Determination of biodiversity of Coprinus comatus using genotyping and metabolic profiling tools

• Authors: Anna Pawlik , Anna Malinowska , Marek Siwulski , Magdalena Frąc , Jerzy Rogalski , Grzegorz Janusz
• Languages of publication: EN

Abstracts

EN

Coprinus comatus strains (CCMs) originating from Poland were identified using ITS region sequencing. Based on the sequences obtained, the genetic relationship between the CCM strains was determined and a clear separation of all strains into two main clusters was obtained. The Coprinus strains were also genetically characterized for the first time by the AFLP technique. The analysis showed that the CCMs separated into four main clusters and a high complication of a UPGMA-based dendrogram was achieved. C. comatus strains included in the analysis displayed an AFLP profile similarity level in the range from 44 to 66%. The highest similarity coefficient, 0.490, was found between CCM12 and CCM13, and the lowest (0.202) between the CCM2 and CCM5 isolates. Biolog FF MicroPlates were applied to obtain data on utilization of 95 carbon sources and mycelial growth. The analysis allowed comparison of the functional diversity of the CCM strains and revealed a broad variability within the analyzed Coprinus species based on substrate utilization profiles. Significant differences (2-48) have been shown in the substrate richness values. The Biolog experiments proved to be a good profiling technology for studying the diversity in shaggy manes due to metabolic differences and demonstrated that all the strains might be considered individually. It is evident that the strain metabolic grouping does not correlate with the grouping based on the ITS sequences and AFLP profiles, however, some similarities may be observed.

Keywords

EN

AFLP; ITS; Biolog; fungal diversity; Coprinus comatus; shaggy mane mushroom

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2015
• Volume: 62
• Issue: 4
• Pages: 683-689

Dates

published

2015

received

2015-07-15

revised

2015-09-17

accepted

2015-10-02

(unknown)

2015-10-26

Contributors

author

Anna Pawlik

• Department of Biochemistry, Maria Curie-Skłodowska University, Lublin, Poland

author

Anna Malinowska

• Department of Biochemistry, Maria Curie-Skłodowska University, Lublin, Poland

author

Marek Siwulski

• Department of Vegetable Crops, Poznań University of Life Sciences, Poznań, Poland

author

Magdalena Frąc

• Department of Plant and Soil System, Laboratory of Molecular and Environmental Microbiology, Institute of Agrophysics PAS, Lublin, Poland

author

Jerzy Rogalski

• Department of Biochemistry, Maria Curie-Skłodowska University, Lublin, Poland

author

Grzegorz Janusz

• Department of Biochemistry, Maria Curie-Skłodowska University, Lublin, Poland

References

• Agger S, Lopez-Gallego F, Schmidt-Dannert C (2009) Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus. Mol Microbiol 72: 1181-1195.
• Borges MJ, Azevedo MO, Bonatelli M, Felipe MSS, Astolfi-Filho S (1990) A practical method for the preparation of total DNA from filamentous fungi. Fungal Genet Newsl 10: 11.
• Cai D, Chen M, Cai Z, Li H, Guo Z, Liao J (2010) SRAP analysis of Coprinus comatus cultivars. Acta Edulis Fungi 17: 16-19.
• Cilerdzic J, Vukojevic J, Stajic M, Stanojkovic T, Glamoclija J (2014) Biological activity of Ganoderma lucidum basidiocarps cultivated on alternative and commercial substrate. J Ethnopharmacol 155: 312-319.
• Druzhinina IS, Komon-Zelazowska M, Atanasova L, Seidl V, Kubicek CP (2010) Evolution and ecophysiology of the industrial producer Hypocrea jecorina (anamorph Trichoderma reesei) and a new sympatric agamospecies related to it. PloS One 5: e9191.
• Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118.
• Hampl V, Pavlicek A, Flegr J (2001) Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Microbiol 51: 731-735.
• Han C, Yuan J, Wang Y, Li L (2006) Hypoglycemic activity of fermented mushroom of Coprinus comatus rich in vanadium. J Trace Elem Med Biol 20: 191-196.
• Hartigan JA (1975) Necessary and sufficient conditions for asymptotic joint normality of a statistic and its subsample values. Ann Stat 3: 573-580.
• Hopple JS, Vilgalys R (1999) Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups, and monophyly. Mol Phylogenet Evol 13: 1-19.
• Hoyos-Carvajal L, Orduz S, Bissett J (2009) Genetic and metabolic biodiversity of Trichoderma from Colombia and adjacent neotropic regions. Fungal Genet Biol 46: 615-631.
• Jaccard P (1912) The Distribution of the flora in the alpine zone New Phytol 11: 37-50.
• Jang MJ, Lee YH, Liu JJ, Ju YC (2009) Optimal conditions for the mycelial growth of Coprinus comatus strains. Mycobiology 37: 103-108.
• Janusz G, Czurylo A, Frac M, Rola B, Sulej J, Pawlik A, Siwulski M, Rogalski J (2015) Laccase production and metabolic diversity among Flammulina velutipes strains. World J Microbiol Biotechnol 31: 121-133.
• Keirle MR, Hemmes DE, Desjardin DE (2004) Agaricales of the Hawaiian Islands. 8. Agaricaceae: Coprinus and Podaxis; Psathyrellaceae: Coprinopsis, Coprinellus and Parasola. Fungal Divers 15: 33-124.
• Ko KS, Lim YW, Kim YH, Jung HS (2001) Phylogeographic divergences of nuclear ITS sequences in Coprinus species sensu lato. Mycol Res 105: 1519-1526.
• Kubicek CP, Bissett J, Druzhinina I, Kullnig-Gradinger C, Szakacs G (2003) Genetic and metabolic diversity of Trichoderma: a case study on South-East Asian isolates. Fungal Genet Biol 38: 310-319.
• Li B, Lu F, Suo X, Nan H (2010) Antioxidant properties of cap and stipe from Coprinus comatus. Molecules 15: 1473-1486.
• Li LH, Yin QY, Liu XH, Yang H (2010) An efficient protoplast isolation and regeneration system in Coprinus comatus. Afr J Microbiol Res 4: 459-465.
• Lindeberg G, Holm G (1952) Occurrence of tyrosinase and laccase in fruit bodies and mycelia of some Hymenomycetes. Physiol Plant 5: 100-114.
• Luo H, Mo M, Huang X, Huang X, Li X, Zhang K (2004) Coprinus comatus: A basidiomycete fungus forms novel spiny structures and infects nematode. Mycologia 96: 1218-1224.
• Luo H, Liu Y, Fang L, Li X, Tang N, Zhang K (2007) Coprinus comatus damages nematode cuticles mechanically with spiny balls and produces potent toxins to immobilize nematodes. Appl Environ Microbiol 73: 3916-3923.
• Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14: 389-394.
• Muraguchi H, Ito Y, Kamada T, Yanagi SO (2003) A linkage map of the basidiomycete Coprinus cinereus based on Random Amplified Polymorphic DNAs and Restriction Fragment Length Polymorphisms. Fungal Genet Biol 40: 93-102.
• Nei M, Li WH (1979) Mathematical model for studying genetic-variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269-5273.
• Page RD (1996) TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
• Pawlik A, Janusz G, Dębska I, Siwulski M, Frąc M, Rogalski J (2015) Genetic and metabolic intraspecific biodiversity of Ganoderma lucidum. BioMed Res Int 2015: 726149.
• Pawlik A, Janusz G, Koszerny J, Małek W, Rogalski J (2012) Genetic diversity of the edible mushroom Pleurotus sp. by Amplified Fragment Length Polymorphism. Curr Microbiol 65: 438-445.
• Redhead SA, Vilgalys R, Moncalvo JM, Johnson J, Hopple JS (2001) Coprinus Pers. and the disposition of Coprinus species sensu lato. Taxon 50: 203-241.
• Ren J, Shi JL, Han C, Liu ZQ, Guo J (2012) Isolation and biological activity of triglycerides of the fermented mushroom of Coprinus comatus. BMC Complement Altern Med 12: 52.
• Sabo A, Stilinovic N, Vukmirovic S, Bukumiric Z, Capo I, Jakovljevic V (2010) Pharmacodynamic action of a commercial preparation of the mushroom Coprinus comatus in rats. Phytother Res 24: 1532-1537.
• Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas P, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, B D, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera G, Hirayama K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, GM K, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, T R, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schussler A, Shearer C, Sotome K, Stefani FO, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiss M, White MM, Xu J, Yahr R, Yang ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109: 6241-6246.
• Stamets P (2000) The gilled mushroom. In Growing gourmet and medicinal mushrooms. Stamets P eds, pp 219-350. Ten Speed Press.
• Stojkovic D, Reis FS, Barros L, Glamoclija J, Ciric A, van Griensven LJ, Sokovic M, Ferreira IC (2013) Nutrients and non-nutrients composition and bioactivity of wild and cultivated Coprinus comatus (O.F.Mull.) Pers. Food Chem Toxicol 59: 289-296.
• Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
• Tripathi BM, Kaushik R, Kumari P, Saxena AK, Arora DK (2011) Genetic and metabolic diversity of streptomycetes in pulp and paper mill effluent treated crop fields. World J Microbiol Biotechnol 27: 1603-1613.
• Tryon RC (1939) Cluster analysis. Edwards Brothers.
• Urbanelli S, Della Rosa V, Punelli F, Porretta D, Reverberi M, Fabbri AA, Fanelli C (2007) DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the Pleurotus eryngii complex. Appl Microbiol Biotechnol 74: 592-600.
• Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
• White TJ, Bruns T, Lee S, Taylor JW (1990) PCR Protocols: A Guide to Methods and Applications. Innis MA, Gelfand DH, Sninsky JJ, White TJ eds, pp 315-322. New York Academic Press.
• Zhao S, Rong CB, Kong C, Liu Y, Xu F, Miao QJ, Wang SX, Wang HX, Zhang GQ (2014) A novel laccase with potent antiproliferative and HIV-1 reverse transcriptase inhibitory activities from mycelia of mushroom Coprinus comatus. BioMed Res Int 2014: 417461.

Identifiers

DOI

10.18388/abp.2015_1102