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Chang W, Feng W, Yang Y, Shen Y, Song T, Li Y, Cai W. Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost. PeerJ 2022; 10:e14426. [PMID: 36523457 PMCID: PMC9745911 DOI: 10.7717/peerj.14426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/30/2022] [Indexed: 12/13/2022] Open
Abstract
Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.
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Affiliation(s)
- Wanqiu Chang
- Jilin Agricultural University, Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Changchun, Jilin, China,Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Zhejiang, China
| | - Weilin Feng
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Zhejiang, China
| | - Yang Yang
- Chinese Academy of Tropical Agricultural Sciences, Environment and Plant Protection Institute, Haikou, Hainan, China
| | - Yingyue Shen
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Zhejiang, China
| | - Tingting Song
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Zhejiang, China
| | - Yu Li
- Jilin Agricultural University, Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Changchun, Jilin, China
| | - Weiming Cai
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Zhejiang, China
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Longley R, Benucci GMN, Mills G, Bonito G. Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors. FEMS Microbiol Lett 2020; 366:5585883. [PMID: 31603508 DOI: 10.1093/femsle/fnz215] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Morel mushrooms (Morchella, Pezizales) are highly prized edible fungi. Approaches to cultivate morels indoors in pasteurized composted substrates have been successful for Morchella rufobrunnea. We used DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) ribosomal DNA and 16S rRNA gene to follow bacterial and fungal communities in substrates during indoor morel cultivation. Our goal was to determine changes in microbial communities at key stages of morel cultivation, which included primordia development, fundament initiation, differentiation and maturation. Additionally, we compared microbial communities between trays that successfully fruited to those that produced conidia and primordia but aborted before ascocarp formation (non-fruiting). The prokaryotic community was dominated by Firmicutes belonging to Bacillus and Paenibacillus with a lower abundance of Flavobacteria. At earlier stages, the fungal community was dominated by Pezizomycetes including Morchella and other species, whereas, later in the cropping cycle Sordariomycetes dominated. Additionally, differences were observed between trays with successful fruiting, which were dominated by Gilmaniella; compared to trays that did not fruit, which were dominated by Cephalotrichum. Our findings inform understanding of microbial community dynamics during morel cultivation, and show that fungal genera, such as Gilmaniella, and prokaryotic genera, such as Bacillus, are abundant in substrates that support M. rufobrunnea fruiting.
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Affiliation(s)
- Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd, East Lansing MI, 48823, USA
| | - Gian Maria Niccoló Benucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing MI, 48824, USA
| | - Gary Mills
- Gourmet Mushrooms Inc., 506 E State St, Scottville MI, 49454, USA
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd, East Lansing MI, 48823, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing MI, 48824, USA
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McGee CF. Microbial ecology of the Agaricus bisporus mushroom cropping process. Appl Microbiol Biotechnol 2017; 102:1075-1083. [PMID: 29222576 DOI: 10.1007/s00253-017-8683-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
Agaricus bisporus is the most widely cultivated mushroom species in the world. Cultivation is commenced by inoculating beds of semi-pasteurised composted organic substrate with a pure spawn of A. bisporus. The A. bisporus mycelium subsequently colonises the composted substrate by degrading the organic material to release nutrients. A layer of peat, often called "casing soil", is laid upon the surface of the composted substrate to induce the development of the mushroom crop and maintain compost environmental conditions. Extensive research has been conducted investigating the biochemistry and genetics of A. bisporus throughout the cultivation process; however, little is currently known about the wider microbial ecology that co-inhabits the composted substrate and casing layers. The compost and casing microbial communities are known to play important roles in the mushroom production process. Microbial species present in the compost and casing are known for (1) being an important source of nitrogen for the A. bisporus mycelium, (2) releasing sugar residues through the degradation of the wheat straw in the composted substrate, (3) playing a critical role in inducing development of the A. bisporus fruiting bodies and (4) acting as pathogens by parasitising the mushroom mycelium/crop. Despite a long history of research into the mushroom cropping process, an extensive review of the microbial communities present in the compost and casing has not as of yet been undertaken. The aim of this review is to provide a comprehensive summary of the literature investigating the compost and casing microbial communities throughout cultivation of the A. bisporus mushroom crop.
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Affiliation(s)
- Conor F McGee
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland.
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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. [DOI: 10.1007/s13213-017-1303-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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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. [PMID: 26436656 PMCID: PMC4593547 DOI: 10.1371/journal.pone.0138909] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/06/2015] [Indexed: 11/18/2022] Open
Abstract
In wheat straw based composting, enabling growth of Agaricus bisporus mushrooms, it is unknown to which extent the carbohydrate-lignin matrix changes and how much is metabolized. In this paper we report yields and remaining structures of the major components. During the Phase II of composting 50% of both xylan and cellulose were metabolized by microbial activity, while lignin structures were unaltered. During A. bisporus’ mycelium growth (Phase III) carbohydrates were only slightly consumed and xylan was found to be partially degraded. At the same time, lignin was metabolized for 45% based on pyrolysis GC/MS. Remaining lignin was found to be modified by an increase in the ratio of syringyl (S) to guaiacyl (G) units from 0.5 to 0.7 during mycelium growth, while fewer decorations on the phenolic skeleton of both S and G units remained.
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Affiliation(s)
- Edita Jurak
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Arjen M. Punt
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Wim Arts
- C4C Grondstoffen B.V. Driekronenstraat 6, 6596 MA, Milsbeek, The Netherlands
| | - Mirjam A. Kabel
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Harry Gruppen
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
- * E-mail:
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Compost Grown Agaricus bisporus Lacks the Ability to Degrade and Consume Highly Substituted Xylan Fragments. PLoS One 2015; 10:e0134169. [PMID: 26237450 PMCID: PMC4523207 DOI: 10.1371/journal.pone.0134169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/06/2015] [Indexed: 11/21/2022] Open
Abstract
The fungus Agaricus bisporus is commercially grown for the production of edible mushrooms. This cultivation occurs on compost, but not all of this substrate is consumed by the fungus. To determine why certain fractions remain unused, carbohydrate degrading enzymes, water-extracted from mushroom-grown compost at different stages of mycelium growth and fruiting body formation, were analyzed for their ability to degrade a range of polysaccharides. Mainly endo-xylanase, endo-glucanase, β-xylosidase and β-glucanase activities were determined in the compost extracts obtained during mushroom growth. Interestingly, arabinofuranosidase activity able to remove arabinosyl residues from doubly substituted xylose residues and α-glucuronidase activity were not detected in the compost enzyme extracts. This correlates with the observed accumulation of arabinosyl and glucuronic acid substituents on the xylan backbone in the compost towards the end of the cultivation. Hence, it was concluded that compost grown A. bisporus lacks the ability to degrade and consume highly substituted xylan fragments.
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Zhang R, Wang H, Liu Q, Ng T. Chemical and ultrastructural studies of lignocellulose biodegradation during Agaricus bisporus cultivation. Biotechnol Appl Biochem 2013; 61:208-16. [PMID: 24033911 DOI: 10.1002/bab.1156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/06/2013] [Indexed: 11/06/2022]
Abstract
During Agaricus bisporus cultivation, lignocellulose degradation is the result of the activity of both the mushroom and microbial communities developed during the composting. To investigate the lignocellulose degradation in detail from the beginning to the end of the process, the functional groups of cellulose, hemicellulose, and lignin have been studied with Fourier transform infrared spectroscopy and the morphological changes of lignocelluloses were elucidated with scanning electron microscopy. The aperture of lignin and cellulose increased to enable the mycelia of A. bisporus to penetrate into the medium and to degrade lignocelluloses in a more direct way. The chemical structure changes implied a preferential use of lignin that could make for better use of cellulose to boost growth of A. bisporus. Changes in chemical structure together with ultrastructural changes induced by the microbial flora during cultivation substrate production by the composting substrate are important in promoting the utilization of lignocelluloses by A. bisporus.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory for Agro-Biotechnology, Department of Microbiology and Immunology, China Agricultural University, Haidian District, Beijing, People's Republic of China
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Farnet AM, Qasemian L, Peter-Valence F, Ruaudel F, Savoie JM, Ferré E. Capacity for colonization and degradation of horse manure and wheat-straw-based compost by different strains of Agaricus subrufescens during the first two weeks of cultivation. BIORESOURCE TECHNOLOGY 2013; 131:266-273. [PMID: 23357087 DOI: 10.1016/j.biortech.2012.12.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 12/21/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
The potential of Agaricus subrufescens strains to colonize and transform horse manure and wheat-straw-based mushroom compost under the physico-chemical conditions typically used for Agaricus bisporus was assessed. Lignocellulolytic activities, H2O2 production and substrate transformation (assessed via CP/MAS NMR of (13)C) for certain A. subrufescens strains were similar or even greater than those obtained for an A. bisporus strain used as control. Moreover, the functional diversity of the microbial communities of the substrate was not altered by the growth of A. subrufescens after 2weeks. These findings obtained with mesocosms simulating the incubation phase of the mushroom production process hold promise for the improvement of cultivation of this tropical Agaricus species on European standard mushroom compost.
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Affiliation(s)
- Anne-Marie Farnet
- Equipe Vulnérabilité des Systèmes Microbiens, IMBE, UMR CNRS IRD 7263, Institut Méditerranéen de Biodiversité et d'Ecologie, Campus de l'Etoile, Aix Marseille Université, 13397 Cedex 20, Marseille, France.
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The medicinal Agaricus mushroom cultivated in Brazil: biology, cultivation and non-medicinal valorisation. Appl Microbiol Biotechnol 2011; 92:897-907. [DOI: 10.1007/s00253-011-3630-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/19/2011] [Accepted: 10/02/2011] [Indexed: 10/16/2022]
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Mata G, Hern�ndez DMM, Andreu LGI. Changes in lignocellulolytic enzyme activites in six Pleurotus spp. strains cultivated on coffee pulp in confrontation with Trichoderma spp. World J Microbiol Biotechnol 2005. [DOI: 10.1007/s11274-004-3041-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Soler-Rivas C, Jolivet S, Arpin N, Olivier JM, Wichers HJ. Biochemical and physiological aspects of brown blotch disease of Agaricus bisporus. FEMS Microbiol Rev 1999; 23:591-614. [PMID: 10525168 DOI: 10.1111/j.1574-6976.1999.tb00415.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Pseudomonas tolaasii is a bacterium endemic to the compost beds where common mushroom (Agaricus bisporus) is cultivated. Under some environmental conditions still not well-determined, but influenced by temperature and relative humidity, the bacterium can become pathogenic and provoke the brown blotch disease. This review describes the interaction between P. tolaasii and A. bisporus that results in the appearance of brown spots on the mushroom caps, typical symptoms of the disease. Firstly, P. tolaasii is studied, the changes in pathogenicity are explained, the compounds that provoke the damage are enumerated as well as various experimental methods to identify the pathogenic form of the bacteria. Secondly, mechanisms involved in the formation of the brown colour on the A. bisporus caps upon infection are briefly mentioned, taking into account the enzymes that catalyse the reaction, their mechanism, substrates and reaction products. Afterwards, a detailed description of the infection process is presented step by step, starting by the chemotactical attraction, fixation, secretion of the toxins, membrane breakdown, effect of the toxin on mushroom polyphenol oxidases and on the discolouration reaction. A possible mechanism of infection is hypothesised at the molecular level. Finally, the strategies tested until now to control the disease are discussed.
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Affiliation(s)
- C Soler-Rivas
- Agrotechnological Research Institute (ATO-DLO), Bornsesteeg 59, 6708 PD, Wageningen, The Netherlands.
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