title: The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled.
abstract: Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.
authors.affiliation: Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, The Netherlands i.u.haq@rug.nl j.d.van.elsas@rug.nl.
authors.forename: Irshad Ul
authors.initials: IU
authors.lastname: Haq
authors.affiliation: Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Graupner
authors.affiliation: Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
authors.forename: Rashid
authors.initials: R
authors.lastname: Nazir
authors.affiliation: Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, The Netherlands i.u.haq@rug.nl j.d.van.elsas@rug.nl.
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
mesh_terms: D019117:Burkholderia / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D012988:Soil Microbiology
keywords: Burkholderia; membrane transporters; pan–core genome; regions of genomic plasticity; secretion systems; synteny