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J Bacteriol. 2010 November; 192(22): 6103–6104.
Published online 2010 September 17. doi:  10.1128/JB.00983-10
PMCID: PMC2976442

Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium Paenibacillus polymyxa E681[down-pointing small open triangle]


Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.

Among the plant-associated microbes, some are beneficial to plants, as they antagonize various plant pathogens, induce immunity, or even promote growth (2, 21, 29). These “plant-probiotic” bacteria (15, 16, 19, 22, 23, 28) have been isolated and commercially developed for use in the biological control of plant diseases or biofertilization (7, 10). Spore-forming bacteria, in particular, members of the phylum Firmicutes and streptomycetes, are considered advantageous in product formulation and stable maintenance in soil (9).

The genus Paenibacillus (1) has grown to encompass more than 110 species (, but its genome information is severely underrepresented. Paenibacillus spp. are important members of soil- or plant-associated ecosystems (3, 8, 20), with Paenibacillus polymyxa as one of the most industrially significant bacteria (13, 17, 25, 31). P. polymyxa E681, an endospore former isolated from the rhizosphere of winter barley in South Korea (14, 27), suppresses plant diseases, produces antibiotics and a plant hormone, secretes a variety of hydrolytic enzymes, and has good root-colonizing ability (4, 26).

We determined the genome sequence of a rifampin-resistant clone of E681. About 62,000 chromatograms (~6.7-fold genome coverage) were produced from plasmid/fosmid/bacterial artificial chromosome libraries with an AB 3700/377 DNA analyzer. Base calling, fragment assembly, contig/scaffold editing, and finishing were performed with Phred/Phrap/Consed. Gaps were closed by primer walking. To improve the sequence quality, 2.4 Gb of 76-bp single-ended sequences were obtained from Illumina Genome Analyzer IIx. Errors were identified using Maq/MapView and rectified by confirmatory sequencing. Yacop-predicted coding sequences were translated and subjected to transitive annotation by searches against UniProt, COG, KEGG Genes, and TIGRFAMs.

The genome is composed of one circular chromosome of 5,394,884 bp (45.8% G+C). It has as many as 12 rRNA operons. No plasmid was found. Three-quarters of the 4,805 genes were assigned putative functions. Protein-coding genes are distributed preferentially on the leading strand. Apparently to cope with an ever-changing environment in the rhizosphere, the genome hosts at least 13 extracytoplasmic function sigma factors (12). There are 19 complete/disrupted insertion sequence elements but few phage-related genes.

Some antibiotic-biosynthetic genes have been characterized. Polymyxin, produced and transported by PmxA to -E (5), is a potent antimicrobial that recently attracted attention for the treatment of multidrug-resistant Gram-negative bacteria (11, 18, 30). Fusaricidin, an antifungal antibiotic consisting of six amino acids, is synthesized by a single-chain nonribosomal peptide synthetase (6). E681 may also synthesize a polyketide, a tridecaptin-like nonribosomal peptide, and a hybrid of polyketide and nonribosomal peptide. A gene cluster is responsible for the production of a novel lantibiotic.

Based on sequence investigation and biochemical analysis, auxin biosynthesis via the indole-3-pyruvic acid pathway was proposed as the only possible mechanism (24). The bacterium also produces volatile compounds that may promote growth and induce resistance of plants and one or more N-acyl-l-homoserine lactonases. Genome analysis revealed a rich set of secreted enzymes that degrade various plant-derived polysaccharides. They include xylanases, pectic enzymes, cellulases, and amylases. Genes involved in nitrogen fixation were not identified.

Nucleotide sequence accession number.

The genome sequence of P. polymyxa E681 is available in GenBank under accession number CP000154, as well as in the Genome Encyclopedia of Microbes (GEM;


We thank Changhoon Kim, Hoon Cheong, Rumi Kim, Dong-Su Yu, and other GEM members for technical assistance and Myung Hee Kim, Byung Kwon Kim, and Ju Yeon Song for helpful comments.

This work was supported by the KRIBB Research Initiative Program and the 21C Frontier Microbial Genomics and Applications Center Program of the Ministry of Education, Science and Technology, Republic of Korea.


[down-pointing small open triangle]Published ahead of print on 17 September 2010.


1. Ash, C., F. G. Priest, and M. D. Collins. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64:253-260. [PubMed]
2. Bloemberg, G. V., and B. J. Lugtenberg. 2001. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr. Opin. Plant Biol. 4:343-350. [PubMed]
3. Cheong, H., S.-Y. Park, C.-M. Ryu, J. F. Kim, S.-H. Park, and C. S. Park. 2005. Diversity of root-associated Paenibacillus spp. in winter crops from the southern part of Korea. J. Microbiol. Biotechnol. 15:1286-1298.
4. Choi, O., J. Kim, C.-M. Ryu, and C. S. Park. 2004. Colonization and population changes of a biocontrol agent. Plant Pathol. J. 20:97-102.
5. Choi, S.-K., S.-Y. Park, R. Kim, S.-B. Kim, C.-H. Lee, J. F. Kim, and S.-H. Park. 2009. Identification of a polymyxin synthetase gene cluster of Paenibacillus polymyxa and heterologous expression of the gene in Bacillus subtilis. J. Bacteriol. 191:3350-3358. [PMC free article] [PubMed]
6. Choi, S.-K., S.-Y. Park, R. Kim, C.-H. Lee, J. F. Kim, and S.-H. Park. 2008. Identification and functional analysis of the fusaricidin biosynthetic gene of Paenibacillus polymyxa E681. Biochem. Biophys. Res. Commun. 365:89-95. [PubMed]
7. Compant, S., B. Duffy, J. Nowak, C. Clement, and E. A. Barka. 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71:4951-4959. [PMC free article] [PubMed]
8. da Mota, F. F., E. A. Gomes, E. Paiva, and L. Seldin. 2005. Assessment of the diversity of Paenibacillus species in environmental samples by a novel rpoB-based PCR-DGGE method. FEMS Microbiol. Ecol. 53:317-328. [PubMed]
9. Francis, I., M. Holsters, and D. Vereecke. 2010. The Gram-positive side of plant-microbe interactions. Environ. Microbiol. 12:1-12. [PubMed]
10. Fravel, D. R. 2005. Commercialization and implementation of biocontrol. Annu. Rev. Phytopathol. 43:337-359. [PubMed]
11. Giamarellou, H., and G. Poulakou. 2009. Multidrug-resistant Gram-negative infections: what are the treatment options? Drugs 69:1879-1901. [PubMed]
12. Helmann, J. D. 2002. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46:47-110. [PubMed]
13. Jeong, H., J. F. Kim, Y.-K. Park, S.-B. Kim, C. Kim, and S.-H. Park. 2006. Genome snapshot of Paenibacillus polymyxa ATCC 842T. J. Microbiol. Biotechnol. 16:1650-1655.
14. Jeong, H., S. H. Yoon, D. S. Yu, T. K. Oh, and J. F. Kim. 2008. Recent progress of microbial genome projects in Korea. Biotechnol. J. 3:601-611. [PubMed]
15. Kim, J. F., C. Kim, H. Jeong, S.-Y. Park, Y.-K. Park, S.-K. Choi, C.-G. Hur, T. K. Oh, Y. H. Moon, C. S. Park, and S.-H. Park. 2003. Genome sequencing and analysis of the plant-probiotic bacterium Paenibacillus polymyxa E681, abstr. P88, p. 46. In Proceedings of the 3rd ASM and TIGR Conference on Microbial Genomes.
16. Kloepper, J. W., R. Rodríguez-Ubana, G. W. Zehnder, J. F. Murphy, E. Sikora, and C. Fernandez. 1999. Plant root-bacterial interactions in biological control of soilborne diseases and potential extension to systemic and foliar diseases. Australas. Plant Pathol. 28:21-26.
17. Lal, S., and S. Tabacchioni. 2009. Ecology and biotechnological potential of Paenibacillus polymyxa: a minireview. Indian J. Microbiol. 49:2-10. [PMC free article] [PubMed]
18. Landman, D., C. Georgescu, D. A. Martin, and J. Quale. 2008. Polymyxins revisited. Clin. Microbiol. Rev. 21:449-465. [PMC free article] [PubMed]
19. Lugtenberg, B., and F. Kamilova. 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63:541-556. [PubMed]
20. McSpadden Gardener, B. B. 2004. Ecology of Bacillus and Paenibacillus spp. in agricultural systems. Phytopathology 94:1252-1258. [PubMed]
21. Ortiz-Castro, R., H. A. Contreras-Cornejo, L. Macias-Rodriguez, and J. Lopez-Bucio. 2009. The role of microbial signals in plant growth and development. Plant Signal. Behav. 4:701-712. [PMC free article] [PubMed]
22. Park, S.-H., J. F. Kim, C. Kim, H. Jeong, S.-K. Choi, C.-G. Hur, T. K. Oh, Y. H. Moon, and C. S. Park. 2002. Genome sequencing and analysis of Paenibacillus polymyxa E681, a plant-probiotic bacterium, abstr. S18-7, p. 68. In Proceedings of the 9th International Symposium on the Genetics of Industrial Microorganisms.
23. Park, S.-H., J. F. Kim, H. Jeong, S.-B. Kim, H. Chung, S.-Y. Park, S. G. Park, C. Lee, Y. H. Moon, C.-G. Hur, S.-Y. Ghim, C. S. Park, and T. K. Oh. 2004. Functional genomics of the plant-probiotic bacterium, Paenibacillus polymyxa E681, abstr. SI-3, p. 30-31. In Proceedings of the 2004 KSPP Annual Meeting and International Symposium on the New Horizons in Plant Pathology: Biotechnology for Plant Health.
24. Phi, Q. T., S.-H. Oh, Y.-M. Park, S.-H. Park, C.-M. Ryu, and S.-Y. Ghim. 2008. Isolation and characterization of transposon-insertional mutants from Paenibacillus polymyxa E681 altering the biosynthesis of indole-3-acetic acid. Curr. Microbiol. 56:524-530. [PubMed]
25. Raza, W., W. Yang, and Q. R. Shen. 2008. Paenibacillus polymyxa: antibiotics, hydrolytic enzymes and hazard assessment. J. Plant Pathol. 90:419-430.
26. Ryu, C.-M., J. Kim, O. Choi, S.-Y. Park, S.-H. Park, and C. S. Park. 2005. Nature of a root-associated Paenibacillus polymyxa from field-grown winter barley in Korea. J. Microbiol. Biotechnol. 15:984-991.
27. Ryu, C.-M., and C. S. Park. 1997. Enhancement of plant growth induced by endospore forming PGPR strain, Bacillus polymyxa E681, p. 186-190. In Proceedings of the 4th International Workshop on Plant Growth-Promoting Rhizobacteria.
28. Timmusk, S., and E. G. Wagner. 1999. The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol. Plant Microbe Interact. 12:951-959. [PubMed]
29. Van Wees, S. C., S. Van der Ent, and C. M. Pieterse. 2008. Plant immune responses triggered by beneficial microbes. Curr. Opin. Plant Biol. 11:443-448. [PubMed]
30. Velkov, T., P. E. Thompson, R. L. Nation, and J. Li. 2010. Structure-activity relationships of polymyxin antibiotics. J. Med. Chem. 53:1898-1916. [PMC free article] [PubMed]
31. Von Bredemann, G. 1908. Untersuchungen über die Variation und das Stickstoffbindungsvermögen des Bacillus asterosporus A. M., ausgeführt an 27 Stämmen verschiedener Herkunft. Ein Beitrag zur Spezies-Frage der Bakterien. Zentralbl. Bakteriol. Parasitenkd. Infektionskrankh. Hyg. 22:44-89.

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