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J Bacteriol. 2012 Jun; 194(12): 3272–3273.
PMCID: PMC3370877

Genome Sequences of Two Plant Growth-Promoting Fluorescent Pseudomonas Strains, R62 and R81


Plant growth-promoting rhizobacterial (PGPR) strains R62 and R81 have previously been isolated and characterized as part of the Indo-Swiss Collaboration in Biotechnology. Here we present the draft genome sequences of these two PGPR strains, with the aim of unraveling the mechanisms behind their ability to promote wheat growth.


Plant growth-promoting rhizobacteria (PGPR) are of considerable interest because they may increase crop yield by increasing the availability of mineral nutrients, by affecting plant development through the production of phytohormones, and also by providing protection against pathogens through the production of secondary metabolites (3, 11, 17, 18). Among the PGPRs are several strains of fluorescent pseudomonads; three of them have been completely sequenced and annotated (15).

Two strains of PGPRs, named R62 and R81, were selected after the screening of more than 3,000 strains of bacteria isolated from wheat (cv. UP2338) roots grown in marginal soils of Bhawanipur, District Budaun, Uttar Pradesh, India (13, 14). These two strains displayed a high potential for use as biofertilizers of wheat in India (7, 14). In long-term field experiments conducted in the Indo-Gangetic plains, they increased the yield and grain quality of wheat and other crop plants substantially, particularly in combination with arbuscular mycorrhizal fungi (12). Here we present the draft genome sequences of these two strains, which were obtained by using an 8-kb paired-end 454 sequencing approach with about 40-fold coverage (∼250,000,000 bp) per genome.

Sequencing was carried out at the Functional Genomics Center, Zürich, Switzerland, with the Roche Genome Sequencer FLX 454 system. Genome assembly was done with the instrument's GS de novo assembler (Newbler v. 2.5.3). We obtained 991 contigs, resulting in two scaffolds (3,877,914 and 2,446,977 bp), for R62 and 151 contigs, resulting in one scaffold (6,215,135 bp), for R81. The GC contents of the R62 and R81 genomes were 59.5 and 61.7%, respectively.

Based on subsystem analysis with the RAST server (1), the R62 genome contained 5,354 protein coding sequences (CDS), whereas the R81 genome had 5,602 CDS. The closest neighbors among completely sequenced pseudomonads were Pseudomonas fluorescens strain Pf0-1 for R62 and P. fluorescens strain SBW25 for R81 (15), each with a genome size of about 6 Mb.

Annotations were made with the xBASE (2) bacterial genome annotation with the GLIMMER (5), tRNAScan-SE (10), and RNAmmer (8) algorithms, respectively. There were 66 and 63 predicted tRNA domains found in R62 and R81, respectively. The number of predicted rRNAs was five for R62 and four for R81. The “Annotate and Predict” menu in the Geneious Pro v. 5.5 software was used to predict key genes and simple sequence repeats with GLIMMER (5) and Phobos 3.3.11 (http://www.rub.de/spezzoo/cm/cm_phobos.htm), respectively. Homology searching was performed with BLASTN for some of the key genes known to encode enzymes involved in the production of secondary metabolites thought to be important for plant growth promotion, such as ferric siderophores, 2,4-diacetylphloroglucinol, hydrogen cyanide, orfamide A, phenazine, pyoluteorin, and pyrrolnitrin (3, 9). As expected, we found numerous homologous sequences to such key genes in R62 and R81. We hope that a more detailed comparative analysis will allow us to understand the genetic and biochemical basis of the known plant growth-promoting properties of R62 and R81, especially for the wheat crops grown in marginal soils of India.

Nucleotide sequence accession numbers.

This whole-genome shotgun project (draft genome sequences) has been deposited in the DDBJ/EMBL/GenBank databases under accession numbers AHZM00000000 and AHZN00000000 for R62 and R81, respectively. The version described in this paper is the first version, AHZM01000000 for R62 and AHZN01000000 for R81, which will be subsequently updated with annotations.


We thank Lucy Poveda at the Functional Genomics Center, Zürich, Switzerland, for performing paired-end 454 sequencing and Weihong Qi for de novo assembly and delivery of data.

This work was supported by the Indo-Swiss Collaboration in Biotechnology, in particular, by a grant for genome sequencing to Thomas Boller, Botanical Institute, University of Basel, Basel, Switzerland.


N.M. and R.S. are joint first authors.

A.K.S. and T.B. are joint last authors.


1. Aziz RK, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. [PMC free article] [PubMed]
2. Chaudhuri RR, et al. 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res. 36:D543–D546 [PMC free article] [PubMed]
3. Compant S, Duffy B, Nowak J, Clement C, Barka EA. 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]
4. Reference deleted.
5. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636–4641 [PMC free article] [PubMed]
6. Reference deleted.
7. Gaur R, et al. 2004. Diacetylphloroglucinol-producing pseudomonads do not influence AM fungi in wheat rhizosphere. Curr. Sci. 86:453–457
8. Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108 [PMC free article] [PubMed]
9. Loper JE, Kobayashi DY, Paulsen IT. 2007. The genomic sequence of Pseudomonas fluorescens Pf-5: insights into biological control. Phytopathology 97:233–238 [PubMed]
10. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964 [PMC free article] [PubMed]
11. Lugtenberg B, Kamilova F. 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63:541–556 [PubMed]
12. Mader P, et al. 2011. Inoculation of root microorganisms for sustainable wheat-rice and wheat-black gram rotations in India. Soil Biol. Biochem. 43:609–619
13. Roesti D, et al. 2006. Plant growth stage, fertiliser management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria affect the rhizobacterial community structure in rain-fed wheat fields. Soil Biol. Biochem. 38:1111–1120
14. Roesti D, et al. 2005. Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum. Appl. Environ. Microbiol. 71:6673–6679 [PMC free article] [PubMed]
15. Silby MW, et al. 2009. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol. 10:R51. [PMC free article] [PubMed]
16. Reference deleted.
17. Vessey JK. 2003. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil. 255:571–586
18. Zahir ZA, Arshad M, Frankenberger WT. 2004. Plant growth promoting rhizobacteria: applications and perspectives in agriculture. Adv. Agron. 81:97–168

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