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Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures Rashid Nazir,a Martin A. Hansen,b Søren Sørensen,b and Jan Dirk van Elsasa Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, Netherlands,a and Molecular Microbial Ecology Group, University of Copenhagen, Copenhagen, Denmarkb
Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately 11.5-Mb (GⴙC content, 61.52%) draft genome sequence of B. terrae BS001 with the aim of providing insight into the genomic basis of its ecological success in fungus-affected soil settings.
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urkholderia terrae strain BS001 is a Gram-negative, rodshaped member of the Betaproteobacteria which was isolated from acidic sandy soil underneath the foot of Laccaria proxima fruiting bodies (8). Similar Burkholderia terrae types were also positively selected in soil by the growing fungus Lyophyllum sp. strain Karsten (4, 9). Remarkably, B. terrae BS001 migrates with growing fungal hyphae and assists other bacteria, e.g., Dyella japonica strain BS003, to comigrate (7). Interestingly, the group of so-called beneficial Burkholderia species (6) also contains the endofungal Burkholderia rhizoxinica (5). The related B. terrae BS001 is also fungus interacting. Such Burkholderia species exhibit characteristics like swimming and twitching motility, chemotaxis (2), and biofilm formation (9). They also reveal the presence of secretion systems (3) which may allow them to attach to, and colonize, fungal surface structures. The ecological success of B. terrae BS001 in the mycosphere may be related to the presence on its genome of a rich plethora of these and other genetic systems which allow it to be optimally fit at the fungus. The total estimated genome size of B. terrae BS001 is 11.5 Mb. Based on its 16S rRNA gene sequence, B. terrae strain BS001 shares high similarity (99%) with the type strain B. terrae KMY02. The genome sequence of B. terrae BS001 was determined via Roche 454 pyrosequencing (541,595 reads). The genome was de novo assembled using Newbler (version 2.5.3) and the Velvet (version 0.7.59) assembler. The best assembly consisted of 330 contigs. The draft genome has an average G⫹C content of 61.52%. Annotation was performed using RAST (1). This predicted 10,975 protein-coding sequences (CDS), with 67.27% assigned to recognizable functional genes. Furthermore, 91 tRNA genes were predicted. Several predicted genes and/or operons that are potentially important in the fungus-interacting behavior of B. terrae BS001, i.e., those involved in motility and chemotaxis (159), regulation, cell signaling (155), iron acquisition and metabolism (35), and transport over the membrane, including secretion systems (208), were found. The draft genome further revealed the presence of several putative ABC transporters, as well as type II, III, IV, and VI secretion systems. Along with many genes involved in metabolism, the genome revealed the presence of 367 genes for the metabolism of aromatic compounds and 1,207 genes for carbohydrate metabolism. This
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indicates the versatility of B. terrae BS001 in utilizing a multitude of C compounds. Moreover, using the Effective (http: //www.effectors.org/) software and T3SE db (http://effectors .bic.nus.edu.sg/T3SEdb/predict.php) for rapid prediction and identification, we found 15 effector proteins that are potentially secreted by the type III secretion system. These secreted proteins may be important in host modification. Finally, several genes for the biosynthesis of bacteriocins (14) and resistance to antibiotics and toxic compounds (178) were found. Nucleotide sequence accession numbers. The draft sequence of this genome has been deposited at DDBJ/EMBL/GenBank under accession number AKAU00000000. The first version, AKAU01000000, is described here in this paper. ACKNOWLEDGMENT Rashid Nazir was supported by the HEC-NUFFIC program of the Government of Pakistan.
REFERENCES 1. Aziz RK, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 2. Furuno S, et al. 2010. Fungal mycelia allow chemotactic dispersal of polycyclic aromatic hydrocarbon-degrading bacteria in water-unsaturated systems. Environ. Microbiol. 12:1391–1398. 3. Nazir R, Warmink JA, Boersma H, van Elsas JD. 2010. Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats. FEMS Microbiol. Ecol. 71:169 –185. 4. Nazir R, Zhang M, de Boer W, van Elsas JD. 2012. The capacity to comigrate with Lyophyllum sp. strain Karsten through different soils is spread among several phylogenetic groups within the genus Burkholderia. Soil Biol. Biochem. 50:221–233. 5. Partida-Martinez LP, et al. 2007. Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plantpathogenic fungus Rhizopus microsporus. Int. J. Syst. Evol. Microbiol. 57: 2583–2590.
Received 27 April 2012 Accepted 6 June 2012 Address correspondence to Jan Dirk van Elsas,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.00725-12
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6. Suárez-Moreno ZR, et al. 2012. Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb. Ecol. 63:249 – 266. 7. Warmink JA, Nazir R, Corten B, van Elsas JD. 2011. Hitchhikers on the fungal highway: the helper effect for bacterial migration via fungal hyphae. Soil Biol. Biochem. 43:760 –765.
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8. Warmink JA, van Elsas JD. 2008. Selection of bacterial populations in the mycosphere of Laccaria proxima: is type III secretion involved? ISME J. 2:887–900. 9. Warmink JA, van Elsas JD. 2009. Migratory response of soil bacteria to Lyophyllum sp. strain Karsten in soil microcosms. Appl. Environ. Microbiol. 75:2820 –2830.
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