Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.

[en] Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.

Disciplines :

Environmental sciences & ecology
Genetics & genetic processes
Microbiology

Author, co-author :

Cornet, Luc ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes

Bertrand, Amandine ; Université de Liège - ULiège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale

Hanikenne, Marc ; Université de Liège - ULiège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale

Javaux, Emmanuelle ; Université de Liège - ULiège > Département de géologie > Paléobiogéologie - Paléobotanique - Paléopalynologie (PPP)

Wilmotte, Annick ; Université de Liège - ULiège > Département des sciences de la vie > Physiologie et génétique bactériennes

Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes

Language :

English

Title :

Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.

Publication date :

2018

Journal title :

Microbial Genomics

eISSN :

2057-5858

Publisher :

Microbiology Society, London, United Kingdom

Volume :

Peer reviewed :

Peer Reviewed verified by ORBi

Tags :

Tier-1 supercomputer
CÉCI : Consortium des Équipements de Calcul Intensif

European Projects :

FP7 - 308074 - ELITE - Early Life Traces, Evolution, and Implications for Astrobiology

Funders :

F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
BELSPO - Politique scientifique fédérale [BE]
FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture [BE]
ULiège - Université de Liège [BE]
CE - Commission Européenne [BE]

Available on ORBi :

since 05 September 2018

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