Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus

LITERATURE CITED

• Berendsen RL, Kalkhove SIC, Lugones LG, Wosten HAB, Bakker PAHM. 2012. Germination of Lecanicillium fungicola in the mycosphere of Agaricus bisporus. Environmental Microbiology Reports 4:227–233.
   PubMed Web of Science ®Google Scholar
• Bernardo D, Cabo AP, Novaes-Ledieu M, Mendoza CG. 2004. Verticillium disease or “dry bubble” of cultivated mushrooms: the Agaricus bisporus lectin recognizes and binds the Verticillium fungicola cell wall glucogalactomannan. Canadian Journal Microbiology 50:729–735.
   PubMed Web of Science ®Google Scholar
• Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF. 2015. Unusual biology across a group comprising more than 15% of domain bacteria. Nature 523:208–211.
   PubMed Web of Science ®Google Scholar
• Calonje M, Garcia Mendoza C, Perez Cabo A, Bernardo D, Novaes-Ledieu M. 2000. Interaction between the mycoparasite Verticillium fungicola and the vegetative mycelial phase of Agaricus bisporus. Mycological Research 104:988–992.
   Web of Science ®Google Scholar
• De Groot PWJ, Visser J, Van Griensven LJLD, Schaap PJ. 1998. Biochemical and molecular aspects of growth and fruiting of the edible mushroom Agaricus bisporus. Mycological Research 102:1297–1308.
   Web of Science ®Google Scholar
• Foulongne-Oriol M, Rodier A, and Savoie JM. 2012. Relationship between yield components and partial resistance to Lecanicillium fungicola in the button mushroom, Agaricus bisporus, assessed by quantitative trait locus mapping. Applied Environmental Microbiology 78:2435–2442.
   PubMed Web of Science ®Google Scholar
• Gea FJ, Carrasco J, Santos M, Dianez F, Navarro, MJ. 2013. Incidence of Lecanicillium fungicola in white-button mushroom (Agaricus bisporus) cultivated with two types of casing soil. Journal of Plant Pathology 95:163–166.
   Web of Science ®Google Scholar
• Genders R. 1969. Mushroom growing for everyone. 1st ed. Albuquerque, New Mexico: Transatlantic Arts. 216 p.
   Google Scholar
• Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, Griffiths RI, Schonrogge K. 2015. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods in Ecology and Evolution 6:973–980.
   PubMed Web of Science ®Google Scholar
• Hirsch PR, Mauchline TH, Clark IM. 2010. Culture-independent molecular techniques for soil microbial ecology. Soil Biology & Biochemistry 42:878–887.
   Web of Science ®Google Scholar
• Hollman F, Gumulya Y, Tolle C, Liese A, Thum O. 2008. Evaluation of the laccase from myceliophthora thermophila as industrial biocatalyst for polymerization reactions. Macromolecules 41:8520–8524.
   Web of Science ®Google Scholar
• Hultman J, Ritari J, Romantschuk M, Paulin L, Auvinen P. 2008. Universal ligation-detection-reaction microarray applied for compost microbes. BMC Microbiology 8:237.
   Web of Science ®Google Scholar
• Hultman J, Vasara T, Partanen P, Kurola J, Kontro MH, Paulin L, Auvinen P, Romantschuk M. 2010. Determination of fungal succession during municipal solid waste composting using a cloning-based analysis. Journal of Applied Microbiology 108:472–487.
   PubMed Web of Science ®Google Scholar
• Jurak E, Patyshakuliyeva A, de Vries RP, Gruppan H, Kabel MA. 2015. Compost grown Agaricus bisporus lacks the ability to degrade and consume highly substituted xylan fragments. PLoS ONE 10:e0134169.
   PubMed Web of Science ®Google Scholar
• Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT. 2004. Methods of studying soil microbial diversity. Journal of Microbiological Methods 58:169–188.
   PubMed Web of Science ®Google Scholar
• Largeteau ML, Savoie JM. 2010. Microbially induced diseases of Agaricus bisporus: biochemical mechanisms and impact on commercial mushroom production. Applied Microbiology and Biotechnology 86:63–73.
   PubMed Web of Science ®Google Scholar
• Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Koljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H. 2013. Fungal community analysis by high-throughput sequencing of amplified markers—a user’s guide. New Phytologist 199:288–299.
   PubMed Web of Science ®Google Scholar
• Moretti MMS, Bocchini-Martins DA, Da Silva R, Rodrigues A, Sette LD, Gomes E. 2012. Selection of thermophilic and thermotolerant fungi for the production of cellulases and xylanases under solid-state fermentation. Brazilian Journal of Microbiology 43:1062–1071.
   PubMed Web of Science ®Google Scholar
• Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling JS, Kennedy PG. 2016. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology 20: 241–248.
   Google Scholar
• Patyshakuliyeva A, Jurak E, Kohler A, Baker A, Battaglia E, de Bruijn W, Burton KS, Challen MP, Coutinho PM, Eastwood DC, Gruben BS, Mäkelä MR, Martin F, Nadal M, Van Den Brink J, Wiebenga A, Zhou M, Henrissat B, Kabel M, Gruppen H, de Vries RP. 2013. Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus. BMC Genomics 14:663.
   Google Scholar
• Patyshakuliyeva A, Post H, Zhou M, Jurack E, Heck AJR, Hilden KS, Kabel MA, Makela MR, Altelaar AFM, de Vries RP. 2015. Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle. Environmental Microbiology 17:3098–3108.
   PubMed Web of Science ®Google Scholar
• Pecchia J, Cortese R, Albert I. 2014. Investigation into the microbial community changes that occur in the casing layer during cropping of the white button mushroom, Agaricus bisporus. In: Singh, M., ed. Proceedings of the 8th International Conference on Mushroom Biology and Mushroom Products, 19–22 November 2014, New Delhi, India. pp. 309–313.
   Google Scholar
• Raghukumar C, D’Souza-Ticlo D, Verma A. 2008. Treatment of coloured effluents with lignin-degrading enzymes: an emerging role of marine-derived fungi. Critical Reviews in Microbiology 34:189–206.
   PubMed Web of Science ®Google Scholar
• Ramos JAT, Barends S, Verhaert RMD, de Graaff LH. 2011. The Aspergillus niger multicopper oxidase family: analysis and overexpression of laccase-like encoding genes. Microbial Cell Factory 10:78.
   Web of Science ®Google Scholar
• Singh S, Madlala AM, Prior BA. 2003. Thermomyces lanuginosus: properties of strains and their hemicellulases. FEMS Microbiology Reviews 27:3–16.
   PubMed Web of Science ®Google Scholar
• Sonnenberg ASM, Baars JJP, Hendrix PM, Lavrijssen B, Gao W, Weijn A, Mes JJ. 2011. Breeding and strain protection in the button mushroom Agaricus bisporus. In: Savoie, J.M, Foulongne-Oriol, M., Largeteau, M., Barroso, G., eds. Proceedings of the 7th International Conference On Mushroom Biology And Mushroom Products, Genomics, Genetics and Breeding, 2011 October 4-7, Arcachon, France. p. 7–15.
   Google Scholar
• Straatsma G, Samson RA, Olijnsma TW, Camp HJMOD, Gerrits JPG, Van Griensven LJLD. 1994. Ecology of thermophilic fungi in mushroom compost, with emphasis on Scytalidium thermophilum and growth stimulation of Agaricus bisporus mycelium. Applied and Environmental Microbiology 60:454–458.
   PubMed Web of Science ®Google Scholar
• Szekely AJ, Sipos R, Berta B, Vajna B, Hajdu C, Marialigeti K. 2009. DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microbial Ecology 57:522–533.
   PubMed Web of Science ®Google Scholar
• Umar MH, Van Griensven LJLD. 1997. Morphological studies on the life span, developmental stages, senescence and death of fruit bodies of Agaricus bisporus. Mycological Research 101:1409–1422.
   Web of Science ®Google Scholar
• Van Griensven LJLD, Van Roestel AJJ. 2004. The cultivation of the button mushroom Agaricus bisporus in The Netherlands: a successful industry. Revista Mexicana de Micologia 19:95–102.
   Google Scholar
• Zhang X, Zhong Y, Yang S, Zhang W, Xu M, Ma A, Zhuang G, Chen G, Liu W. 2014. Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production. Bioresource Technology 170:183–195.
   PubMed Web of Science ®Google Scholar
• Zoll J, Snelders E, Verweij P, Melchers W.J.G. 2016. Next-generation sequencing in the mycology lab. Current Fungal Infection Reports 10:37–42.
   PubMedGoogle Scholar