Abstract
We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France).
GENOME ANNOUNCEMENT
Minerals represent the main source of nutritive cations in acidic and nutrient-poor forest soils in temperate regions (1). However, the nutrients entrapped in their structure are not directly accessible to the tree roots, which rely on soil microorganisms to weather the minerals (2, 3). Functional screening of bacterial strains isolated from the Scleroderma citrinum ectomycorrhizosphere and the surrounding bulk soil revealed an enrichment of effective mineral-weathering bacteria in the tree root vicinity (4–7). Notably, cultivation-dependent and -independent approaches revealed that the Burkholderia genus was the most abundant and the most effective mineral-weathering genus (6–9). A significant positive correlation was observed between the abundance of Burkholderia on minerals incubated in forest soils and the weathering level of these minerals (9, 10). Among Burkholderia strains tested, strain PML1(12) appeared the most effective and capable of improving tree growth in nutrient-poor condition microcoms (11). With the goal of characterizing this strain and of identifying the molecular mechanisms involved in its mineral-weathering ability, we determined the complete sequence of its genome.
Genomic DNA was obtained using the protocol of Pospiech and Neumann (12). The genomic DNA was sequenced on a genome sequencer (GS) FLX 454 System (Roche) at Cogenics (Meylan, France). A half-run was used to perform 3-kb paired-end tags (L-PET) yielding 1,452,141 reads that were 385 bp long on average. A de novo assembly was performed using Newbler 2.6. The draft genome has 293 contigs larger than 500 bp, which were assembled in 8 scaffolds, with a calculated total length of 9,340,894 bp (35× average depth of coverage), a G+C content of 60.83%, and an N50 contig size of 70,828 bp. The largest contig generated was 272,460 bp long. We aligned the draft genome with the 10 closest neighboring complete genomes (chromosomes and plasmids) of the Burkholderia genus using average nucleotide identity (ANI) tools (http://enve-omics.ce.gatech.edu/ani/) (13). The best ANI score (80.83% average nucleotide identity) was obtained with Burkholderia glathei strain LMG14190T, indicating that strain PML1(12) could represent a novel species within the Burkholderia genus.
According to the automated annotation done using RAST, the genome contains a total of 8,761 predicted protein-coding genes, from which 2,241 (25.6%) were annotated as encoding hypothetical proteins. The genome contains a total of 46 tRNA coding genes. In addition, the genome of strain PML1(12) contains at least 4 complete copies of ribosomal operons of the following structure: 5S/23S/tRNA-ala-TGC/tRNAile-GAT/16S. The genome of strain PML1(12) presents genes related to plant growth promotion, including the genes for the production of indole-3-acetic acid (accD). The genome presents one N-acylhomoserine lactone quorum-sensing system. Interestingly, the PML1(12) genome shows a large number of genes (690) for the metabolism of sugars and carbohydrates, including genes for the synthesis and transport of gluconate, an organic acid for which production has been previously linked with the ability of bacteria to weather minerals. The genome possesses 15 genes annotated as siderophore transporters, which indicates the ability of the strain to scavenge Fe-loaded siderophores synthesized by other bacteria.
Nucleotide sequence accession number.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AEJF00000000 (project ID PRJNA53985; sample ID 53985).
ACKNOWLEDGMENTS
This work was supported by grants from the EC2CO program of the CNRS to S.U. and P.O. and the ANR JCJC Bactoweather from the French National Research Agency (ANR) to S.U. The UMR1136 and UR1138 are supported by the ANR through the Laboratory of Excellence Arbre (ANR-11-LABX-0002-01).
Footnotes
Citation Uroz S, Oger P. 2015. Draft genome sequence of Burkholderia sp. strain PML1(12), an ectomycorrhizosphere-inhabiting bacterium with effective mineral-weathering ability. Genome Announc 3(4):e00798-15. doi:10.1128/genomeA.00798-15.
REFERENCES
- 1.Uroz S, Oger P, Lepleux C, Collignon C, Frey-Klett P, Turpault MP. 2011. Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems. Res Microbiol 162:820–831. doi: 10.1016/j.resmic.2011.01.013. [DOI] [PubMed] [Google Scholar]
- 2.Landeweert R, Hoffland E, Finlay RD, Kuyper TW, van Breemen N. 2001. Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals. Trends Ecol Evol 16:248–253. doi: 10.1016/S0169-5347(01)02122-X. [DOI] [PubMed] [Google Scholar]
- 3.Uroz S, Calvaruso C, Turpault MP, Frey-Klett P. 2009. Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 17:378–387. doi: 10.1016/j.tim.2009.05.004. [DOI] [PubMed] [Google Scholar]
- 4.Calvaruso C, Turpault MP, Leclerc E, Ranger J, Garbaye J, Uroz S, Frey-Klett P. 2010. Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere. Appl Environ Microbiol 76:4780–4787. doi: 10.1128/AEM.03040-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Uroz S, Calvaruso C, Turpault MP, Pierrat JC, Mustin C, Frey-Klett P. 2007. Effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. Appl Environ Microbiol 73:3019–3027. doi: 10.1128/AEM.00121-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Uroz S, Buée M, Murat C, Frey-Klett P, Martin F. 2010. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288. doi: 10.1111/j.1758-2229.2009.00117.x. [DOI] [PubMed] [Google Scholar]
- 7.Uroz S, Tech JJ, Sawaya NA, Frey-Klett P, Leveau JHJ. 2014. Structure and function of bacterial communities in ageing soils: insights from the Mendocino ecological staircase. Soil Biol Biochem 69:265–274. doi: 10.1016/j.soilbio.2013.11.002. [DOI] [Google Scholar]
- 8.Collignon C, Uroz S, Turpault M, Frey-Klett P. 2011. Seasons differently impact the structure of mineral weathering bacterial communities in beech and spruce stands. Soil Biol Biochem 43:2012–2022. doi: 10.1016/j.soilbio.2011.05.008. [DOI] [Google Scholar]
- 9.Lepleux C, Turpault M-P, Oger P, Frey-Klett P, Uroz S. 2012. Correlation of the abundance of betaproteobacteria on mineral surfaces with mineral weathering in forest soils. Appl Environ Microbiol 78:7114–7119. doi: 10.1128/AEM.00996-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Uroz S, Turpault MP, Delaruelle C, Mareschal L, Pierrat J-, Frey-Klett P. 2012. Minerals affect the specific diversity of forest soil bacterial communities. Geomicrobiol J 29:88–98. doi: 10.1080/01490451.2010.523764. [DOI] [Google Scholar]
- 11.Calvaruso C, Turpault M-P, Frey-Klett P. 2006. Root-associated bacteria contribute to mineral weathering and to mineral nutrition in trees: a budgeting analysis. Appl Environ Microbiol 72:1258–1266. doi: 10.1128/AEM.72.2.1258-1266.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Pospiech A, Neumann B. 1995. A versatile quick-prep of genomic DNA from Gram-positive bacteria. Trends Genet 11:217–218. doi: 10.1016/S0168-9525(00)89052-6. [DOI] [PubMed] [Google Scholar]
- 13.Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. doi: 10.1099/ijs.0.64483-0. [DOI] [PubMed] [Google Scholar]