in

Dynamics of microbial community and enzyme activities during preparation of Agaricus bisporus compost substrate

[adace-ad id="91168"]
  • Royse DJ. A global perspective on the high five: Agaricus, Pleurotus, Lentinula, Auricularia and Flammulina. In: Singh M, editor. Proceedings of the 8th International Conference on Mushroom Biology and Mushroom Products. New Delhi; 2014. p. 1–6.

  • Vos AM, Heijboer A, Boschker HTS, Bonnet B, Lugones LG, Wosten HAB. Microbial biomass in compost during colonization of Agaricus bisporus. AMB Express. 2017; 7:12.

  • Jurak E, Punt AM, Arts W, Kabel MA, Gruppen H. Fate of carbohydrates and lignin during composting and mycelium growth of Agaricus bisporus on wheat straw based compost. PLoS ONE. 2015;10:e0138909.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Beyer DM. Basic procedures for Agaricus mushroom growing PennState Extension: the Pennsylvania State University. 2003. https://extension.psu.edu/basic-procedures-for-agaricus-mushroom-growing.

  • Wang L, Mao J, Zhao H, Li M, Wei Q, Zhou Y, et al. Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for Agaricus bisporus production. J Ind Microbiol Biotechnol. 2016;43:1249–60.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Adams JDW, Frostick LE. Investigating microbial activities in compost using mushroom (Agaricus bisporus) cultivation as an experimental system. Bioresour Technol. 2008;99:1097–102.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Liu L, Wang S, Guo X, Zhao T, Zhang B. Succession and diversity of microorganisms and their association with physicochemical properties during green waste thermophilic composting. Waste Manage. 2018;73:101–12.

    CAS 
    Article 

    Google Scholar 

  • Reyes-Torres M, Oviedo-Ocana ER, Dominguez I, Komilis D, Sanchez A. A systematic review on the composting of green waste: feedstock quality and optimization strategies. Waste Manage. 2018;77:486–99.

    CAS 
    Article 

    Google Scholar 

  • Pardo‐Giménez A, González JEP, Zied DC. Casing materials and techniques in Agaricus bisporus cultivation. In: Zied DC, Pardo‐Giménez A, editors. Edible and medicinal mushrooms technology and applications. Chichester, UK: Wiley; 2017. p. 149–74.

  • Baars JJP, Scholtmeijer K, Sonnenberg ASM, van Peer A. Critical factors involved in primordia building in Agaricus bisporus: a review. Molecules. 2020;25:2984.

  • Vieira FR, Pecchia JA. Bacterial community patterns in the Agaricus bisporus cultivation system, from compost raw materials to mushroom caps. Microb Ecol. 2021;84:20–32.

    PubMed 
    Article 

    Google Scholar 

  • Kristensen JB, Thygesen LG, Felby C, Jorgensen H, Elder T. Cell-wall structural changes in wheat straw pretreated for bioethanol production. Biotechnol Biofuels. 2008;1:1–9.

    Article 

    Google Scholar 

  • Jurak E, Patyshakuliyeva A, de Vries RP, Gruppen H, Kabel MA. Compost grown Agaricus bisporus lacks the ability to degrade and consume highly substituted xylan fragments. PLoS ONE. 2015;10:e0134169.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ryckeboer J, Mergaert J, Vaes K, Klammer S, De Clercq D, Coosemans J, et al. A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol. 2003;53:349–410.

    Google Scholar 

  • Kutzner HJ. Microbiology of composting. In: Rehm H-J, Reed G, editors. Biotechnology. 11c. 2nd ed. Verlag: Wiley-VCH; 2000. p. 35–100.

  • Carrasco J, Garcia-Delgado C, Lavega R, Tello ML, De Toro M, Barba-Vicente V, et al. Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation. Microb Biotechnol. 2020;13:1933–47.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Vieira FR, Pecchia JA. Bacterial community patterns in the Agaricus bisporus cultivation system, from compost raw materials to mushroom caps. Microb Ecol. 2021;82. https://doi.org/10.1007/s00248-021-1833-5.

  • Vieira FR, Pecchia JA. An exploration into the bacterial community under different pasteurization conditions during substrate preparation (composting–Phase II) for Agaricus bisporus cultivation. Microb Ecol. 2018;75:318–30.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Cao GT, Song TT, Shen YY, Jin QL, Feng WL, Fan LJ, et al. Diversity of bacterial and fungal communities in wheat straw compost for Agaricus bisporus cultivation. Hortscience. 2019;54:100–9.

    CAS 
    Article 

    Google Scholar 

  • Wiegant WM. Growth characteristics of the thermophilic fungus Scytalidium thermophilum in relation to production of mushroom compost. Appl Environ Microbiol. 1992;58:1301–7.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fermor T, Randle P, Smith J. Compost as a substrate and its preparation. In: Flegg PB, Spencer DM, Wood D, editors. The biology and technology of the cultivated mushroom. Chichester, UK: John Wiley & Sons, Ltd; 1985. p. 81–109.

  • Straatsma G, Samson RA, Olijnsma TW, Op den Camp HJM, Gerrits JPG, Griensven LJLDV. Ecology of thermophilic fungi in mushroom compost, with emphasis on Scytalidium thermophilum and growth stimulation of Agaricus bisporus mycelium. Appl Environ Microbiol. 1994;60:454–8.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ross RC, Harris PJ. An investigation into the selective nature of mushroom compost. Sci Hortic. 1983;19:55–64.

    Article 

    Google Scholar 

  • Coello-Castillo MM, Sanchez JE, Royse DJ. Production of Agaricus bisporus on substrates pre-colonized by Scytalidium thermophilum and supplemented at casing with protein-rich supplements. Bioresour Technol. 2009;100:4488–92.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Szekely A, Sipos R, Berta B, Vajna B, Hajdu C, Marialigeti K. DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microb Ecol. 2009;57:522–33.

    PubMed 
    Article 

    Google Scholar 

  • Kertesz M, Safianowicz K, Bell TL. New insights into the microbial communities and biological activities that define mushroom compost. Sci Cultiv Edible Fungi. 2016;19:161–5.

    Google Scholar 

  • McGee CF, Byrne H, Irvine A, Wilson J. Diversity and dynamics of the DNA and cDNA-derived bacterial compost communities throughout the Agaricus bisporus mushroom cropping process. Ann Microbiol. 2017;67:751–61.

    CAS 
    Article 

    Google Scholar 

  • McGee CF, Byrne H, Irvine A, Wilson J. Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus. Mycologia. 2017;109:475–84.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Yeates C, Gillings MR. Rapid purification of DNA from soil for molecular biodiversity analysis. Lett Appl Microbiol. 1998;27:49–53.

    CAS 
    Article 

    Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor JW. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. New York: Academic Press; 1990. p. 315–22.

    Google Scholar 

  • Lever MA, Torti A, Eickenbusch P, Michaud AB, Santl-Temkiv T, Jorgensen BB. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types. Front Microbiol. 2015;6:476.

  • Muyzer G, Waal ECD, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59:695–700.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation For Statistical Computing; 2019.

  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina aplicon data. Nat Meth. 2016;13:581–3.

    CAS 
    Article 

    Google Scholar 

  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res. 2012;41:D590–6.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2010;27:592–3.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wright ES. Using DECIPHER v2.0 to analyze big biological sequence data in R. R J. 2016;8:352–9.

    Article 

    Google Scholar 

  • McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dixon P. VEGAN, a package of R functions for community ecology. J Veget Sci. 2003;14:927–30.

    Article 

    Google Scholar 

  • Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer; 2016.

  • Sharma HS, Kilpatrick M. Mushroom (Agaricus bisporus) compost quality factors for predicting potential yield of fruiting bodies. Can J Microbiol. 2000;46:515–9.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Seaby DA. Mushroom (Agaricus bisporus) yield modelling for the bag method of mushroom production using commercial yields and from micro plots. Sci Cultiv Edible Fungi. 1995;14:409–16.

    Google Scholar 

  • O’Donoghue DC. Relationship between some compost factors and their effects on yield of Agaricus. Mushroom Sci. 1965;6:245–54.

    Google Scholar 

  • Andersen B, Sorensen JL, Nielsen KF, van den Ende BG, de Hoog S. A polyphasic approach to the taxonomy of the Alternaria infectoria species-group. Fungal Genet Biol. 2009;46:642–56.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • van den Brink J, Samson RA, Hagen F, Boekhout T, de Vries RP. Phylogeny of the industrial relevant, thermophilic genera Myceliophthora and Corynascus. Fungal Divers. 2012;52:197–207.

    Article 

    Google Scholar 

  • Souza TP, Marques SC, Santos D, Dias ES. Analysis of thermophilic fungal populations during phase II of composting for the cultivation of Agaricus subrufescens. World J Microbiol Biotechnol. 2014;30:2419–25.

    PubMed 
    Article 

    Google Scholar 

  • Vajna B, Szili D, Nagy A, Márialigeti K. An improved sequence-aided T-RFLP analysis of bacterial succession during oyster mushroom substrate preparation. Microb Ecol. 2012;64:702–13.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Du R, Yan J, Li S, Zhang L, Zhang S, Li J, et al. Cellulosic ethanol production by natural bacterial consortia is enhanced by Pseudoxanthomonas taiwanensis. Biotechnol Biofuels. 2015;8:10.

  • Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl Environ Microbiol. 2005;71:7099–106.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Haruta S, Cui Z, Huang Z, Li M, Ishii M, Igarashi Y. Construction of a stable microbial community with high cellulose-degradation ability. Appl Microbiol Biotechnol. 2002;59:529–34.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Vajna B, Adrienn N, Sajben-Nagy E, Manczinger L, Szijártó N, Kádár Z, et al. Microbial community structure changes during oyster mushroom substrate preparation. Appl Microbiol Biotechnol. 2010;86:367–75.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Karadag D, Özkaya B, Ölmez E, Nissilä ME, Çakmakçı M, Yıldız Ş, et al. Profiling of bacterial community in a full-scale aerobic composting plant. Int Biodeter Biodeg. 2013;77:85–90.

    CAS 
    Article 

    Google Scholar 

  • Rathinam NK, Gorky, Bibra M, Salem DR, Sani RK. Bioelectrochemical approach for enhancing lignocellulose degradation and biofilm formation in Geobacillus strain WSUCF1. Bioresour Technol. 2020;295:122271.

  • Song TT, Shen YY, Jin QL, Feng WL, Fan LJ, Cao GT, et al. Bacterial community diversity, lignocellulose components, and histological changes in composting using agricultural straws for Agaricus bisporus production. PeerJ. 2021;9:e10452.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhang X, Zhong Y, Yang S, Zhang W, Xu M, Ma A, et al. Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production. Bioresour Technol. 2014;170:183–95.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Goodfellow M, Maldonado LA, Quintana ET. Reclassification of Nonomuraea flexuosa (Meyer 1989) Zhang et al. 1998 as Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev. Int J Syst Evol Microbiol. 2005;55:1979–83.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Lin SB, Stutzenberger FJ. Purification and characterization of the major beta-1,4-endoglucanase from Thermomonospora curvata. J Appl Bacteriol. 1995;79:447–53.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Kukolya J, Nagy I, Láday M, Tóth E, Oravecz O, Márialigeti K, et al. Thermobifida cellulolytica sp. nov., a novel lignocellulose-decomposing actinomycete. Int J Syst Evol Microbiol. 2002;52:1193–9.

    CAS 
    PubMed 

    Google Scholar 

  • Weon H-Y, Lee S-Y, Kim B-Y, Noh H-J, Schumann P, Kim J-S, et al. Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts. Int J Syst Evol Microbiol. 2007;57:2908–11.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Poli A, Laezza G, Gul-Guven R, Orlando P, Nicolaus B. Geobacillus galactosidasius sp. nov., a new thermophilic galactosidase-producing bacterium isolated from compost. Syst Appl Microbiol. 2011;34:419–23.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Gavande PV, Basak A, Sen S, Lepcha K, Murmu N, Rai V, et al. Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization. Sci Rep. 2021;11:3032.

  • Xu JQ, Lu YY, Shan GC, He XS, Huang JH, Li QL. Inoculation with compost-born thermophilic complex microbial consortium induced organic matters degradation while reduced nitrogen loss during co-composting of dairy manure and sugarcane leaves. Waste Biomass Valor. 2019;10:2467–77.

    CAS 
    Article 

    Google Scholar 

  • Yoon JH, Kang SJ, Im WT, Lee ST, Oh TK. Chelatococcus daeguensis sp nov., isolated from wastewater of a textile dye works, and emended description of the genus Chelatococcus. Int J Syst Evol Microbiol. 2008;58:2224–8.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhou C, Liu Z, Huang Z-L, Dong M, Yu X-L, Ning P. A new strategy for co-composting dairy manure with rice straw: addition of different inocula at three stages of composting. Waste Manage. 2015;40:38–43.

    CAS 
    Article 

    Google Scholar 

  • Gómez A. New technology in Agaricus bisporus cultivation. In: Zied DC, Pardo-Giménez A, editors. Edible and medicinal mushrooms. Chichester, UK: John Wiley & Sons; 2017. p. 211–20.

  • von Minnigerode HF, editor. Method for controlling and regulating the composting process. Proceedings of the Eleventh International Scientific Congress on the Cultivation of Edible Fungi. Sydney, Australia: The International Society for Mushroom Science; 1981.

  • Jurak E, Gruppen H, Kabel MA, Eggink G, Meyer AS, van der Maarel MJEC, et al. How mushrooms feed on compost: conversion of carbohydrates and lignin in industrial wheat straw based compost enabling the growth of Agaricus bisporus. Wageningen University—Graduate School VLAG; 2015.

  • Miller FC, Macauley BJ, Harper ER. Investigation of various gases, pH and redox potential in mushroom composting Phase-I stacks. Aust J Exper Agric. 1991;31:415–25.

    Article 

    Google Scholar 

  • Miller FC, Harper ER, Macauley BJ, Gulliver A. Composting based on moderately thermophilic and aerobic conditions for the production of commercial growing compost. Aust J Exper Agric. 1990;30:287–96.

    Article 

    Google Scholar 

  • Carrasco J, Preston GM. Growing edible mushrooms: a conversation between bacteria and fungi. Environ Microbiol. 2020;22:858–72.

    PubMed 
    Article 

    Google Scholar 


  • Source: Ecology - nature.com

    Ultrasonic antifouling devices negatively impact Cuvier’s beaked whales near Guadalupe Island, México

    Estimating leaf area index of maize using UAV-based digital imagery and machine learning methods