Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Adrien C. Pozzi; Hector H. Bautista-Guerrero; Sophie S. Abby; Aude Herrera-Belaroussi; Danis Abrouk; Philippe Normand; Frédéric Menu; Maria P. Fernandez

doi:10.1016/j.syapm.2018.03.002

Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Adrien C. Pozzi, Hector H. Bautista-Guerrero, Sophie S. Abby, Aude Herrera-Belaroussi, Danis Abrouk, Philippe Normand, Frédéric Menu, Maria P. Fernandez

Ecology, Evolution and Behavior

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

Diazotrophic Actinobacteria of the genus Frankia represent a challenge to classical bacterial taxonomy as they include many unculturable strains. As a consequence, we still have a poor understanding of their diversity, evolution and biogeography. In this study, a Multi-Locus Sequence Analysis (MLSA) using atpD, dnaA, ftsZ, pgk, and rpoB loci was done on a large set of cultured and uncultured strains, compared to 16S rRNA and correlated to Average Nucleotide Identity (ANI) from available Frankia genomes. MLSA provided a robust resolution of Frankia genus phylogeny and clarified the status of unresolved species and complex of species. The robustness of single-gene topologies and their congruence with the MLSA tree were tested. Lateral Gene Transfers (LGT) were few and scattered, suggesting they had no impact on the concatenate topology. The pgk marker – providing the longest sequence, highest mean genetic divergence and least occurrence of LGT – was used to survey an unequalled number of Alnus-infective Frankia — mainly uncultured strains from a broad range of host-species and geographic origins. This marker allowed reliable Single-Locus Strain Typing (SLST) below the species level, revealed an undiscovered taxonomical diversity, and highlighted the effect of cultivation, sporulation phenotype and host plant species on symbiont richness, diversity and phylogeny.

Original language	English (US)
Pages (from-to)	311-323
Number of pages	13
Journal	Systematic and Applied Microbiology
Volume	41
Issue number	4
DOIs	https://doi.org/10.1016/j.syapm.2018.03.002
State	Published - Jul 2018

Bibliographical note

Funding Information:
This study could never have existed without the immense and strenuous work of the entire community of Frankia researchers who have isolated and cultivated strains since 1978. This paper is dedicated to them. Particular thanks are expressed to Louis S. Tisa (University of Durham, New Hampshire) for granting access to IMGer genome data, and to Hiroyuki Tobita (Forestry and Forest Products Research Institute, Tsukuba, Japan), Monique Gardes and Mélanie Roy (University of Toulouse, France), Roger Ruess and Michaela Swanson (University of Fairbanks, Alaska) for the help in nodule samplings. We also thank Ramon Rossello-Mora and one anonymous reviewer for their comments that contributed to improve this paper. This work was supported by the National Center for Scientific Research (CNRS, grant EC2CO), the Mexico-France ECOS program and the research cluster FR41 BioEnviS. A.C. Pozzi was granted a doctoral fellowship by the Ministry of Higher Education and Research (France) and H. Bautista Guerrero had a PhD grant from CONACYT (Mexico). None of the authors have competing interests to declare.

Publisher Copyright:
© 2018 Elsevier GmbH

Keywords

Diversity
Evolution
Frankia
Genomospecies
MLSA phylogeny
Taxonomy

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10.1016/j.syapm.2018.03.002

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Pozzi, A. C., Bautista-Guerrero, H. H., Abby, S. S., Herrera-Belaroussi, A., Abrouk, D., Normand, P., Menu, F., & Fernandez, M. P. (2018). Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size. Systematic and Applied Microbiology, 41(4), 311-323. https://doi.org/10.1016/j.syapm.2018.03.002

Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size. / Pozzi, Adrien C.; Bautista-Guerrero, Hector H.; Abby, Sophie S. et al.

In: Systematic and Applied Microbiology, Vol. 41, No. 4, 07.2018, p. 311-323.

Research output: Contribution to journal › Article › peer-review

Pozzi, AC, Bautista-Guerrero, HH, Abby, SS, Herrera-Belaroussi, A, Abrouk, D, Normand, P, Menu, F & Fernandez, MP 2018, 'Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size', Systematic and Applied Microbiology, vol. 41, no. 4, pp. 311-323. https://doi.org/10.1016/j.syapm.2018.03.002

Pozzi AC, Bautista-Guerrero HH, Abby SS, Herrera-Belaroussi A, Abrouk D, Normand P et al. Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size. Systematic and Applied Microbiology. 2018 Jul;41(4):311-323. doi: 10.1016/j.syapm.2018.03.002

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abstract = "Diazotrophic Actinobacteria of the genus Frankia represent a challenge to classical bacterial taxonomy as they include many unculturable strains. As a consequence, we still have a poor understanding of their diversity, evolution and biogeography. In this study, a Multi-Locus Sequence Analysis (MLSA) using atpD, dnaA, ftsZ, pgk, and rpoB loci was done on a large set of cultured and uncultured strains, compared to 16S rRNA and correlated to Average Nucleotide Identity (ANI) from available Frankia genomes. MLSA provided a robust resolution of Frankia genus phylogeny and clarified the status of unresolved species and complex of species. The robustness of single-gene topologies and their congruence with the MLSA tree were tested. Lateral Gene Transfers (LGT) were few and scattered, suggesting they had no impact on the concatenate topology. The pgk marker – providing the longest sequence, highest mean genetic divergence and least occurrence of LGT – was used to survey an unequalled number of Alnus-infective Frankia — mainly uncultured strains from a broad range of host-species and geographic origins. This marker allowed reliable Single-Locus Strain Typing (SLST) below the species level, revealed an undiscovered taxonomical diversity, and highlighted the effect of cultivation, sporulation phenotype and host plant species on symbiont richness, diversity and phylogeny.",

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note = "Funding Information: This study could never have existed without the immense and strenuous work of the entire community of Frankia researchers who have isolated and cultivated strains since 1978. This paper is dedicated to them. Particular thanks are expressed to Louis S. Tisa (University of Durham, New Hampshire) for granting access to IMGer genome data, and to Hiroyuki Tobita (Forestry and Forest Products Research Institute, Tsukuba, Japan), Monique Gardes and M{\'e}lanie Roy (University of Toulouse, France), Roger Ruess and Michaela Swanson (University of Fairbanks, Alaska) for the help in nodule samplings. We also thank Ramon Rossello-Mora and one anonymous reviewer for their comments that contributed to improve this paper. This work was supported by the National Center for Scientific Research (CNRS, grant EC2CO), the Mexico-France ECOS program and the research cluster FR41 BioEnviS. A.C. Pozzi was granted a doctoral fellowship by the Ministry of Higher Education and Research (France) and H. Bautista Guerrero had a PhD grant from CONACYT (Mexico). None of the authors have competing interests to declare. Publisher Copyright: {\textcopyright} 2018 Elsevier GmbH",

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AU - Normand, Philippe

AU - Menu, Frédéric

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Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Abstract

Bibliographical note

Keywords

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