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3 Biotech

, 9:256 | Cite as

Draft genome sequence of a cold-adapted phosphorous-solubilizing Pseudomonas koreensis P2 isolated from Sela Lake, India

  • Alok Kumar SrivastavaEmail author
  • Pragya Saxena
  • Anjney Sharma
  • Ruchi Srivastava
  • Hena Jamali
  • Akhilendra Pratap Bharati
  • Jagriti Yadav
  • Anchal Kumar Srivastava
  • M. Kumar
  • Hillol Chakdar
  • Prem Lal KashyapEmail author
  • Anil Kumar Saxena
Genome Reports
  • 40 Downloads

Abstract

The draft genome sequence of a cold-adapted phosphorus-solubilizing strain Pseudomonas koreensis P2 isolated from the Sela Lake contains 6,436,246 bp with G + C content of 59.8%. The genome sequence includes 5743 protein coding genes, 68 non-protein coding genes, 1007 putative proteins, 5 rRNA genes, 64 tRNAs and two prophage regions in 40 contigs. Besides these, genes involved in phosphate solubilization, siderophore production, iron uptake, heat shock and cold shock tolerance, multidrug resistance and glycine-betaine production were also identified.

Keywords

Phosphorus (P) Pseudomonas koreensis Genome Phosphate solubilization PGPR 

Notes

Acknowledgements

We thankfully acknowledge the financial assistance under CRP-Genomics Platform of Indian Council of Agricultural Research (ICAR), India. The assistance of M/S Bionivid technology Pvt. Ltd., Kasturi Nagar, Bengaluru, India is acknowledged.

Author contributions

AKS conceived the idea. AKS, PS, HC, MK and PLK are associated with the wet lab experiments and sequencing. JY, Anjney Sharma, and Anchal K. Srivastava contributed in sequencing and analysis. APB, RS and AKS analyzed the genome data. Anil K. Saxena gave critical inputs. APB and AKS wrote the paper.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13205_2019_1784_MOESM1_ESM.docx (4 mb)
Supplementary material 1 (DOCX 4090 kb)

References

  1. Ahmad F, Ahmad I, Khan MS (2008) Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181CrossRefGoogle Scholar
  2. Alikhan NF, Petty NK, Zakour NLB, Beatson SA (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402CrossRefGoogle Scholar
  3. Awasthi S, Sharma A, Saxena P, Yadav J, Pandiyan K, Kumar M, Singh A, Chakdar H, Bhowmik A, Kashyap PL, Srivastava AK, Saxena AK (2019) Molecular detection and in silico characterization of cold shock protein coding gene (cspA) from cold adaptive Pseudomonas koreensis. J Plant Biochem Biotechnol.  https://doi.org/10.1007/s13562-019-00500-8 CrossRefGoogle Scholar
  4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75.  https://doi.org/10.1186/1471-2164-9-75 CrossRefGoogle Scholar
  5. Bric JM, Bostock RM, Silverstone SE (1991) Rapid in situ assay for indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane. Appl Environ Microbiol 57:535–538PubMedPubMedCentralGoogle Scholar
  6. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H (2014) PlasmidFinder and pMLST: in silico detection and typing of plasmids. Antimicrob Agents Chemother 58:3895–3903CrossRefGoogle Scholar
  7. Fiske CH, Subbarow Y (1925) The colorimetric determination of phosphorus. J Biol Chem 66:375–400Google Scholar
  8. Galardini M, Biondi EG, Bazzicalup M, Mengoni A (2011) CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 6:11CrossRefGoogle Scholar
  9. Green MR, Sambrook J (2018) The basic polymerase chain reaction (PCR). Cold Spring Harbor Protoc.  https://doi.org/10.1101/pdb-prot095117 CrossRefGoogle Scholar
  10. Hernandez-Salmeron JE, Hernandez-Leon R, Orozco-Mosqueda MDC, Valencia-Cantero E, Moreno-Hagelsieb G, Santoyo G (2016) Draft Genome sequence of the biocontrol and plant growth-promoting rhizobacterium Pseudomonas fluorescens strain UM270. Stand Genomic Sci 11:1.  https://doi.org/10.1186/s40793-015-0123-9 CrossRefGoogle Scholar
  11. ICAR-NBAIM Annual Report (2014–2015) ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Mau, UP, IndiaGoogle Scholar
  12. Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731.  https://doi.org/10.1016/j.jmb.2015.11.006 CrossRefGoogle Scholar
  13. Kashyap PL, Chakdar H, Saxena P, Soni AP, Srivastava AK, Sharma AK (2015) Characterization and evaluation of plant growth promoting capabilities of phosphate solubilizing psychrotolerant bacteria from Cold Desert of Arunachal Pradesh. In: Presented at international conference on low temperature science and biotechnological advances held at NBPGR, Pusa Campus, New Delhi from 27–30th April 2015, p 112Google Scholar
  14. Kwak Y, Park G-S, Shin J-H (2016) High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium. Stand Genom Sci 11(1):51CrossRefGoogle Scholar
  15. Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJ (2003) Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. Int J Syst Evol Microbiol 53:21–27CrossRefGoogle Scholar
  16. Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM (2016) Draft genome sequence of the phosphate-solubilizing bacterium Pseudomonas argentinensis strain SA190 isolated from the desert plant Indigofera argentea. Genome Announc 4:e01431-16.  https://doi.org/10.1128/genomeA.01431-16 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108.  https://doi.org/10.1093/nar/gkm160 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359.  https://doi.org/10.1038/nmeth.1923 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16.  https://doi.org/10.1093/nar/gkh152 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Lin H, Hu S, Liu R, Chen P, Ge C, Zhu B, Guo L (2016) Genome sequence of Pseudomonas koreensis CRS05-R5, an antagonistic bacterium isolated from rice paddy field. Front Microbiol 7:1756PubMedPubMedCentralGoogle Scholar
  21. Lorck H (1948) Production of hydrocyanic acid by bacteria. Physiol Plantarum 1:142–146CrossRefGoogle Scholar
  22. Lozano GL, Park HB, Bravo JI, Armstrong EA, Denu JM, Stabb EV, Broderick NA, Crawford JM, Handelsman J (2019) Bacterial analogs of plant tetrahydropyridine alkaloids mediate microbial interactions in a rhizosphere model system. Appl Environ Microbiol.  https://doi.org/10.1128/AEM.03058-18 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Ann Rev Microbiol 63:541–556.  https://doi.org/10.1146/annurev.micro.62.081307.162918 CrossRefGoogle Scholar
  24. Lujan KM, Eisen JA, Coil DA (2017) Draft genome sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. strain UCD-KL20, Shewanella sp. strain UCD-KL12, and Shewanella sp. strain UCD-KL21, isolated from Seagrass. Genome Announc 5(13):e00023-17CrossRefGoogle Scholar
  25. Monds RD, Newell PD, Schwartzman JA, O'Toole GA (2006) Conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1. Appl Environ Microbiol 72(3):1910–1924CrossRefGoogle Scholar
  26. Oteino N, Lally RD, Kiwanuka S, Lloyd A, Ryan D, Germaine KJ, Dowling DN (2015) Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microbiol. 6:745CrossRefGoogle Scholar
  27. Reva ON, Weinel C, Weinel M, Bohm K, Stjepandic D, Hoheisel D Jr, Tummler B (2006) Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 188:4079–4092CrossRefGoogle Scholar
  28. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56CrossRefGoogle Scholar
  29. Selvakumar G, Kundu S, Joshi P, Nazim S, Gupta AD, Mishra PK, Gupta HS (2008) Characterization of a cold-tolerant plant growth-promoting bacterium Pantoea dispersa 1A isolated from a sub-alpine soil in the North Western Indian Himalayas. World J Microbiol Biotechnol 24:955–960CrossRefGoogle Scholar
  30. Selvakumar G, Joshi P, Suyal P, Mishra PK, Joshi GK, Bisht JK, Bhatt JC, Gupta HS (2011) Pseudomonas lurida M2RH3 (MTCC 9245), a psychrotolerant bacterium from the Uttarakhand Himalayas, solubilizes phosphate and promotes wheat seedling growth. World J Microbiol Biotechnol 27:1129–1135CrossRefGoogle Scholar
  31. Sharma D, Gupta M, Gupta S, Kashyap PL, Zargar SM, Mallick SA (2018) Antibiotic gene specific characterization and ARDRA analysis of native isolates of Pseudomonas spp. from Jammu, India. Indian Phytopathol 71(2):225–233CrossRefGoogle Scholar
  32. Solanki MK, Singh RK, Srivastava S, Kumar S, Kashyap PL, Srivastava AK, Arora DK (2014) Isolation and characterization of siderophore producing antagonistic rhizobacteria against Rhizoctonia solani. J Basic Microbiol 54(6):585–597CrossRefGoogle Scholar
  33. Srivastava AK, Sharma A, Srivastava R, Tiwari PK, Singh AK, Yadav J, Jamali H, Bharati AP, Srivastava AK, Kashyap PL, Chakdar H, Kumar M, Saxena AK (2019) Draft genome sequence of halotolerant bacterium Chromohalobacter salexigens ANJ207, isolated from salt crystal deposits in pipelines. Microbiol Resour Announc 8(15):e00049-19CrossRefGoogle Scholar
  34. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729CrossRefGoogle Scholar
  35. Zerbino D, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829CrossRefGoogle Scholar
  36. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acid Res 39:W347–W352CrossRefGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM)MauIndia
  2. 2.ICAR-Indian Institute of Wheat and Barley Research (IIWBR)KarnalIndia

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