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Wang H, Qin Y, Xin L, Nan Q, Xu X, Zhao C, Wu W. Pilot-scale study of innovative mechanically-enhanced dynamic composting for treating kitchen waste. BIORESOURCE TECHNOLOGY 2024; 394:130176. [PMID: 38086465 DOI: 10.1016/j.biortech.2023.130176] [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: 10/12/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
This study introduced a novel mechanically-enhanced dynamic composting (MEDC) method for treating kitchen waste (KW) through partial-mixing and stratified fermentation. A pilot test varied aeration frequencies (AF) to refine control parameters and explore the maturation mechanism. Results showed that a moderate AF (10 min/4 h) achieved optimal efficiency, with a compost germination index of 123 % within 15 d. Moderate AF enhanced the growth of Corynebacterium_1 (25.4 %) and Saccharomonospora (10.5 %) during the low-temperature stage and Bacillus growth (91.3 %) during the maturation stage. Moreover, it enhanced microbial interactions (with an average degree of 19.9) and promoted substrate degradation and transformation, expediting heating and maturation. Multivariate dimensionality reduction analysis showed the MEDC accomplished rapid composting through stratified composting, dividing the reactor into distinct functional zones: feeding, low-temperature, high-temperature, and maturation. This enabled efficient microorganism enrichment and material degradation, expediting KW decomposition and maturation. This study offers a promising alternative for accelerated KW composting.
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Affiliation(s)
- Haoshu Wang
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China; Zhejiang Transper Environmental Protection Technology Co., Ltd., Hangzhou 310058, PR China
| | - Yong Qin
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China.
| | - Liqing Xin
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China
| | - Qiong Nan
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China
| | - Xingkun Xu
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China
| | - Changxun Zhao
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China
| | - Weixiang Wu
- Institute of Environment Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang 310058, PR China
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Ameen HA, Dohuki MSSM. The effect of leaching and bulking agents on the quality of municipal solid waste compost. ENVIRONMENTAL TECHNOLOGY 2024; 45:144-157. [PMID: 35816131 DOI: 10.1080/09593330.2022.2101026] [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: 04/25/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Compost quality varies greatly depending on the feedstocks used and the composting process. Thus, improving the quality of compost is highly important for producing a high-quality agricultural product. Accordingly, the effect of leaching and addition of wheat straw (WS) and wood shaving (WSH) as bulking agents (BAs) on the organic fraction of municipal solid waste (OFMSW) was evaluated through assessing their effects on composting process and final product quality. Two pilot-scale experiments were prepared, each consisting of 3 piles of 1.2 m3. The first experiment (A) has three plies: A1 = (100% OFMSW), A2 = (88.5% OFMSW + 11.5% WS) and A3 = (90.1% OFMSW + 9.9% WSH). The second one (B), where OFMSW was subjected to leaching, has also three piles: B1 = (100% OFMSW), B2 = (96.2% OFMSW + 3.8% WS) and B3 = (97.1% OFMSW + 2.9% WSH). The results showed that the addition of BAs and leaching treatments accelerated the starting step, raised the temperature and decomposing process, and reduced the duration of the thermophilic phase. The addition of BAs, primarily WS, increased compost stability and maturity in terms of greater total organic carbon (TOC) 22.8-25.5%, total kjeldahl nitrogen (TKN) 1.73-2.37%, germination index (GI) 84.6-107.2%, and reduced C/N 10.8-14 ratio and CO2 evolution rate 2.67-3.69 mg CO2 - C/g OM/d. The use of the leaching process and BAa decreased EC values and heavy metal content in the final products. The implementation of these experimental approaches can be used successfully to reduce the undesired high salt and heavy metal content in the final composts.
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3
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Rocha Vieira F, Andrew Pecchia J. Fungal community assembly during a high-temperature composting under different pasteurization regimes used to elaborate the Agaricus bisporus substrate. Fungal Biol 2021; 125:826-833. [PMID: 34537178 DOI: 10.1016/j.funbio.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/10/2021] [Accepted: 05/24/2021] [Indexed: 01/04/2023]
Abstract
Agaricus bisporus cultivation is based on a selective substrate prepared by a meticulous composting process where thermophilic and/or thermotolerant fungi might play an important role in straw biomass depolymerization. Since fungi have physiological limitations to survive and grow in high-temperature environments, we set out different pasteurization regimes (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h) to evaluate the impact on the fungal community assembly. The fungal community profile generated by high-throughput sequencing showed shifts in community diversity and composition under different pasteurization regimes. Most of the recovered sequences belong to the Ascomycota phylum. Among 73 species detected, Mycothermus thermophilus, Talaromyces thermophilus, and Thermomyces lanuginosus were the most abundant. In the current study, we outlined that pasteurization regimes can reshape the fungal community in compost which can potentially impact the A. bisporus development.
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Affiliation(s)
- Fabricio Rocha Vieira
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.
| | - John Andrew Pecchia
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
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4
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Moreno J, López-González JA, Arcos-Nievas MA, Suárez-Estrella F, Jurado MM, Estrella-González MJ, López MJ. Revisiting the succession of microbial populations throughout composting: A matter of thermotolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145587. [PMID: 33592470 DOI: 10.1016/j.scitotenv.2021.145587] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Composting has been traditionally considered a process in which a succession of mesophilic and thermophilic microbial populations occurs due to temperature changes. In order to deepen in this model, 1380 bacterial and fungal strains (the entire culturable microbiota isolated from a composting process) were investigated for their ability to grow across a wide range of temperatures (20 to 60 °C). First, qualitative tests were performed to establish a thermal profile for each strain. Then, quantitative tests allowed ascertaining the extent of growth for each strain at each of the tested temperatures. The identity of the isolates enabled to position them taxonomically and permitted tracking the strains throughout the process. Results showed that 90% of the isolates were classified as thermotolerant (they grew at all tested temperatures). Only 9% and 1% of the studied strains showed to be strictly mesophilic or thermophilic, respectively. Firmicutes exhibited the greatest thermal plasticity, followed by Actinobacteria and Ascomycota. Most of the Proteobacteria and all Basidiomycota strains were also able to grow at all the assayed temperatures. Thermotolerance was clearly demonstrated among the composting microbiota, suggesting that the idea of the succession of mesophilic and thermophilic populations throughout the process might need a reassessment.
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Affiliation(s)
- J Moreno
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - J A López-González
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain.
| | - M A Arcos-Nievas
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - F Suárez-Estrella
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - M M Jurado
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - M J Estrella-González
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - M J López
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, Agrifood Campus of International Excellence ceiA3; CIAIMBITAL, University of Almería, 04120 Almería, Spain
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5
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Papale M, Romano I, Finore I, Lo Giudice A, Piccolo A, Cangemi S, Di Meo V, Nicolaus B, Poli A. Prokaryotic Diversity of the Composting Thermophilic Phase: The Case of Ground Coffee Compost. Microorganisms 2021; 9:microorganisms9020218. [PMID: 33494462 PMCID: PMC7911569 DOI: 10.3390/microorganisms9020218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 01/22/2023] Open
Abstract
Waste biomass coming from a local coffee company, which supplied burnt ground coffee after an incorrect roasting process, was employed as a starting material in the composting plant of the Experimental Station of the University of Naples Federico II at Castel Volturno (CE). The direct molecular characterization of compost using 13C-NMR spectra, which was acquired through cross-polarization magic-angle spinning, showed a hydrophobicity index of 2.7% and an alkyl/hydroxyalkyl index of 0.7%. Compost samples that were collected during the early "active thermophilic phase" (when the composting temperature was 63 °C) were analyzed for the prokaryotic community composition and activities. Two complementary approaches, i.e., genomic and predictive metabolic analysis of the 16S rRNA V3-V4 amplicon and culture-dependent analysis, were combined to identify the main microbial factors that characterized the composting process. The whole microbial community was dominated by Firmicutes. The predictive analysis of the metabolic functionality of the community highlighted the potential degradation of peptidoglycan and the ability of metal chelation, with both functions being extremely useful for the revitalization and fertilization of agricultural soils. Finally, three biotechnologically relevant Firmicutes members, i.e., Geobacillus thermodenitrificans subsp. calidus, Aeribacillus pallidus, and Ureibacillus terrenus (strains CAF1, CAF2, and CAF5, respectively) were isolated from the "active thermophilic phase" of the coffee composting. All strains were thermophiles growing at the optimal temperature of 60 °C. Our findings contribute to the current knowledge on thermophilic composting microbiology and valorize burnt ground coffee as waste material with biotechnological potentialities.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council of Italy, Spianata San Raineri 86, 98122 Messina, Sicilia, Italy; (M.P.); (A.L.G.)
| | - Ida Romano
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
| | - Ilaria Finore
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council of Italy, Spianata San Raineri 86, 98122 Messina, Sicilia, Italy; (M.P.); (A.L.G.)
| | - Alessandro Piccolo
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agro-alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055 Portici, Naples, Italy; (A.P.); (S.C.)
| | - Silvana Cangemi
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agro-alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055 Portici, Naples, Italy; (A.P.); (S.C.)
| | - Vincenzo Di Meo
- Dipartimento di Agraria, Università Federico II, Via Università 100, 80055 Portici, Naples, Italy;
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
| | - Annarita Poli
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
- Correspondence: ; Tel.: +39-081-867-5311
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6
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Bioprospecting of Thermophilic Fungal Enzymes and Potential Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Lin H, Ye J, Sun W, Yu Q, Wang Q, Zou P, Chen Z, Ma J, Wang F, Ma J. Solar composting greenhouse for organic waste treatment in fed-batch mode: Physicochemical and microbiological dynamics. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 113:1-11. [PMID: 32502764 DOI: 10.1016/j.wasman.2020.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Composting is a sustainable means of managing organic waste, and solar composters offer a viable solution in rural areas lacking connection to municipal power supplies. This study tracked the physicochemical and microbiological changes that occur in a solar composting greenhouse during the treatment of food and green cellulosic waste in fed-batch mode, which remain poorly understood. Solar composting greenhouse performed well on waste reduction and nutrient retention, resulting in a 45.0-58.8% decrease in feedstock volume over 12-day composting cycles, a 41% removal in dry matter after three batches of composting, and 29.5%, 252.9% and 96.6% increase in the nitrogen, phosphorus and potassium content respectively after 42 days of composting. Batch feeding and composting jointly influenced microbiological succession by altering the physicochemical properties of compost. The contents of nitrogen and phosphorus, pH, and electrical conductivity significantly accounts for variations in culturable microbial populations. The succession of dominant bacterial genera such as Lactobacillus, Pseudoxanthomonas, Bacillus, and Pseudomonas were closely related to pH, cellulose, NH4+-N, carbon content, and temperature. In addition, Pichia kudriavzevii, Thermomyces lanuginosus, and Scopulariopsis brevicaulis successively became the dominant fungal species during composting. Preliminary compost quality assessments showed that solar composting greenhouse has a high potentiality to transform organic waste into organic fertilizer. Additionally, corresponding purposeful suggestions were proposed for future optimization in this system, mainly from a microbiological aspect.
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Affiliation(s)
- Hui Lin
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Ye
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wanchun Sun
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qiaogang Yu
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qiang Wang
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ping Zou
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhaoming Chen
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jinchuan Ma
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Feng Wang
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Junwei Ma
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Chang F, Jia F, Lv R, Zhen L, Li Y, Wang Y. Changes in structure and function of bacterial and fungal communities in open composting of Chinese herb residues. Can J Microbiol 2019; 66:194-205. [PMID: 31790274 DOI: 10.1139/cjm-2019-0347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In this study, dynamic changes in bacterial and fungal communities, metabolic characteristics, and trophic modes in Chinese herb residues open composting for 30 days were analyzed by using high-throughput sequencing, PICRUSt, and FUNGuild, respectively. Bacillaceae and Basidiomycota predominated at the early composting stage, while Proteobacteria and Ascomycota became the dominant phyla during the active phase. Aerobic composting had a significant effect on bacterial metabolic characteristics and fungal trophic modes over the composting time. The function of the bacterial communities changed from environmental information processing to metabolism. Fungal communities changed as well, with the pathogenic fungi decreasing and wood saprotrophs increasing. These results indicated that open composting of Chinese herb residues not only influenced microbial community structure but also changed metabolic characteristics and trophic modes, which became the internal dynamics of composting.
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Affiliation(s)
- Fan Chang
- Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China.,Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China
| | - Fengan Jia
- Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China.,Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China
| | - Rui Lv
- Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China.,Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China
| | - Lisha Zhen
- Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China.,Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China
| | - Yan Li
- Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China.,Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China
| | - Yan Wang
- Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China.,Research Center for Metabolites, Shaanxi Institute of Microbiology, 76 Xiying Road, Xi'an, Shaanxi 710043, P.R. China
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9
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Calabi-Floody M, Medina J, Suazo J, Ordiqueo M, Aponte H, Mora MDLL, Rumpel C. Optimization of wheat straw co-composting for carrier material development. WASTE MANAGEMENT (NEW YORK, N.Y.) 2019; 98:37-49. [PMID: 31425837 DOI: 10.1016/j.wasman.2019.07.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
In modern agriculture large amounts of harvesting residues are produced each year due to the increase of agricultural activities in order to maintain food production for the growing population. The development of innovative fertilizers, able to satisfy nutrient needs without adverse effects on the environment. In order to allow for effective production of a carrier material for smart fertilizers, the objective of this study is to propose a statistical method to optimize the water holding capacity (WHC) and organic matter stability properties of co-composted wheat straw (WS) by using a multi response method. We varied WS size (<1, 1-2, >2 cm), charge of Trichoderma harzianum (0, 7 and 14 discs), and nitrogen addition (0, 0.95 and 1.95 g kg-1). Optimized carrier material was characterized by a higher porosity (WHC 91.7%) than raw WS, associated to structural changes and slightly increased stability as indicated by C:N ratio of the 59.5, slightly alkaline (pH ∼ 8.0), with high OM structural complexity (E4:E6 ∼ 7,9) and enhanced sorption properties (total acidity ∼ 11.6). We conclude that the optimal treatment included co-composting of WS with fine particle size (<1 cm), with a charge of T. harzianum (14 discs), and 0.98 g kg-1 of NH4NO3 to obtain a suitable WS carrier material with high possibility to improve nutrient and water holding capacity in soil.
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Affiliation(s)
- Marcela Calabi-Floody
- Nano-biotechnology Laboratory, Universidad de La Frontera, Temuco, Chile; Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus, BIOREN-UFRO, Av. Francisco Salazar 01145, Universidad de La Frontera, Temuco, Chile.
| | - Jorge Medina
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA), Scientific and Technological Bioresources Nucleus-BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Jonathan Suazo
- Nano-biotechnology Laboratory, Universidad de La Frontera, Temuco, Chile; Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus, BIOREN-UFRO, Av. Francisco Salazar 01145, Universidad de La Frontera, Temuco, Chile
| | - Manuel Ordiqueo
- Nano-biotechnology Laboratory, Universidad de La Frontera, Temuco, Chile
| | - Humberto Aponte
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA), Scientific and Technological Bioresources Nucleus-BIOREN, Universidad de La Frontera, Temuco, Chile
| | - María de La Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus, BIOREN-UFRO, Av. Francisco Salazar 01145, Universidad de La Frontera, Temuco, Chile
| | - Cornelia Rumpel
- CNRS, Institute for Ecology and Environmental Sciences IEES (UMR 7618, CNRS-UPMC-UPEC-IRD-INRA), Thiverval-Grignon, France
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10
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Sandona K, Billingsley Tobias TL, Hutchinson MI, Natvig DO, Porras-Alfaro A. Diversity of thermophilic and thermotolerant fungi in corn grain. Mycologia 2019; 111:719-729. [PMID: 31348716 DOI: 10.1080/00275514.2019.1631137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Corn bins in the midwestern United States can reach temperatures up to 52 C. High temperatures combined with sufficient moisture and humidity in bins provide the perfect environment to promote the growth of thermophilic and thermotolerant fungi. In this article, we characterize for the first time thermophilic and thermotolerant fungi in corn grain bins using culture-based methods and pyrosequencing techniques. Corn samples were collected from local farms in western Illinois. Samples were plated and incubated at 50 C using a variety of approaches. Of several hundred kernels examined, more than 90% showed colonization. Species identified using culture methods included Thermomyces lanuginosus, Thermomyces dupontii, Aspergillus fumigatus, Thermoascus crustaceus, and Rhizomucor pusillus. Pyrosequencing was also performed directly on corn grain using fungal-specific primers to determine whether thermophilic fungi could be detected using this technique. Sequences were dominated by pathogenic fungi, and thermophiles were represented by less than 2% of the sequences despite being isolated from 90% of the grain samples using culturing techniques. The high abundance of previously undocumented viable fungi in corn could have negative implications for grain quality and pose a potential risk for workers and consumers of corn-derived products in the food industry. Members of the Sordariales were absent among thermophile isolates and were not represented in nuc rDNA internal transcribed spacer (ITS) sequences. This is in striking contrast with results obtained with other substrates such as litter, dung, and soils, where mesophilic and thermophilic members of the Sordariaceae and Chaetomiaceae are common. This absence appears to reflect an important difference between the ecology of Sordariales and other orders within the Ascomycota in terms of their ability to compete in microhabitats rich in sugars and living tissues.
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Affiliation(s)
- Katrina Sandona
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Terri L Billingsley Tobias
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Miriam I Hutchinson
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Donald O Natvig
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Andrea Porras-Alfaro
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455.,Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
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11
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Dust at Various Workplaces-Microbiological and Toxicological Threats. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15050877. [PMID: 29702619 PMCID: PMC5981916 DOI: 10.3390/ijerph15050877] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 01/14/2023]
Abstract
The aim of the present study was to evaluate the relation between the chemical (analysis of elements and pH) and microbiological composition (culture and metagenomics analysis) of the dust at various workplaces (cement plant, composting plant, poultry farm, and cultivated area) and the cytotoxicity effect on the human adenocarcinoma lung epithelial adherent cell line A-549 (MTT assay test). Analysis of the Particulate Matter (PM) fraction showed that the dust concentration in cultivated areas exceeded the OELs. For the remaining workplaces examined, the dust concentration was lower than OELs limits. The number of microorganisms in the dust samples was 3.8 × 102–1.6 × 108 CFU/g bacteria and 1.5 × 102–6.5 × 106 CFU/g fungi. The highest number of microorganisms was noted for dust from cultivated areas (total number of bacteria, actinomycetes, P. fluorescens) and composting plants (xerophilic fungi and staphylococci), while the least number of microorganisms was observed for dust from cement plants. Many types of potentially pathogenic microorganisms have been identified, including bacteria, such as Bacillus, Actinomyces, Corynebacterium, Prevotella, Clostridium, and Rickettsia, and fungi, such as Alternaria, Cladosporium, Penicillium, and Aspergillus. The most cytotoxic to the human lung cell line A-549 was dust from cultivated areas (IC50 = 3.8 mg/mL after 72 h). The cytotoxicity of the tested dust samples depends on the PM concentration, the number of microorganisms, including potentially pathogenic genera, and the exposure time.
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12
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Guo L, Okamoto A. Fluorescence-switching RNA for detection of bacterial ribosomes. Chem Commun (Camb) 2018; 53:9406-9409. [PMID: 28765840 DOI: 10.1039/c7cc04818a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an efficient chemical system that allows quantification of bacterial ribosomes by fluorescence-based analysis. The key component in the system is the exciton-controlled fluorescent RNA aptamer, which recognizes neomycin B. The intensity of fluorescence from such a ribosome-sensing system increased drastically in the presence of Escherichia coli.
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Affiliation(s)
- Lihao Guo
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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13
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Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms. Appl Microbiol Biotechnol 2018; 102:1639-1650. [PMID: 29362825 DOI: 10.1007/s00253-018-8777-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.
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Galitskaya P, Biktasheva L, Saveliev A, Grigoryeva T, Boulygina E, Selivanovskaya S. Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing. PLoS One 2017; 12:e0186051. [PMID: 29059245 PMCID: PMC5653195 DOI: 10.1371/journal.pone.0186051] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023] Open
Abstract
Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 106 and (0.4±0.0) x 107 g-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) x105 and (6.1±0.2) x105 ITS copies g-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the dynamics of the bacterial and fungal communities were not similar. Analysis by non-metric multidimensional scaling (NMDS) revealed that the bacterial communities of the two composts became progressively more similar; a similar trend was followed by the fungal community.
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Affiliation(s)
- Polina Galitskaya
- Department of Applied Ecology, Institute of Environmental Sciences, Kazan Federal University, Kazan, Russian Federation
| | - Liliya Biktasheva
- Department of Applied Ecology, Institute of Environmental Sciences, Kazan Federal University, Kazan, Russian Federation
- * E-mail:
| | - Anatoly Saveliev
- Department of Ecological Systems Modeling, Institute of Environmental Sciences, Kazan Federal University, Kazan, Russian Federation
| | - Tatiana Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Eugenia Boulygina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Svetlana Selivanovskaya
- Department of Applied Ecology, Institute of Environmental Sciences, Kazan Federal University, Kazan, Russian Federation
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15
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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; 109:475-484. [PMID: 28759322 DOI: 10.1080/00275514.2017.1349498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Commercial cultivation of the button mushroom Agaricus bisporus is performed through the inoculation of a semipasteurized composted material. Pasteurization of the compost material prior to inoculation results in a substrate with a fungal community that becomes dominated by A. bisporus. However, little is known about the composition and activity in the wider fungal community beyond the presence of A. bisporus in compost throughout the mushroom cropping process. In this study, the fungal cropping compost community was characterized by sequencing nuc rDNA ITS1-5.8S-ITS2 amplified from extractable DNA and RNA. The fungal community generated from DNA extracts identified a diverse community containing 211 unique species, although only 51 were identified from cDNA. Agaricus bisporus was found to dominate in the DNA-derived fungal community for the duration of the cropping process. However, analysis of cDNA extracts found A. bisporus to dominate only up to the first crop flush, after which activity decreased sharply and a much broader fungal community became active. This study has highlighted the diverse fungal community that is present in mushroom compost during cropping.
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Affiliation(s)
- C F McGee
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
| | - H Byrne
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
| | - A Irvine
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
| | - J Wilson
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
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16
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Paula FS, Tatti E, Abram F, Wilson J, O'Flaherty V. Stabilisation of spent mushroom substrate for application as a plant growth-promoting organic amendment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 196:476-486. [PMID: 28343049 DOI: 10.1016/j.jenvman.2017.03.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/13/2017] [Accepted: 03/14/2017] [Indexed: 05/22/2023]
Abstract
Over three million tonnes of spent mushroom substrate (SMS) are produced in Europe every year as a by-product of the cultivation of Agaricus bisporus. The management of SMS has become an increasing challenge for the mushroom production industry, and finding environmentally and economically sustainable solutions for this organic residue is, therefore, highly desirable. Due to its physical properties and nutrient content, SMS has great potential to be employed in agricultural and horticultural sectors, and further contribute to reduce the use of non-renewable resources, such as peat. However, SMS is often regarded as not being stable and/or mature, which hampers its wide use for crop production. Here, we demonstrate the stabilisation of SMS and its subsequent use as organic fertiliser and partial peat replacement in horticulture. The stabilisation was performed in a laboratory-scale composting system, with controlled temperature and aeration. Physical and chemical parameters were monitored during composting and provided information on the progress of the process. Water soluble carbohydrates (WSC) content was found to be the most reliable parameter to predict SMS stability. In situ oxygen consumption indicated the main composting phases, reflecting major changes in microbial activity. The structure of the bacterial community was also found to be a potential predictor of stability, as the compositional changes followed the composting progress. By contrast, the fungal community did not present clear successional process along the experiment. Maturity and quality of the stabilised SMS were assessed in a horticultural growing trial. When used as the sole fertiliser source, SMS was able to support Lolium multiflorum (Italian ryegrass) growth and significantly improved grass yield with a concentration-dependent response, increasing grass biomass up to 300%, when compared to the untreated control. In summary, the results indicated that the method employed was efficient in generating a stable and mature product, which has a great potential to be applied in horticulture. This study represents a step forward in the management of SMS residue, and also provides an alternative to reduce the use of peat in horticulture, alleviating environmental impacts to peatland ecosystems.
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Affiliation(s)
- Fabiana S Paula
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland; Research and Development Department, Monaghan Mushrooms, Tyholland, Ireland.
| | - Enrico Tatti
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland; Research and Development Department, Monaghan Mushrooms, Tyholland, Ireland
| | - Florence Abram
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - Jude Wilson
- Research and Development Department, Monaghan Mushrooms, Tyholland, Ireland
| | - Vincent O'Flaherty
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
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17
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Hanajík P, Zvarík M, Fritze H, Šimkovic I, Kanka R. Composition of microbial PLFAs and correlations with topsoil characteristics in the rare active travertine spring-fed fen. EKOLÓGIA (BRATISLAVA) 2016. [DOI: 10.1515/eko-2016-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
We studied soil PLFAs composition and specific soil properties among transect of small-scale fen in Stankovany, Slovakia. The aim of this study was to determine potential differences in the microbial community structure of the fen transect and reveal correlations among PLFAs and specific soil characteristics. PCA analyses of 43 PLFAs showed a separation of the samples along the axis largely influenced by i14:0, 16:1ω5, br17:0, 10Me16:0, cy17:0, cy17:1, br18:0 and 10Me17:0. We measured a high correlation of sample scores and distance from fen edge (Kendall’s test τ = 0.857, P < 0.01). Kendall’s test showed a negative correlation of PLFAs content (mol%) and distance from the fen border for Gram (+) bacteria, Actinomycetes, mid-chain branched saturated PLFAs and total PLFAs. The redundancy analysis of the PLFA data set for the eight samples using PLFAs as species and 21 environmental variables identified soil properties significantly associated with the PLFA variables, as tested by Monte Carlo permutation showing most significant environmental variables including dichlormethan extractables, water extractables, Klason lignin, acid-soluble lignin, holocellulose, total extractables, organic matter content, total PLFA amount, bacterial PLFA and total nitrogen negatively correlated to axis 1 and dry weight and carbonate carbon positively correlated to axis 1. The amounts of Klason lignin, acid-soluble lignin, holocellulose total extractables, total PLFA, bacterial PLFA and total nitrogen were significantly correlated positively to the distance from fen border while moisture and total carbonate carbon were correlated negatively.
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Affiliation(s)
- Peter Hanajík
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 845 15 Bratislava, Slovakia
| | - Milan Zvarík
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Hannu Fritze
- Natural Resources Institute Finland (Luke), Jokiniemenkuja 1, BOX 18, FI-01301 Vantaa, Finland
| | - Ivan Šimkovic
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 845 15 Bratislava, Slovakia
| | - Róbert Kanka
- Institute of Landscape Ecology SAS, Štefánikova 3, P.O.Box 254, 814 99, Bratislava, Slovakia
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Oliveira TBD, Lopes VCP, Barbosa FN, Ferro M, Meirelles LA, Sette LD, Gomes E, Rodrigues A. Fungal communities in pressmud composting harbour beneficial and detrimental fungi for human welfare. MICROBIOLOGY-SGM 2016; 162:1147-1156. [PMID: 27170376 DOI: 10.1099/mic.0.000306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pressmud is a substrate derived from sugarcane juice filtrate, and around 26-40 kg of this residue are produced per ton of sugarcane. It is mainly used as fertilizer in crops, and its application in the field is often made without any prior treatment, but, in this research, it was studied for the risk this practice poses for human health. This research was stimulated by previous results indicating the presence of opportunistic pathogens in residues used in various composting systems and the extensive use of fresh pressmud in agriculture. Here, It was assessed the fungal diversity present in both fresh and composting pressmud using 454 pyrosequencing. In addition, heat-tolerant fungi were isolated and surveyed for their enzymatic repertoire of biomass-degrading enzymes (cellulase, xylanase, laccase and polygalacturonase). A wide range of opportunistic pathogens was found among the most abundant taxa in the fresh pressmud, such as Lomentospora prolificans (43.13 %), Trichosporon sp. (10.07 %), Candida tropicalis (7.91 %), and Hormographiella aspergillata (8.19 %). This indicates that fresh pressmud might be a putative source of human pathogenic fungi, presenting a potential threat to human health if applied as fertilizer without any treatment. With regard to the heat-tolerant fungi found in this substrate, all the 110 isolates screened were able to produce at least one of the tested enzymes. The pressmud composting process not only effectively reduces the load of pathogenic fungi, but also creates an interesting environment for fungi able to produce thermostable hydrolytic and oxidative enzymes with biotechnological applications.
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Affiliation(s)
- Tássio Brito de Oliveira
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
| | | | | | - Milene Ferro
- Center for the Study of Social Insects, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
| | - Lucas Andrade Meirelles
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil.,Division of Biology and Biological Engineering, Caltech - California Institute of Technology, Pasadena, CA, USA
| | - Lara Durães Sette
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
| | - Eleni Gomes
- Department of Biology, UNESP - Univ Estadual Paulista, Sao Jose do Rio Preto, SP, Brazil
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
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Singh B, Poças-Fonseca MJ, Johri BN, Satyanarayana T. Thermophilic molds: Biology and applications. Crit Rev Microbiol 2016; 42:985-1006. [DOI: 10.3109/1040841x.2015.1122572] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples. Appl Microbiol Biotechnol 2015; 99:10271-82. [DOI: 10.1007/s00253-015-6866-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/16/2015] [Accepted: 07/18/2015] [Indexed: 11/25/2022]
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21
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Liu D, Li M, Xi B, Zhao Y, Wei Z, Song C, Zhu C. Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. Microb Biotechnol 2015; 8:950-60. [PMID: 25989417 PMCID: PMC4621448 DOI: 10.1111/1751-7915.12290] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 01/14/2023] Open
Abstract
Composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. We employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. The investigation of microbial succession revealed that Bacillales, Actinobacteria and Saccharomyces increased significantly with respect to abundance in composting process. The key microbiologic population for cellulose degradation in different composting stages was different. Fungi were found to be the main producers of cellulase in earlier phase. However, the cellulolytic fungal communities were gradually replaced by a purely bacterial one in active phase, which did not support the concept that the thermophilic fungi are active through the thermophilic phase. The effective decomposition of cellulose required the synergy between bacteria and fungi in the curing phase.
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Affiliation(s)
- Dongming Liu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.,Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Mingxiao Li
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Beidou Xi
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Yue Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zimin Wei
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Caihong Song
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.,Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Chaowei Zhu
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
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22
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López-González JA, Vargas-García MDC, López MJ, Suárez-Estrella F, Jurado MDM, Moreno J. Biodiversity and succession of mycobiota associated to agricultural lignocellulosic waste-based composting. BIORESOURCE TECHNOLOGY 2015; 187:305-313. [PMID: 25863208 DOI: 10.1016/j.biortech.2015.03.124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
A comprehensive characterization of the culturable mycobiota associated to all stages of lignocellulose-based composting was achieved. A total of 77 different isolates were detected, 69 of which were identified on the basis of the 5.8-ITS region sequencing. All the isolates were assigned to the phyla Ascomycota and Basidiomycota, with prevalence of the Sordariomycetes (19) and Eurotiomycetes (17) classes. Penicillium was the most represented genus (11 species), while the species Gibellulopsis nigrescens and Microascus brevicaulis were detected at all the composting stages and showed the highest relative abundances. Fungal diversity decreased as the process proceed, while similarity between fungal communities associated to different samples were maximal for those phases closely connected chronologically and showing similar biological activity degree. Thus, the structure of the lignocellulose-based composting mycobiota can be divided into two major stages corresponding to bio-oxidative phase and maturation phase together with the final product, with a transitional cooling stage joining both of them.
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Affiliation(s)
- Juan Antonio López-González
- Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence CeiA3, 04120 Almeria, Spain
| | - María Del Carmen Vargas-García
- Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence CeiA3, 04120 Almeria, Spain.
| | - María José López
- Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence CeiA3, 04120 Almeria, Spain
| | - Francisca Suárez-Estrella
- Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence CeiA3, 04120 Almeria, Spain
| | - Macarena Del Mar Jurado
- Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence CeiA3, 04120 Almeria, Spain
| | - Joaquín Moreno
- Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence CeiA3, 04120 Almeria, Spain
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23
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López-González JA, Suárez-Estrella F, Vargas-García MC, López MJ, Jurado MM, Moreno J. Dynamics of bacterial microbiota during lignocellulosic waste composting: Studies upon its structure, functionality and biodiversity. BIORESOURCE TECHNOLOGY 2015; 175:406-416. [PMID: 25459849 DOI: 10.1016/j.biortech.2014.10.123] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/21/2014] [Accepted: 10/24/2014] [Indexed: 06/04/2023]
Abstract
An intensive isolation program carried out in three replicated composting piles allowed the identification of the resident and transient components of the composting microbiome. More than 4000 bacterial strains were isolated, enzymatically characterized and identified by partial sequencing of their 16S rRNA gene. While microorganisms isolated under mesophilic conditions were prominent throughout the process, thermophilic stages gathered the highest total counts and spore-forming bacteria prevailed at the bio-oxidative phase of composting. Enzymatic capabilities related to the degradation of polymeric materials were exhibited by most of the isolates and as a result of these activities, more soluble compounds could be made available to the entire composting microbiota. A high proportion of isolates showed to be thermotolerant as they were detected at mesophilic and thermophilic phases. Isolated strains belonged to 187 bacterial species. Biodiversity was greater at the central stages of composting and mesophilic, thermophilic and cooling phases shared 50% of species.
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Affiliation(s)
- J A López-González
- Unit of Microbiology, Department of Biology and Geology, University of Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain
| | - F Suárez-Estrella
- Unit of Microbiology, Department of Biology and Geology, University of Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain
| | - M C Vargas-García
- Unit of Microbiology, Department of Biology and Geology, University of Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain
| | - M J López
- Unit of Microbiology, Department of Biology and Geology, University of Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain
| | - M M Jurado
- Unit of Microbiology, Department of Biology and Geology, University of Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain
| | - J Moreno
- Unit of Microbiology, Department of Biology and Geology, University of Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain.
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24
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An investigation of the biodiversity of thermophilic and thermotolerant fungal species in composts using culture-based and molecular techniques. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.05.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Mehta CM, Palni U, Franke-Whittle IH, Sharma AK. Compost: its role, mechanism and impact on reducing soil-borne plant diseases. WASTE MANAGEMENT (NEW YORK, N.Y.) 2014; 34:607-22. [PMID: 24373678 DOI: 10.1016/j.wasman.2013.11.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 05/14/2023]
Abstract
Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.
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Affiliation(s)
- C M Mehta
- Department of Biological Sciences, College of Basic Science and Humanities, G. B. P. U. A. & T. Pantnagar, U.S. Nagar, Uttarakhand, India; Department of Botany, D.S.B. Campus, Kumaun University Nainital, Uttarakhand, India
| | - Uma Palni
- Department of Botany, D.S.B. Campus, Kumaun University Nainital, Uttarakhand, India
| | - I H Franke-Whittle
- Leopold-Franzens University, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria
| | - A K Sharma
- Department of Biological Sciences, College of Basic Science and Humanities, G. B. P. U. A. & T. Pantnagar, U.S. Nagar, Uttarakhand, India.
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Langarica-Fuentes A, Zafar U, Heyworth A, Brown T, Fox G, Robson GD. Fungal succession in an in-vessel composting system characterized using 454 pyrosequencing. FEMS Microbiol Ecol 2014; 88:296-308. [DOI: 10.1111/1574-6941.12293] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 11/21/2013] [Accepted: 01/24/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Urooj Zafar
- Faculty of Life Sciences; University of Manchester; Manchester UK
| | | | | | - Graeme Fox
- Faculty of Life Sciences; University of Manchester; Manchester UK
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Neher DA, Weicht TR, Bates ST, Leff JW, Fierer N. Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times. PLoS One 2013; 8:e79512. [PMID: 24278144 PMCID: PMC3836849 DOI: 10.1371/journal.pone.0079512] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/25/2013] [Indexed: 12/01/2022] Open
Abstract
Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.
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Affiliation(s)
- Deborah A. Neher
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America
| | - Thomas R. Weicht
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America
| | - Scott T. Bates
- Department of Plant Pathology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jonathan W. Leff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, United States of America
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, United States of America
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
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28
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Neher DA, Weicht TR, Bates ST, Leff JW, Fierer N. Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times. PLoS One 2013. [PMID: 24278144 DOI: 10.1371/journal.pone.0079512,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.
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Affiliation(s)
- Deborah A Neher
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America
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29
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Fungal communities associated with the biodegradation of polyester polyurethane buried under compost at different temperatures. Appl Environ Microbiol 2013; 79:7313-24. [PMID: 24056469 DOI: 10.1128/aem.02536-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plastics play an essential role in the modern world due to their low cost and durability. However, accumulation of plastic waste in the environment causes wide-scale pollution with long-lasting effects, making plastic waste management expensive and problematic. Polyurethanes (PUs) are heteropolymers that made up ca. 7% of the total plastic production in Europe in 2011. Polyester PUs in particular have been extensively reported as susceptible to microbial biodegradation in the environment, particularly by fungi. In this study, we investigated the impact of composting on PUs, as composting is a microbially rich process that is increasingly being used for the processing of green waste and food waste as an economically viable alternative to landfill disposal. PU coupons were incubated for 12 weeks in fresh compost at 25°C, 45°C, and 50°C to emulate the thermophilic and maturation stages of the composting process. Incubation at all temperatures caused significant physical deterioration of the polyester PU coupons and was associated with extensive fungal colonization. Terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of the fungal communities on the PU surface and in the surrounding compost revealed that the population on the surface of PU was different from the surrounding compost community, suggesting enrichment and selection. The most dominant fungi identified from the surfaces of PU coupons by pyrosequencing was Fusarium solani at 25°C, while at both 45°C and 50°C, Candida ethanolica was the dominant species. The results of this preliminary study suggest that the composting process has the potential to biodegrade PU waste if optimized further in the future.
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Vítězová M, Mach P, Vítěz T, Lošák T. Development of microbial community in the course of composting of garden waste. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2013. [DOI: 10.11118/actaun201260030225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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De Gannes V, Eudoxie G, Hickey WJ. Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety. Front Microbiol 2013; 4:164. [PMID: 23785368 PMCID: PMC3682178 DOI: 10.3389/fmicb.2013.00164] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/03/2013] [Indexed: 01/18/2023] Open
Abstract
Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health.
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Affiliation(s)
- Vidya De Gannes
- Department of Food Production, Faculty of Food and Agriculture, University of the West Indies, St. Augustine Campus St. Augustine, Republic of Trinidad and Tobago
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Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms. PLoS One 2013; 8:e61928. [PMID: 23637931 PMCID: PMC3637033 DOI: 10.1371/journal.pone.0061928] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/15/2013] [Indexed: 12/19/2022] Open
Abstract
Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.
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Maeda K, Toyoda S, Hanajima D, Yoshida N. Denitrifiers in the surface zone are primarily responsible for the nitrous oxide emission of dairy manure compost. JOURNAL OF HAZARDOUS MATERIALS 2013; 248-249:329-336. [PMID: 23416476 DOI: 10.1016/j.jhazmat.2013.01.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 01/08/2013] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
During the dairy manure composting process, significant nitrous oxide (N2O) emissions occur just after the pile turnings. To understand the characteristics of this N2O emission, samples were taken from the compost surface and core independently, and the N2O production was monitored in laboratory incubation experiments. Equal amounts of surface and core samples were mixed to simulate the turning, and the (15)N isotope ratios within the molecules of produced N2O were analyzed by isotopomer analysis. The results showed that the surface samples emitted significant levels of N2O, and these emissions were correlated with NOx(-)-N accumulation. Moreover, the surface samples and surface-core mixed samples incubated at 30°C produced N2O with a low site preference (SP) value (-0.9 to 7.0‰) that was close to bacteria denitrification (0‰), indicating that denitrifiers in the surface samples are responsible for this N2O production. On the other hand, N2O produced by NO2(-)-amended core samples and surface samples incubated at 60°C showed unrecognized isotopic signatures (SP=11.4-20.3‰). From these results, it was revealed that the N2O production occurring just after the turnings was mainly derived from bacterial denitrification (including nitrifier denitrification) of NOx(-)-N under mesophilic conditions, and surface denitrifying bacteria appeared to be the main contributor to this process.
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Affiliation(s)
- Koki Maeda
- Dairy Research Division, National Agricultural Research Center for Hokkaido Region, National Agricultural and Food Research Organization, 1 Hitsujigaoka, Sapporo 062-8555, Japan.
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Ritari J, Koskinen K, Hultman J, Kurola JM, Kymäläinen M, Romantschuk M, Paulin L, Auvinen P. Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation. BMC Microbiol 2012; 12:121. [PMID: 22727142 PMCID: PMC3408363 DOI: 10.1186/1471-2180-12-121] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 06/22/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD. RESULTS The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%. CONCLUSIONS The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.
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Affiliation(s)
- Jarmo Ritari
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00790, Helsinki, Finland.
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Houbraken J, Spierenburg H, Frisvad JC. Rasamsonia, a new genus comprising thermotolerant and thermophilic Talaromyces and Geosmithia species. Antonie Van Leeuwenhoek 2012; 101:403-21. [PMID: 21965082 PMCID: PMC3261388 DOI: 10.1007/s10482-011-9647-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 09/16/2011] [Indexed: 11/29/2022]
Abstract
The phylogenetic relationship among Geosmithia argillacea, Talaromyces emersonii, Talaromyces byssochlamydoides and other members of the Trichocomaceae was studied using partial RPB2 (RNA polymerase II gene, encoding the second largest protein subunit), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences. The results showed that these species form a distinct clade within the Trichocomaceae and Trichocoma paradoxa is phylogenetically most closely related. Based on phenotypic and physiological characters and molecular data, we propose Rasamsonia gen. nov. to accommodate these species. This new genus is distinct from other genera of the Trichocomaceae in being thermotolerant or thermophilic and having conidiophores with distinctly rough walled stipes, olive-brown conidia and ascomata, if present, with a scanty covering. Species within the genus Rasamsonia were distinguished using a combination of phenotypic characters, extrolite patterns, ITS and partial calmodulin and β-tubulin sequences. Rasamsonia brevistipitata sp. nov. is described and five new combinations are proposed.
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Affiliation(s)
- J Houbraken
- Department of Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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Dehghani R, Asadi MA, Charkhloo E, Mostafaie G, Saffari M, Mousavi GA, Pourbabaei M. Identification of Fungal Communities in Producing Compost by Windrow Method. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/jep.2012.31008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Maeda K, Hanajima D, Toyoda S, Yoshida N, Morioka R, Osada T. Microbiology of nitrogen cycle in animal manure compost. Microb Biotechnol 2011; 4:700-9. [PMID: 21375720 PMCID: PMC3815407 DOI: 10.1111/j.1751-7915.2010.00236.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 10/17/2010] [Indexed: 11/29/2022] Open
Abstract
Composting is the major technology in the treatment of animal manure and is a source of nitrous oxide, a greenhouse gas. Although the microbiological processes of both nitrification and denitrification are involved in composting, the key players in these pathways have not been well identified. Recent molecular microbiological methodologies have revealed the presence of dominant Bacillus species in the degradation of organic material or betaproteobacterial ammonia-oxidizing bacteria on nitrification on the surface, and have also revealed the mechanism of nitrous oxide emission in this complicated process to some extent. Some bacteria, archaea or fungi still would be considered potential key players, and the contribution of some pathways, such as nitrifier denitrification or heterotrophic nitrification, might be involved in composting. This review article discusses these potential microbial players in nitrification-denitrification within the composting pile and highlights the relevant unknowns through recent activities that focus on the nitrogen cycle within the animal manure composting process.
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Affiliation(s)
- Koki Maeda
- Hokkaido Research Subteam for Waste Recycling System, National Agricultural Research Center for Hokkaido Region, National Agricultural and Food Research Organization, 1 Hitsujigaoka, Sapporo 062-8555, Japan.
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Rainisalo A, Romantschuk M, Kontro MH. Evolution of clostridia and streptomycetes in full-scale composting facilities and pilot drums equipped with on-line temperature monitoring and aeration. BIORESOURCE TECHNOLOGY 2011; 102:7975-7983. [PMID: 21719280 DOI: 10.1016/j.biortech.2011.05.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/30/2011] [Accepted: 05/30/2011] [Indexed: 05/31/2023]
Abstract
The evolution of sporulating bacteria in full-scale composting facilities with online temperature monitoring has been poorly studied, although organic matter recycling increases. We analysed Clostridium perfringens and sulphite-reducing clostridia (SRC) by cultivation, and streptomycetes by real-time PCR in five full-scale, temperature-monitored and aerated composting processes, and two pilot-scale drum composters. Facilities composted woodchips, sawdust, peat, or bark amended sludge or source-separated biowaste. Streptomycetes genes of 0.21-110×10(7)copies/g feed increased fast to 0.019-33×10(9)copies/g, and then were equal or decreased. SRC of 0.06-2.2×10(7)cfu/g feed decreased to 0-600 cfu/g, with re-growth in two facilities. End products were clean of C. perfringens, detected in sludge composts. Although processes contained large quantities of spore-forming bacteria, in the best facilities end products had the high quality. Temperature (>55°C,>2d) was not related to the end compost quality, but relations between waste and bulking agent qualities, aeration, and processing time should be better controlled.
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Affiliation(s)
- Aija Rainisalo
- Helsinki University, Department of Environmental Sciences, Niemenkatu 73, 15140 Lahti, Finland
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Kurola JM, Arnold M, Kontro MH, Talves M, Romantschuk M. Wood ash for application in municipal biowaste composting. BIORESOURCE TECHNOLOGY 2011; 102:5214-5220. [PMID: 21349704 DOI: 10.1016/j.biortech.2011.01.092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/25/2011] [Accepted: 01/28/2011] [Indexed: 05/30/2023]
Abstract
This study aimed to clarify the impacts of pH control by wood ash amendment on biowaste composting processes. To achieve this, fresh source separated municipal biowaste was mixed with low doses (2-8% wt/vol) of wood ash and processed in a pilot and large-scale composting systems. The results indicated a correlation between a low initial pH and delay in the early rise of the process temperature. Wood ash elevated the composting temperatures and pH, and stimulated the mineralisation both in the pilot scale and the industrial large-scale processes. According to the results addition of amounts of 4-8% wood ash is sufficient for efficient biowaste composting process and yields a safe end product. However, to minimise the environmental risk for heavy metal contamination, and meet the criteria for the limit values of the impurities in wood ash, strict quality control of the applied wood ashes should be implemented.
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Affiliation(s)
- Jukka M Kurola
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73 C, FIN-15140 Lahti, Finland.
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40
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Sundberg C, Franke-Whittle IH, Kauppi S, Yu D, Romantschuk M, Insam H, Jönsson H. Characterisation of source-separated household waste intended for composting. BIORESOURCE TECHNOLOGY 2011; 102:2859-67. [PMID: 21075618 PMCID: PMC3024507 DOI: 10.1016/j.biortech.2010.10.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 10/06/2010] [Accepted: 10/16/2010] [Indexed: 05/07/2023]
Abstract
Large-scale composting of source-separated household waste has expanded in recent years in the Nordic countries. One problem can be low pH at the start of the process. Incoming biowaste at four composting plants was characterised chemically, physically and microbiologically. The pH of food waste ranged from 4.7 to 6.1 and organic acid concentration from 24 to 81 mmol kg(-1). The bacterial diversity in the waste samples was high, with all samples dominated by Gammaproteobacteria, particularly Pseudomonas and Enterobacteria (Escherichia coli, Klebsiella, Enterobacter). Lactic acid bacteria were also numerically important and are known to negatively affect the composting process because the lactic acid they produce lowers the pH, inhibiting other bacteria. The bacterial groups needed for efficient composting, i.e. Bacillales and Actinobacteria, were present in appreciable amounts. The results indicated that start-up problems in the composting process can be prevented by recycling bulk material and compost.
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Affiliation(s)
- Cecilia Sundberg
- Department of Energy and Technology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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41
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Hui N, Jumpponen A, Niskanen T, Liimatainen K, Jones KL, Koivula T, Romantschuk M, Strömmer R. EcM fungal community structure, but not diversity, altered in a Pb-contaminated shooting range in a boreal coniferous forest site in Southern Finland. FEMS Microbiol Ecol 2011; 76:121-32. [PMID: 21223331 DOI: 10.1111/j.1574-6941.2010.01038.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Boreal forests contain diverse fungal communities that form essential ectomycorrhizal symbioses with trees. To determine the effects of lead (Pb) contamination on ectomycorrhizal fungal communities associated with the dominant pine (Pinus sylvestris L.), we surveyed sporocarps for 3 years, analyzed morphotyped ectomycorrhizal root tips by direct sequencing, and 454-sequenced fungal communities that grew into in-growth bags during a 2-year incubation at a shooting range where sectors vary in the Pb load. We recorded a total of 32 ectomycorrhizal fungi that formed conspicuous sporocarps, 27 ectomycorrhizal fungal phylotypes from 294 root tips, and 116 ectomycorrhizal fungal operation taxonomic unit (OTUs) from a total of 8194 internal transcribed spacer-2 454 sequences. Our ordination analyses by nonparametric multidimensional scaling (NMS) indicated that the Pb enrichment induced a shift in the ectomycorrhizal community composition. This was visible as indicative trends in the sporocarp and root tip data sets, but was explicitly clear in the communities observed in the in-growth bags. The compositional shift in the ectomycorrhizal community was mainly attributable to an increase in the frequencies of OTUs assigned to genus Thelephora and to a decrease in the OTUs assigned to Pseudotomentella, Suillus, and Tylospora in Pb-contaminated areas when compared with the control. While the compositional shifts are clear, their functional consequences for the dominant trees or soil ecosystem function remain undetermined.
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Affiliation(s)
- Nan Hui
- Department of Environmental Sciences, University of Helsinki, Lahti, Finland.
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Ntougias S, Kavroulakis N, Papadopoulou KK, Ehaliotis C, Zervakis GI. Characterization of cultivated fungi isolated from grape marc wastes through the use of amplified rDNA restriction analysis and sequencing. J Microbiol 2010; 48:297-306. [PMID: 20571946 DOI: 10.1007/s12275-010-9193-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 04/09/2010] [Indexed: 11/28/2022]
Abstract
Microbial assessment of grape marc wastes, the residual solid by-product of the wine-industry, was performed by identifying phylogenetically the fungal culturable diversity in order to evaluate environmental and disposal safety issues and to discuss ecological considerations of applications on agricultural land. Fungal spores in grape marc were estimated to 4.7 x 10(6) per g dry weight. Fifty six fungal isolates were classified into eight operational taxonomic units (OTUs) following amplified ribosomal DNA restriction analysis (ARDRA) and colony morphology. Based on 18S rRNA gene and 5.8S rRNA gene-ITS sequencing, the isolates representing OTUs #1, #2, #3, and #4, which comprised 44.6%, 26.8%, 12.5%, and 5.3%, respectively, of the number of the total isolates, were identified as Aspergillus fumigatus, Bionectria ochroleuca, Haematonectria haematococca, and Trichosporon mycotoxinivorans. The isolates of OTU#5 demonstrated high phylogenetic affinity with Penicillium spp., while members of OTUs #6 and #7 were closer linked with Geotrichum candidum var. citri-aurantii and Mycocladus corymbifer, respectively (95.4 and 97.9% similarities in respect to their 5.8S rRNA gene-ITS sequences). The OTU#8 with a single isolate was related with Aspergillus strains. It appears that most of the fungal isolates are associated with the initial raw material. Despite the fact that some of the species identified may potentially act as pathogens, measures such as the avoidance of maintaining large and unprocessed quantities of grape marc wastes in premises without adequate aeration, together with its suitable biological treatment (e.g., composting) prior to any agriculture-related application, could eliminate any pertinent health risks.
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Affiliation(s)
- Spyridon Ntougias
- National Agricultural Research Foundation, Institute of Kalamata, Lakonikis 87, 24100, Kalamata, Greece
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Partanen P, Hultman J, Paulin L, Auvinen P, Romantschuk M. Bacterial diversity at different stages of the composting process. BMC Microbiol 2010; 10:94. [PMID: 20350306 PMCID: PMC2907838 DOI: 10.1186/1471-2180-10-94#citeas] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/29/2010] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. RESULTS Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. CONCLUSIONS Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.
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Affiliation(s)
- Pasi Partanen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00014 University of Helsinki, Finland
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland
| | - Jenni Hultman
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00014 University of Helsinki, Finland
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00014 University of Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00014 University of Helsinki, Finland
| | - Martin Romantschuk
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland
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Partanen P, Hultman J, Paulin L, Auvinen P, Romantschuk M. Bacterial diversity at different stages of the composting process. BMC Microbiol 2010; 10:94. [PMID: 20350306 PMCID: PMC2907838 DOI: 10.1186/1471-2180-10-94] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/29/2010] [Indexed: 11/10/2022] Open
Abstract
Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.
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Affiliation(s)
- Pasi Partanen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00014 University of Helsinki, Finland
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