Québec, Canada
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Alessandra Giani
2Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Laisa Corrêa Braga Marques
2Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Nathalie Fortin
3National Research Council of Canada, Montreal, Québec, Canada
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B. Jesse Shapiro
1Département de Sciences Biologiques, Université́ de Montréal, Montréal, Québec, Canada
4Department of Microbiology & Immunology, McGill University, Montreal, Québec, Canada
5McGill Genome Centre, McGill University, Montreal, Québec, Canada
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  • ORCID record for B. Jesse Shapiro
  • For correspondence: jesse.shapiro@mcgill.ca olga.maria.perez-carrascal@umontreal.ca nicolas.tromas@umontreal.ca
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Abstract

Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria – their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies – including cyanobacteria and associated bacterial genomes – isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. We found 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely-related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter, suggesting long-term evolutionary associations. Roseomonas and Rhodobacter genomes encode functions which could complement the metabolic repertoire of Microcystis, such as cobalamin and carotenoid biosynthesis, and nitrogen fixation. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 17, 2020.
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Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome
Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laisa Corrêa Braga Marques, Nathalie Fortin, B. Jesse Shapiro
bioRxiv 2020.11.17.386995; doi: https://doi.org/10.1101/2020.11.17.386995
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Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome
Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laisa Corrêa Braga Marques, Nathalie Fortin, B. Jesse Shapiro
bioRxiv 2020.11.17.386995; doi: https://doi.org/10.1101/2020.11.17.386995

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