The complete genome of the antifungal bacterium Pseudomonas sp. strain MS82
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The genomic sequence of Pseudomonas sp. strain MS82 isolated from the rhizosphere of a soybean plant is reported and analyzed in relation to its extensive antifungal activity. Broth media used for production of the antifungal extract from strain MS82 against the mushroom pathogen Trichoderma viride were optimized using the routine plate bioassays. Culture extract of strain 82 in the peptone–K2HPO4–MgSO4 medium (PKM; peptone 20 g/L, K2HPO4 1.5 g/L, MgSO4 1.5 g/L and sterilized water) showed the best antifungal activity with an inhibition rate of 88.69 ± 3.87% to the fungal pathogen. Control efficacy of the T. viride contamination was investigated in mushroom production compost. The disease severity index of P. ostreatus hyphae infected by T. viride of treatment mixed with MS82 supernatant (38.33 ± 5.20%) was lower than that of the compost mixed with non-inoculated broth (97.50 ± 2.50%). The multilocus sequence analysis, containing four partial sequences from the gyrB, rpoB, recA and rpoD, suggests that strain MS82 is a Pseudomonas strain. The strain MS82 genome consists of a circular chromosome of 6,207,556 bp that was predicted to encode 5401 proteins and 131 RNA genes. Genome analysis revealed the presence of the gene clusters for biosynthesis of antifungal compounds, such as phenazine, pyocyanin, pyoverdine, volatile HCN and cyclic lipopeptides (arthrofactin). Genome analysis presented in the report will provide insights into development of biological control for fungal contamination in mushroom cultivation.
KeywordsPseudomonas sp. strain MS82 Complete genome Antifungal activity Mushroom cultivation Secondary metabolites
Nutrient broth yeast extract
Clusters of Orthologous Groups
Inferred from direct assay
Kyoto Encyclopedia of Genes and Genomes
Non-Redundant Protein database
Traceable author statement
This research was supported in part by Natural Science Foundation of Jiangsu Province for Youth (BK20150547 to ML) and China Agriculture Research System (CARS20 to ML). This research was funded in part by the USDA NIFA (Grant MIS-401170 to S-EL.).
LM and SL designed the experiments; SQ, JL, JJ, SB, NJ, HL and LH performed the experiments; LM and SL wrote the manuscript, and all authors read, critiqued and edited the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
- Chi XY, Wang YH, Miao J, Feng ZB, Zhang HQ, Zhai JJ, Zhang HY, Tian LQ, Xue WW, Yang TT, Huang R, Hu XM, Ge YH (2017) Development and characterization of a fusion mutant with the truncated lacZ to screen regulatory genes for phenazine biosynthesis in Pseudomonas chlororaphis G05. Biol Control 108:70–76CrossRefGoogle Scholar
- Hennessy RC, Phippen CBW, Nielsen KF, Olsson S, Stougaard P. (2017) Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR-type transcriptional regulator NunF. Microbiologyopen. https://doi.org/10.1002/mbo3.516
- Hernandez-Salmeron JE, Hernandez-Leon R, Orozco-Mosqueda MD, 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. https://doi.org/10.1186/s40793-015-0123-9
- Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P (2016) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 44:286–293CrossRefGoogle Scholar
- Kimbrel JA, Givan SA, Halgren AB, Creason AL, Mills DI, Banowetz GM, Armstrong DJ, Chang JH (2010) An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genom 11:522. https://doi.org/10.1186/1471-2164-11-522 CrossRefGoogle Scholar
- Ma L, Qu S, Wang X, Deng P, Lin J, Li H, Hou L, Jiang N, Song J, Lu SE (2016) Identification of an antifungal bacterium against mushroom pathogen Trichoderma viride and characterization of genes associated with antifungal activity. Jiangsu J Agric Sci 32:528–533Google Scholar
- Martinez-Garcia PM, Ruano-Rosa D, Schiliro E, Prieto P, Ramos C, Rodriguez-Palenzuela P, Mercado-Blanco J. (2015) Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae. Stand Genomic Sci. https://doi.org/10.1186/1944-3277-10-10
- O’Rawe J, Jiang T, Sun GQ, Wu YY, Wang W, Hu JC, Bodily P, Tian LF, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. https://doi.org/10.1186/gm432
- Scholz-Schroeder BK, Hutchison ML, Grgurina I, Gross DC (2001) The contribution of syringopeptin and syringomycin to virulence of Pseudomonas syringae pv. syringae strain B301D on the basis of sypA and syrB1 biosynthesis mutant analysis. Mol Plant Microbe Interact 14:336–348CrossRefPubMedGoogle Scholar
- Tazawa J, Watanabe K, Yoshida H, Sato M, Homma Y (2017) Simple method of detection of the strains of fluorescent Pseudomonas spp. producing antibiotics, pyrrolnitrin and phloroglucinol. Soil Microorganisms 54:61–67Google Scholar
- Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE. (2016) The rare codon AGA is involved in regulation of pyoluteorin biosynthesis in Pseudomonas protegens Pf-5. Front Microbiol. https://doi.org/10.3389/fmicb.2016.00497