Evaluation of API 20E system in fluorescent Pseudomonas identification from button mushroom Agaricus bisporus cultivation casing soil

  • Anwar O. MOHAMMAD University of Sulaimani, Natural Resources Department, College of Agricultural Engineering Sciences, Al-Sulaymaniyah https://orcid.org/0000-0003-4082-5974
  • Abdulkareem E.S. ALKURTANY Tikrit University, Department of Soil and Water Science, College of Agriculture, Tikrit
  • Abdullah A. HASSAN Tikrit University, Department of Plant Protection, College of Agriculture, Tikrit
Keywords: bacteria; biochemical tests; classification; fluorescent Pseudomonas; PCR


Bacterial activity, mainly Pseudomonas spp. plays a vital role in the fruiting process of white button mushroom, hence a rapid procedure to identify these bacteria is crucial. In the current study, the validity of commercial identification system, Analytical profile index API 20E to identify Pseudomonas isolates from mushroom casing soil were assessed. Using API strips fifty bacterial isolates from a selective medium (King B medium) were examined, all isolates were belonged to the genus Pseudomonas according to API 20E identification systems. However, only 74% of Pseudomonas bacteria were identified to species level. The molecular identification using 16S rRNA gene was used as a reference tool to identify bacteria at the species level. The results show that the accuracy of the system to classify florescent Pseudomonas to species level was 60%. This was species dependant, and the system accuracy were 100%, 87.5%, 81.3% and 63% in identifying P. aeruginosa, P. putida, P. fluorescens and P. tolaasii respectively. Our finding indicates that although the classification of the Pseudomonas genus with API 20E system is useful, but it is not enough to distinguish these bacteria to species level, genomic studies are necessary to confirm the exact taxonomic position of Pseudomonas spp.


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Beveridge TJ, Lawrence JR, Murray RGE (2007). Sampling and staining for light microscopy. Methods for General and Molecular Microbiology 3:19-33. https://doi.org/10.1128/9781555817497.ch2

Bosshard PP, Zbinden R, Abels S, Böddinghaus B, Altwegg M, Böttger EC (2006). 16S rRNA gene sequencing versus the API 20 NE System and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory. Journal of Clinical Microbiology 44:1359-1366. https://doi.org/10.1128/JCM.44.4.1359-1366.2006

Clarridge JE (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiology Reviews 17:840-862.

Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D (2000). 16S Ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. Journal of Clinical Microbiology 38:3623-3630.

Franzetti L, Scarpellini M (2007). Characterisation of Pseudomonas spp. isolated from foods. Annals of Microbiology 57:39-47. https://doi.org/10.1007/BF03175048

Gill WM (1995). Bacterial diseases of Agaricus mushrooms. Reports of the Tottori Mycological Institute (Japan).

Godfrey SAC, Harrow SA, Marshall JW, Klena JD (2001). Characterization by 16S rRNA sequence analysis of pseudomonads causing blotch disease of cultivated Agaricus bisporus. Applied and Environmental Microbiology 67:4316-4323. https://doi.org/10.1128/AEM.67.9.4316-4323.2001

King EO, Ward MK, Raney DE (1954). Two simple media for the demonstration of pyocyanin and fluorescin. The Journal of Laboratory and Clinical Medicine 44:301-307.

Kiska DL, Gilligan PH (2003). Pseudomonas. In: Manual of Clinical Microbiology. ASM Press, Washington DC, pp 719-728.

Kolbert CP, Persing DH (1999). Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Current Opinion in Microbiology 2:299-305.

Koneman EW, Allen SD, Janda WM, Schreckenberger PC, Winn WC (1997). The Enterobacteriaceae. Color atlas and textbook of diagnostic microbiology. B Lippincott Co, Philadelphia, pp 71-230.

Kosanovic D, Sheehan G, Grogan H, Kavanagh K (2019). Characterisation of the interaction of Pseudomonas putida and Pseudomonas tolaasii with Trichoderma aggressivum. European Journal of Plant Pathology 1-11.

Long PE, Jacobs L (1974). Aseptic fruiting of the cultivated mushroom, Agaricus bisporus. Transactions of the British Mycological Society 63:99-107. https://doi.org/10.1016/S0007-1536(74)80140-3

Mohammad A, Sabaa A (2015). In vitro and in vivo impact of some Pseudomonas spp. on growth and yield of cultivated mushroom (Agaricus bisporus). The Egyptian Society of Experimental Biology 11(2):163-167.

Munsch P, Alatossava T, Marttinen N, Meyer J-M, Christen R, Gardan L (2002). Pseudomonas costantinii sp. nov., another causal agent of brown blotch disease, isolated from cultivated mushroom sporophores in Finland. International Journal of Systematic and Evolutionary Microbiology 52:1973-1983. https://doi.org/10.1099/ijs.0.02090-0

Noble R, Fermor TR, Lincoln S, Dobrovin-Pennington A, Evered C, Mead A, Li R (2003). Primordia initiation of mushroom (Agaricus bisporus) strains on axenic casing materials. Mycologia 95:620-629.

O’Hara CM (2005). Manual and automated instrumentation for identification of Enterobacteriaceae and other aerobic gram-negative bacilli. Clinical Microbiology Reviews 18:147-162. https://doi.org/10.1128/CMR.18.1.147-162.2005

O’Hara CM, Rhoden DL, Miller JM (1992). Re-evaluation of the API 20E identification system versus conventional biochemicals for identification of members of the family Enterobacteriaceae: a new look at an old product. Journal of Clinical Microbiology 30:123-125.

Porteous LA, Widmer F, Seidler RJ (2002). Multiple enzyme restriction fragment length polymorphism analysis for high resolution distinction of Pseudomonas (sensu stricto) 16S rRNA genes. Journal of Microbiological Methods 51:337-348. https://doi.org/10.1016/S0167-7012(02)00108-2

Scarpellini M, Franzetti L, Galli A (2004). Development of PCR assay to identify Pseudomonas fluorescens and its biotype. FEMS Microbiology Letters 236:257-260.

Topic Popovic N, Benussi Skukan A, Strunjak-Perovic I, Coz-Rakovac R, Hacmanjek M, Hunjak B (2004). Comparison of the API 20E and BBL crystal E/NF identification systems for differentiating bacterial isolates from apparently healthy reared sea bass (Dicentrarchus labrax). Veterinary Research Communications 28:93-101. https://doi.org/10.1023/B:VERC.0000012113.95479.2f

How to Cite
MOHAMMAD, A. O., ALKURTANY, A. E., & HASSAN, A. A. (2020). Evaluation of API 20E system in fluorescent Pseudomonas identification from button mushroom Agaricus bisporus cultivation casing soil. Notulae Scientia Biologicae, 12(2), 258-263. https://doi.org/10.15835/nsb12210628
Research articles