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Zhou L, Xie Y, Wang X, Wang Z, Sa R, Li P, Yang X. Effect of microbial inoculation on nitrogen transformation, nitrogen functional genes, and bacterial community during cotton straw composting. BIORESOURCE TECHNOLOGY 2024; 403:130859. [PMID: 38777228 DOI: 10.1016/j.biortech.2024.130859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/07/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
The effects of microbial agents on nitrogen (N) conversion during cotton straw composting remains unclear. In this study, inoculation increased the germination index and total nitrogen (TN) by 24-29 % and 7-10 g/kg, respectively. Inoculation enhanced the abundance of nifH, glnA, and amoA and reduced that of major denitrification genes (nirK, narG, and nirS). Inoculation not only produced high differences in the assembly process and strong community replacement but also weakened environmental constraints. Partial least squares path modelling demonstrated that enzyme activity and bacterial community were the main driving factors influencing TN. In addition, network analysis and the random forest model showed distinct changing patterns of bacterial communities after inoculation and identified keystone microorganisms in maintaining network complexity and synergy, as well as system function to promote nitrogen preservation. Findings provide a novel perspective on high-quality resource recovery of agricultural waste.
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Affiliation(s)
- Liuyan Zhou
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
| | - Yuqing Xie
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
| | - Xiaowu Wang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
| | - Zhifang Wang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
| | - Renna Sa
- Research Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
| | - Pengbing Li
- Comprehensive Testing Ground, Xinjiang Academy of Agricultural Sciences, Urumqi 830013, China.
| | - Xinping Yang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
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Quiroz LF, Ciosek T, Grogan H, McKeown PC, Spillane C, Brychkova G. Unravelling the Transcriptional Response of Agaricus bisporus under Lecanicillium fungicola Infection. Int J Mol Sci 2024; 25:1283. [PMID: 38279283 PMCID: PMC10815960 DOI: 10.3390/ijms25021283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Mushrooms are a nutritionally rich and sustainably-produced food with a growing global market. Agaricus bisporus accounts for 11% of the total world mushroom production and it is the dominant species cultivated in Europe. It faces threats from pathogens that cause important production losses, including the mycoparasite Lecanicillium fungicola, the causative agent of dry bubble disease. Through quantitative real-time polymerase chain reaction (qRT-PCR), we determine the impact of L. fungicola infection on the transcription patterns of A. bisporus genes involved in key cellular processes. Notably, genes related to cell division, fruiting body development, and apoptosis exhibit dynamic transcriptional changes in response to infection. Furthermore, A. bisporus infected with L. fungicola were found to accumulate increased levels of reactive oxygen species (ROS). Interestingly, the transcription levels of genes involved in the production and scavenging mechanisms of ROS were also increased, suggesting the involvement of changes to ROS homeostasis in response to L. fungicola infection. These findings identify potential links between enhanced cell proliferation, impaired fruiting body development, and ROS-mediated defence strategies during the A. bisporus (host)-L. fungicola (pathogen) interaction, and offer avenues for innovative disease control strategies and improved understanding of fungal pathogenesis.
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Affiliation(s)
- Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Tessa Ciosek
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Helen Grogan
- Teagasc, Horticulture Development Department, Ashtown Research Centre, D15 KN3K Dublin, Ireland;
| | - Peter C. McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Galina Brychkova
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
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Noble R, Thai M, Kertesz MA. Nitrogen balance and supply in Australasian mushroom composts. Appl Microbiol Biotechnol 2024; 108:151. [PMID: 38240861 PMCID: PMC10798912 DOI: 10.1007/s00253-023-12933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 01/22/2024]
Abstract
Mushrooms are an important source of protein in the human diet. They are increasingly viewed as a sustainable meat replacement in an era of growing populations, with button mushrooms (Agaricus bisporus) the most popular and economically important mushroom in Europe, Australia and North America. Button mushrooms are cultivated on a defined, straw-derived compost, and the nitrogen (N) required to grow these high-protein foods is provided mainly by the addition of poultry manure and horse manure. Using the correct balance of carbon (C) and N sources to produce mushroom compost is critically important in achieving maximum mushroom yields. Changes in the amount and form of N added, the rate and timing of N addition and the other compost components used can dramatically change the proportion of added N recovered in the mushroom caps, the yield and quality of the mushrooms and the loss of N as ammonia and nitrogen oxide gases during composting. This review examines how N supply for mushroom production can be optimised by the use of a broad range of inorganic and organic N sources for mushroom composting, together with the use of recycled compost leachate, gypsum and protein-rich supplements. Integrating this knowledge into our current molecular understanding of mushroom compost biology will provide a pathway for the development of sustainable solutions in mushroom production that will contribute strongly to the circular economy. KEY POINTS: • Nitrogen for production of mushroom compost can be provided as a much wider range of organic feedstocks or inorganic compounds than currently used • Most of the nitrogen used in production of mushroom compost is not recovered as protein in the mushroom crop • The sustainability of mushroom cropping would be increased through alternative nitrogen management during composting and cropping.
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Affiliation(s)
- Ralph Noble
- Microbiotech Ltd, Pershore Centre, Pershore, Worcestershire, WR103JP, UK
| | - Meghann Thai
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, LEES Building, Sydney, NSW, 2006, Australia
| | - Michael A Kertesz
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, LEES Building, Sydney, NSW, 2006, Australia.
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Liu D, Diao W, Sun X, Zong J, Qi X, Liang C. Application of Miscanthus substrates in the cultivation of Ganoderma lingzhi. Arch Microbiol 2023; 205:384. [PMID: 37975884 DOI: 10.1007/s00203-023-03720-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Ganoderma lingzhi is a traditional Chinese medicine that has been used to improve health and longevity for thousands of years. It is usually cultivated on hardwood log- or sawdust-based formulations. Conversely, in this study, we used Miscanthus sacchariflorus (MSF), M. floridulus, and M. sinensis (MSS), fast-growing perennial grasses widely distributed in China, for G. lingzhi cultivation. Mycelial growth rate, activities of lignin-degrading enzymes on colonized mushroom substrates, and expression levels of CAZymes and laccase genes based on different substrates were analyzed. Total triterpenoids, sterols, and polysaccharides content of fruiting bodies obtained from different substrates were investigated. The activities of laccase and manganese peroxidase in mycelia increased in the MSF- and MSS-based formulations compared with that in the sawdust-based formulation. The results of mycelial growth- and cultivation-related experiments showed that the Miscanthus substrates could be used as the substrates for cultivating G. lingzhi. The content of active ingredients, namely triterpenoids, sterols, and polysaccharides, in fruiting bodies cultivated on the Miscanthus substrates did not decrease compared with those in substrate obtained from the sawdust-based formulation. Therefore, the present study provides alternative substrates for the cultivation of G. lingzhi, and a reference for better utilization of inexpensive substrate in future.
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Affiliation(s)
- Dongmei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Wentong Diao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xueyan Sun
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Junqin Zong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
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Lu H, Liu S, Wang A, Yang H, Liang X, Chen X, Li Q. Transmission and regulation insights into antibiotic resistance genes in straw-sludge composting system amended with calcium peroxide. BIORESOURCE TECHNOLOGY 2023; 386:129539. [PMID: 37488016 DOI: 10.1016/j.biortech.2023.129539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
This study developed a Fenton-like system by adding calcium peroxide (CaO2) to a composting system containing straw and sludge. The objective was to examine the influence of antibiotic resistance genes (ARGs) and the structure of the bacterial community. The findings indicated that the inclusion of CaO2 facilitated the reduction of ARGs. ARGs abundance in the test group (T) with CaO2 was 19.02% lower than that in the control check group (CK) without CaO2, and the abundance of ARGs in both groups after composting was lower than the initial abundance. Additionally, the structure of bacterial community in both groups underwent significant changes. Redundancy analysis (RDA) revealed that the CaO2-induced Fenton-like reaction predominantly affected temperature, pH, and the bacterial community by means of reactive oxygen species (ROS). In conclusion, the addition of CaO2 enhanced the removal of ARGs from sewage-sludge and improved compost quality in the composting.
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Affiliation(s)
- Heng Lu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Shuaipeng Liu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Ao Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hongmei Yang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xueling Liang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xiaojing Chen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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Duran K, Magnin J, America AH, Peng M, Hilgers R, de Vries RP, Baars JJ, van Berkel WJ, Kuyper TW, Kabel MA. The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation. iScience 2023; 26:107087. [PMID: 37426348 PMCID: PMC10329178 DOI: 10.1016/j.isci.2023.107087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Despite substantial lignocellulose conversion during mycelial growth, previous transcriptome and proteome studies have not yet revealed how secretomes from the edible mushroom Agaricus bisporus develop and whether they modify lignin models in vitro. To clarify these aspects, A. bisporus secretomes collected throughout a 15-day industrial substrate production and from axenic lab-cultures were subjected to proteomics, and tested on polysaccharides and lignin models. Secretomes (day 6-15) comprised A. bisporus endo-acting and substituent-removing glycoside hydrolases, whereas β-xylosidase and glucosidase activities gradually decreased. Laccases appeared from day 6 onwards. From day 10 onwards, many oxidoreductases were found, with numerous multicopper oxidases (MCO), aryl alcohol oxidases (AAO), glyoxal oxidases (GLOX), a manganese peroxidase (MnP), and unspecific peroxygenases (UPO). Secretomes modified dimeric lignin models, thereby catalyzing syringylglycerol-β-guaiacyl ether (SBG) cleavage, guaiacylglycerol-β-guaiacyl ether (GBG) polymerization, and non-phenolic veratrylglycerol-β-guaiacyl ether (VBG) oxidation. We explored A. bisporus secretomes and insights obtained can help to better understand biomass valorization.
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Affiliation(s)
- Katharina Duran
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Joris Magnin
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Antoine H.P. America
- Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roelant Hilgers
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Johan J.P. Baars
- CNC Grondstoffen, Driekronenstraat 6, 6596 MA Milsbeek, the Netherlands
| | - Willem J.H. van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Thomas W. Kuyper
- Soil Biology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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Santos-Pereira C, Sousa J, Costa ÂMA, Santos AO, Rito T, Soares P, Franco-Duarte R, Silvério SC, Rodrigues LR. Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12627-9. [PMID: 37417976 PMCID: PMC10390414 DOI: 10.1007/s00253-023-12627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
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Affiliation(s)
- Cátia Santos-Pereira
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Joana Sousa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Ângela M A Costa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Andréia O Santos
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Teresa Rito
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Soares
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara C Silvério
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal.
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
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