Advertisement

Archives of Microbiology

, Volume 200, Issue 5, pp 803–810 | Cite as

Draft genome of the fungicidal biological control agent Burkholderia anthina strain XXVI

  • S. de los Santos-Villalobos
  • J. M. Kremer
  • F. I. Parra-Cota
  • A. C. Hayano-Kanashiro
  • L. F. García-Ortega
  • S. K. Gunturu
  • J. M. TiedjeEmail author
  • S. Y. He
  • J. J. Peña-Cabriales
Original Paper
  • 456 Downloads

Abstract

Burkholderia anthina XXVI is a rhizosphere bacterium isolated from a mango orchard in Mexico. This strain has a significant biological control activity against the causal agent of mango anthracnose, Colletotrichum gloeosporioides, likely through the production of siderophores and other secondary metabolites. Here, we present a draft genome sequence of B. anthina XXVI (approximately 7.7 Mb; and G + C content of 67.0%), with the aim of gaining insight into the genomic basis of antifungal modes of action, ecological success as a biological control agent, and full biosynthetic potential.

Keywords

Burkholderia Biocontrol agent Colletotrichum Genome Sequencing Siderophore 

Notes

Acknowledgements

Illumina sequencing was performed at the Research Technology Support Facility at Michigan State University, East Lansing, Michigan. We acknowledge funding from the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02-07ER64494) to James Tiedje, and the Gordon and Betty Moore Foundation (GBMF3037) to Sheng-Yang He. We also thank Araceli Fernández for technical support. Nucleotide sequence accession numbers: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession LFZP00000000. The version described in this paper is: LFZP01000000.

Supplementary material

203_2018_1490_MOESM1_ESM.docx (24 kb)
Supplementary material 1 (DOCX 23 KB)

References

  1. Alteri CJ, Mobley HLT (2016) The versatile type VI secretion system. Microbiol Spectr.  https://doi.org/10.1128/microbiolspec.VMBF-0026-2015 PubMedPubMedCentralCrossRefGoogle Scholar
  2. Araújo WL, Creason AL, Mano ET, Camargo-Neves AA, Minami SN, Chang JH, Loper JE (2016) Genome sequencing and transposon mutagenesis of Burkholderia seminalis TC3.4.2R3 identify genes contributing to suppression of orchid necrosis caused by B. gladioli. Mol Plant Microbe Interact 29(6):435–446.  https://doi.org/10.1094/MPMI-02-16-0047-R CrossRefPubMedGoogle Scholar
  3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75.  https://doi.org/10.1186/1471-2164-9-75 CrossRefGoogle Scholar
  4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.  https://doi.org/10.1089/cmb.2012.0021 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84:11–18.  https://doi.org/10.1007/s00253-009-2092-7 CrossRefPubMedGoogle Scholar
  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.  https://doi.org/10.1093/bioinformatics/btu170 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365.  https://doi.org/10.1038/srep08365 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552CrossRefPubMedGoogle Scholar
  9. Chain PSG, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103:15280–15287.  https://doi.org/10.1073/pnas.0606924103 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chung W-H, Chung W-C, Peng M-T, Yang H-R, Huang J-W (2010) Specific detection of benzimidazole resistance in Colletotrichum gloeosporioides from fruit crops by PCR-RFLP. N Biotechnol 27:17–24.  https://doi.org/10.1016/j.nbt.2009.10.004 CrossRefPubMedGoogle Scholar
  11. Cipolla L, Rocca F, Martinez C, Aguerre L, Barrios R, Prieto M (2017) Prevalencia de especies del complejo Burkholderia cepacia en pacientes con fibrosis quística en Argentina durante el período 2011–2015. Enfermedades Infecciosas y Microbiología Clínica.  https://doi.org/10.1016/j.eimc.2017.09.002
  12. Coenye T, Vandamme P (2003) Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729CrossRefPubMedGoogle Scholar
  13. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147.  https://doi.org/10.1371/journal.pone.0011147 CrossRefPubMedPubMedCentralGoogle Scholar
  14. de los Santos-Villalobos S, de-Folter S, Délano-Frier J, Gómez-Lim M, Guzmán-Ortiz D, Sánchez-García P, Peña-Cabriales JJ (2011) Puntos críticos en el manejo integral de mango: floración, antracnosis y residuos industriales. Revista mexicana de ciencias agrícolas 2:221–234Google Scholar
  15. de los Santos-Villalobos S, Barrera-Galicia GC, Miranda-Salcedo MA, Peña-Cabriales JJ (2012) Burkholderia cepacia XXVI siderophore with biocontrol capacity against Colletotrichum gloeosporioides. World J Microbiol Biotechnol 28:2615–2623.  https://doi.org/10.1007/s11274-012-1071-9 CrossRefPubMedGoogle Scholar
  16. de los Santos-Villalobos S, de Folter S, Délano-Frier JP, Gómez-Lim MA, Guzmán-Ortiz DA, Peña-Cabriales JJ (2013) Growth promotion and flowering induction in mango (Mangifera indica L. cv “Ataulfo”) trees by Burkholderia and rhizobium inoculation: morphometric, biochemical, and molecular events. J Plant Growth Regul 32:615–627.  https://doi.org/10.1007/s00344-013-9329-5 CrossRefGoogle Scholar
  17. Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414–430.  https://doi.org/10.1111/j.1364-3703.2011.00783.x CrossRefPubMedGoogle Scholar
  18. DeLeon-Rodriguez N, Lathem TL, Rodriguez-R LM, Barazesh JM, Anderson BE, Beyersdorf AJ, Ziemba LD, Bergin M, Nenes A, Konstantinidis KT (2013) Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications. Proc Natl Acad Sci USA 110:2575–2580.  https://doi.org/10.1073/pnas.1212089110 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Deng P, Wang X, Baird SM, Showmaker KC, Smith L, Peterson DG, Lu S (2016) Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. Microbiologyopen 5:353–369.  https://doi.org/10.1002/mbo3.333 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  21. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MCJ (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158:1005–1015.  https://doi.org/10.1099/mic.0.055459-0 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kandel SL, Firrincieli A, Joubert PM, Okubara PA, Leston ND, McGeorge KM, Mugnozza GS, Harfouche A, Kim SH, Doty SL (2017) An in vitro study of bio-control and plant growth promotion potential of salicaceae endophytes. Front Microbiol 8:386.  https://doi.org/10.3389/fmicb.2017.00386 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Lackner G, Moebius N, Partida-Martinez L, Hertweck C (2011) Complete genome sequence of Burkholderia rhizoxinica, an endosymbiont of rhizopus microsporus. J Bacteriol 193:783–784.  https://doi.org/10.1128/JB.01318-10 CrossRefPubMedGoogle Scholar
  24. Mahenthiralingam E, Urban TA, Goldberg JB (2005) The multifarious, multireplicon Burkholderia cepacia complex. Nat Rev Microbiol 3:144–156.  https://doi.org/10.1038/nrmicro1085 CrossRefPubMedGoogle Scholar
  25. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214.  https://doi.org/10.1093/nar/gkt1226 CrossRefPubMedGoogle Scholar
  26. Parnell JJ, Berka R, Young HA, Sturino JM, Kang Y, Barnhart DM, DiLeo MV (2016) From the lab to the farm: an industrial perspective of plant beneficial microorganisms. Front Plant Sci 7:1110.  https://doi.org/10.3389/fpls.2016.01110 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Ramette A, LiPuma JJ, Tiedje JM (2005) Species abundance and diversity of Burkholderia cepacia complex in the environment. Appl Environ Microbiol 71:1193–1201.  https://doi.org/10.1128/AEM.71.3.1193-1201.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT (2009) Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 25:2071–2073.  https://doi.org/10.1093/bioinformatics/btp356 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9(3):111–118Google Scholar
  30. Rodriguez-R LM, Konstantinidis KT (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 4:e1900v1.  https://doi.org/10.7287/peerj.preprints.1900v1
  31. Schliep KP (2011) phangorn: phylogenetic analysis in R. Bioinformatics 27:592–593.  https://doi.org/10.1093/bioinformatics/btq706 CrossRefPubMedGoogle Scholar
  32. Schwarz S, Singh P, Robertson JD, LeRoux M, Skerrett SJ, Goodlett DR, West TE, Mougous JD (2014) VgrG-5 is a Burkholderia type VI secretion system-exported protein required for multinucleated giant cell formation and virulence. Infect Immun 82:1445–1452.  https://doi.org/10.1128/IAI.01368-13 CrossRefPubMedPubMedCentralGoogle Scholar
  33. Shommu NS, Vogel HJ, Storey DG (2015) Potential of metabolomics to reveal Burkholderia cepacia complex pathogenesis and antibiotic resistance. Front Microbiol 6:668.  https://doi.org/10.3389/fmicb.2015.00668 CrossRefPubMedPubMedCentralGoogle Scholar
  34. Ussery DW, Kiil K, Lagesen K, Sicheritz-Pontén T, Bohlin J, Wassenaar TM (2009) The genus Burkholderia: analysis of 56 genomic sequences. In: de Reuse H, Bereswill S (eds) Microbial pathogenomics. KARGER, Basel, pp 140–157CrossRefGoogle Scholar
  35. Vargas-Straube MJ, Cámara B, Tello M, Montero-Silva F, Cárdenas F, Seeger M (2016) Genetic and functional analysis of the biosynthesis of a non-ribosomal peptide siderophore in Burkholderia xenovorans LB400. PLoS One 11(3):e0151273.  https://doi.org/10.1371/journal.pone.0151273 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243.  https://doi.org/10.1093/nar/gkv437 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Winsor GL, Khaira B, Van Rossum T, Lo R, Whiteside MD, Brinkman FSL (2008) The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. Bioinformatics 24:2803–2804.  https://doi.org/10.1093/bioinformatics/btn524 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • S. de los Santos-Villalobos
    • 1
  • J. M. Kremer
    • 2
    • 3
    • 10
  • F. I. Parra-Cota
    • 4
  • A. C. Hayano-Kanashiro
    • 5
  • L. F. García-Ortega
    • 6
  • S. K. Gunturu
    • 3
  • J. M. Tiedje
    • 2
    • 3
    Email author
  • S. Y. He
    • 2
    • 7
    • 9
  • J. J. Peña-Cabriales
    • 8
  1. 1.CONACYT-Instituto Tecnológico de SonoraCiudad ObregónMexico
  2. 2.Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingUSA
  3. 3.Center for Microbial EcologyMichigan State UniversityEast LansingUSA
  4. 4.Campo Experimental Norman E. BorlaugSonoraMexico
  5. 5.Departamento de Investigaciones Científicas y TecnológicasUniversidad de SonoraHermosilloMexico
  6. 6.División de Biología MolecularInstituto Potosino de Investigación Científica y Tecnológica, A. C. (IPICYT, AC.)San Luis PotosíMexico
  7. 7.Howard Hughes Medical Institute-Gordon and Betty Moore FoundationMichigan State UniversityEast LansingUSA
  8. 8.Centro de Investigación y de Estudios Avanzados-IPN (CINVESTAV)IrapuatoMexico
  9. 9.Department of Plant BiologyMichigan State UniversityEast LansingUSA
  10. 10.AgBiomeResearch Triangle ParkUSA

Personalised recommendations