1
|
Yang M, Guo Y, Yang F, Wang J, Gao Y, Wang M, Liang X, He S. Dynamic changes in and correlations between microbial communities and physicochemical properties during the composting of cattle manure with Penicillium oxalicum. BMC Microbiol 2024; 24:301. [PMID: 39134942 PMCID: PMC11318117 DOI: 10.1186/s12866-024-03449-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 07/30/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Penicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed. RESULTS The results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH4+-N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting. CONCLUSIONS In conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum.
Collapse
Affiliation(s)
- Mengmeng Yang
- College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, Ningxia, China
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, 750002, Ningxia, China
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750002, China
| | - Yanan Guo
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, 750002, Ningxia, China.
| | - Fei Yang
- College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Jiandong Wang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, 750002, Ningxia, China
| | - Yunhang Gao
- School of Animal Science and Technology, Jilin Agricultural University, Changchun, 130000, China
| | - Mingcheng Wang
- School of Biological and Food Engineering, Huanghuai University, Zhumadian, 463000, China
| | - Xiaojun Liang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, 750002, Ningxia, China
| | - Shenghu He
- College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, Ningxia, China.
| |
Collapse
|
2
|
Premarathna KSD, Gayara Degamboda N, Fernando BHR, Sandanayake S, Pathirana C, Jayarathna L, Ranasinghe CS, Vithanage M. Plastics and plastic-bound toxic metals in municipal solid waste compost from Sri Lanka. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:306. [PMID: 39002030 DOI: 10.1007/s10653-024-02081-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/16/2024] [Indexed: 07/15/2024]
Abstract
This study examined plastics and toxic metals in municipal solid waste compost from various regions in Sri Lanka. Plastics were extracted using density separation, digested using wet peroxidation, and identified using Fourier Transform Infra-Red Spectroscopy in Attenuated Total Reflection mode. Compost and plastics were acid-digested to quantify total Cd, Cu, Co, Cr, Pb, and Zn concentrations and analyzed for the bioavailable fraction using 0.01 M CaCl2. Notably, plastics were highly abundant in most compost samples. The main plastic types detected were polyethylene, polypropylene, and cellophane. However, the average Cd, Cu, Co, Cr, Pb, and Zn levels were 0.727, 60.78, 3.670, 25.44, 18.95, and 130.7 mg/kg, respectively, which are well below the recommended levels. Zn was the most bioavailable (2.476 mg/kg), and Cd was the least bioavailable (0.053 mg/kg) metal associated with compost. The Contamination factor data show that there is considerable enhancement of Cd and Cu, however, Cr, Cu, Co, and Pb are at low contamination levels. Mean geo accumulation index values were 1.39, 1.07, - 1.06, - 0.84, - 0.32, and 0.08 for Cd, Cu, Co, Cr, Pb, and Zn. Therefore, the contamination level of compost samples with Cd and Cu ranges from uncontaminated to contaminated levels, whereas Co, Cr, Pb, and Zn are at uncontaminated levels. Despite no direct metal-plastic correlation, plastics in compost could harm plants, animals, and humans due to ingestion. Hence, reducing plastic and metal contamination in compost is crucial.
Collapse
Affiliation(s)
- K S D Premarathna
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - N Gayara Degamboda
- Department of Forestry and Environmental Science, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - B H R Fernando
- Coconut Research Institute of Sri Lanka, Bandirippuwa Estate, Lunuwila, Sri Lanka
| | - Sandun Sandanayake
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Chaamila Pathirana
- Department of Forestry and Environmental Science, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Lakmal Jayarathna
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - C S Ranasinghe
- Coconut Research Institute of Sri Lanka, Bandirippuwa Estate, Lunuwila, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
| |
Collapse
|
3
|
Zhou Z, Shi X, Bhople P, Jiang J, Chater CCC, Yang S, Perez-Moreno J, Yu F, Liu D. Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120895. [PMID: 38626487 DOI: 10.1016/j.jenvman.2024.120895] [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: 11/10/2023] [Revised: 03/01/2024] [Accepted: 04/10/2024] [Indexed: 04/18/2024]
Abstract
Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.
Collapse
Affiliation(s)
- Ziyan Zhou
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Parag Bhople
- Crops, Environment, And Land Use Department, Environment Research Centre, Teagasc, Johnstown Castle, Wexford, Y35TC98, Ireland
| | - Jishao Jiang
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; Plants, Photosynthesis, and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Shimei Yang
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jesus Perez-Moreno
- Colegio de Postgraduados, Campus Montecillo, Edafologia, Texcoco, 56230, Mexico
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Dong Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| |
Collapse
|
4
|
Kim HS, Noh MH, White EM, Kandefer MV, Wright AF, Datta D, Lim HG, Smiggs E, Locklin JJ, Rahman MA, Feist AM, Pokorski JK. Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration. Nat Commun 2024; 15:3338. [PMID: 38688899 PMCID: PMC11061138 DOI: 10.1038/s41467-024-47132-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.
Collapse
Affiliation(s)
- Han Sol Kim
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Myung Hyun Noh
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30 Jongga-ro, Ulsan, 44429, Republic of Korea
| | - Evan M White
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | | | - Austin F Wright
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | - Debika Datta
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Ethan Smiggs
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Jason J Locklin
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | - Md Arifur Rahman
- Thermoplastic Polyurethane Research, BASF Corporation, 1609 Biddle Ave., Wyandotte, MI, 48192, USA.
| | - Adam M Feist
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark.
| | - Jonathan K Pokorski
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
- Institute for Materials Discovery and Design, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
| |
Collapse
|
5
|
Peng T, Yue S, Mao W, Yang Q, Jiang G. Preparation of high-temperature and low-temperature-resistant solid microbial agent for cattle manure fermentation and effect on composting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:29017-29032. [PMID: 38561539 DOI: 10.1007/s11356-024-32830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
We used microbiology and molecular biology techniques to screen out high-temperature and low-temperature-resistant saprobiotics for compost and prepared a compound fermentation bacteria agent to rapidly ferment cattle manure into high-quality organic fertilizer in low-temperature season. Conventional composting and high-throughput techniques were used to analyze the changes of physical and chemical indexes and biodiversity in the process of composting, from which high and low-temperature-resistant strains were obtained, and high-temperature and low-temperature-resistant solid composite bactericides were prepared and added to composting to verify the effects of composite bactericides on composting. The conventional composting cycle took 22 days, and the diversity of microflora increased first and then decreased. Composting temperature and microbial population were the key factors for the success or failure of composting. Two strains of high-temperature-resistant bacteria and six strains of low-temperature-resistant bacteria were screened out, and they were efficient in degrading starch, cellulose, and protein. The high-temperature and low-temperature-resistant solid bacterial agent was successfully prepared with adjuvant. The preparation could make the compost temperature rise quickly at low temperature, the high temperature lasted for a long time, the water content, C/N, and organic matter fell quickly, the contents of total phosphorus and total potassium were increased, and the seed germination index was significantly improved. Improve the composting effect. The solid composite bacterial agent can shorten the composting time at low temperature and improve the composting efficiency and quality.
Collapse
Affiliation(s)
- Tao Peng
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Shilin Yue
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Wenshuai Mao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Qing Yang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Guojun Jiang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China.
| |
Collapse
|
6
|
Zhang D, Sun J, Wang D, Peng S, Wang Y, Lin X, Yang X, Hua Q, Wu P. Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:94347-94360. [PMID: 37531050 DOI: 10.1007/s11356-023-29056-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.
Collapse
Affiliation(s)
- Dan Zhang
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 101400, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Jianbin Sun
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 101400, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Danqing Wang
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Shuang Peng
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Yiming Wang
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 101400, China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
- College of Agriculture, Ningxia University, Yinchuan, 750021, China.
| | - Xiangui Lin
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Xiaoqian Yang
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Qingqing Hua
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Pan Wu
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| |
Collapse
|
7
|
Li P, Zhu F, Weiping W, Zhou Y, Yao Y, Hong L, Zhu W, Hong C, Liu X, Chen H, Yu Y. Physicochemical properties and risk assessment of perishable waste primary products. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 337:117549. [PMID: 36934502 DOI: 10.1016/j.jenvman.2023.117549] [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: 10/28/2022] [Revised: 01/29/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Fertilization has become one of the most important ways to recycle perishable waste. In order to reveal the effect of the nutrient of the perishable waste primary products on the market and the possible impact of their application, 136 perishable waste primary products were sampled in nine cities in Zhejiang province, China. The result shows that these products have high nutrient content (average nutrient content was 5.00%). However, the conductivity (7.19 mS/cm) total soluble salt content (12.07%), and grease content (5.99%) were too high. The excessive salt and grease may cause harm to soil and crops, and become the main limiting factors for the fertilizer utilization of perishable waste. Heavy metal content of most of the samples met current commercial organic fertilizer standards, except that lead and chromium content of some samples exceeded the limit standard. Toluene, ethylbenzene, m & p-xylene were generally detected in the samples. These toxic and harmful substances have brought risks to the safe use of perishable waste into fertilizers.
Collapse
Affiliation(s)
- Penghao Li
- Zhejiang University of Technology, Hangzhou 310014 China; Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China
| | - Fengxiang Zhu
- Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China
| | - Wang Weiping
- Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China
| | - Ying Zhou
- Zhejiang University of Technology, Hangzhou 310014 China
| | - Yanlai Yao
- Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China
| | - Leidong Hong
- Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China
| | - Weijing Zhu
- Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China
| | - Chunlai Hong
- Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021 China.
| | - Xiaoxia Liu
- Zhejiang Cultivated Land Quality and Fertilizer Administration Station, Hangzhou 310019, China
| | - Hongjin Chen
- Zhejiang Cultivated Land Quality and Fertilizer Administration Station, Hangzhou 310019, China
| | - Yijun Yu
- Zhejiang Cultivated Land Quality and Fertilizer Administration Station, Hangzhou 310019, China
| |
Collapse
|
8
|
Glushakova АМ, Kachalkin АV. Yeast community succession in cow dung composting process. Fungal Biol 2023; 127:1075-1083. [PMID: 37344009 DOI: 10.1016/j.funbio.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
Yeast complexes in the composting process of cow dung prepared to fertilize the soil for growing vegetables and fruits were studied. The average abundance of yeasts changed during the four temperature stages of the composting process. The highest abundance of yeasts, 1.38 × 104 cfu/g, was observed in the second stage of heating from 20 to 40 °C; the lowest was studied in the stage with the highest temperature (65 °C), 1.68 × 103 cfu/g. A total of 19 yeast species were observed and identified: 11 ascomycetes and 8 basidiomycetes, belonging to five subphyla of Fungi: Saccharomycotina (10), Pezizomycotina (1), Agaricomycotina (5), Pucciniomycotina (2), and Ustilaginomycotina (1). The greatest diversity of yeasts was found in the initial (20 °C) and second (heating up to 40 °C) temperature stages of composting (Aureobasidium pullulans (yeast-like fungus), Candida parapsilosis, Candida saitoana, Candida santamariae, Candida tropicalis, Curvibasidium cygneicollum, Cutaneotrichosporon moniliforme, Debaryomyces fabryi, Debaryomyces hansenii, Filobasidium magnum, Kazachstania sp., Moesziomyces bullatus, Naganishia globosa, Papiliotrema flavescens, Rhodotorula mucilaginosa, Scheffersomyces insectosa, Torulaspora delbrueckii, Vanrija musci), and the lowest in the stage of maximum heating (65 °C) (C. parapsilosis, C. tropicalis, Cyberlindnera jadinii).The opportunistic yeasts C. parapsilosis and C. tropicalis were obtained not only in the initial, second and third temperature stages of the composting process, but also in mature compost in the final stage prepared for soil application. This study shows that the cow dung, used in the farm studied did not meet the microbiological safety criteria. The reduction of opportunistic yeast species was not achieved with the composting method used. The likelihood of these species entering agricultural products via compost and soil and developing as endophytes in the internal tissues of fruits is very high. Since some strains of opportunistic Candida species from cow dung exhibited virulent characteristics (they produced hydrolytic enzymes and were resistant to antifungal compounds), additional phenotypic and genetic studies of the compost strains and their comparison with clinical isolates should be pursued.
Collapse
Affiliation(s)
- Аnna М Glushakova
- M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.
| | - Аleksey V Kachalkin
- M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia
| |
Collapse
|
9
|
Changes of bacterial and fungal communities and relationship between keystone taxon and physicochemical factors during dairy manure ectopic fermentation. PLoS One 2022; 17:e0276920. [PMID: 36534655 PMCID: PMC9762577 DOI: 10.1371/journal.pone.0276920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Due to interactions with variety of environmental and physicochemical factors, the composition and diversity of bacteria and fungi in manure ectopic fermentation are constantly changing. The purpose of this study was to investigated bacterial and fungal changes in dairy manure ectopic fermentation, as well as the relationships between keystone species and physicochemical characteristics. METHODS Ectopic fermentation was carried out for 93 days using mattress materials, which was combined with rice husk and rice chaff (6:4, v/v), and dairy waste mixed with manure and sewage. Physicochemical characteristics (moisture content, pH, NH4+-N (NN), total organic carbon (TO), total nitrogen (TN) and the C/N ratio) of ectopic fermentation samples were measured, as well as enzymatic activity (cellulose, urease, dehydrogenase and alkaline phosphatase). Furthermore, the bacterial and fungal communities were studied using 16S rRNA and 18S rRNA gene sequencing, as well as network properties and keystone species were analyzed. RESULTS During the ectopic fermentation, the main pathogenic bacteria reduced while fecal coliform increased. The C/N ratio gradually decreased, whereas cellulase and dehydrogenase remained at lower levels beyond day 65, indicating fermentation maturity and stability. During fermentation, the dominant phyla were Chloroflexi, Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria of bacteria, and Ascomycota of fungi, while bacterial and fungal community diversity changed dramatically and inversely. The association between physicochemical characteristics and community keystone taxon was examined, and C/N ratio was negative associated to keystone genus. CONCLUSION These data indicated that microbial composition and diversity interacted with fermentation environment and parameters, while regulation of keystone species management of physicochemical factors might lead to improved maturation rate and quality during dairy manure ectopic fermentation. These findings provide a reference to enhance the quality and efficiency of waste management on dairy farm.
Collapse
|
10
|
Sun N, Wang L, Sun Y, Li H, Liao S, Ding J, Wang G, Suo L, Li Y, Zou G, Huang S. Positive Effects of Organic Substitution in Reduced-Fertilizer Regimes on Bacterial Diversity and N-Cycling Functionality in Greenhouse Ecosystem. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16954. [PMID: 36554835 PMCID: PMC9779496 DOI: 10.3390/ijerph192416954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Conventional fertilization in the greenhouses of North China used excessive amounts of chemical and organic fertilizer, resulting in soil degradation and severe agricultural non-point source pollution. A nine-year study was conducted on a loamy clay soil in Shijiazhuang, Hebei province, to investigate the effects of reduced-fertilizer input regimes on soil property, bacterial diversity, nitrogen (N) cycling and their interactions. There were four treatments, including high organic + chemical fertilizer application rate and three reduced-fertilizer treatments with swine manure, maize straw or no substitution of 50% chemical N. Treatments with reduced-fertilizer input prevented soil salinization and acidification as in local conventional fertilization after being treated for nine years. In comparison to chemical fertilizer only, swine manure or maize straw substitution maintained higher nutrient availability and soil organic C contents. Fertilizer input reduction significantly increased bacterial richness and shifted bacterial community after nine years, with decisive factors of EC, Olsen P and C/N ratio of applied fertilizer. Soil chemical characteristics (EC, pH and nutrients), aggregation and C/N ratio of applied fertilizer selected certain bacterial groups, as well as N-cycling functions. Reduced-fertilizer input decreased the potential nitrification and denitrification functioning of bacterial community, but only in organic substitution treatments. The results of this study suggested that fertilizer input reduction combined with organic C input has potential in reducing non-point source pollution and increasing N-use efficiency in greenhouse vegetable production in North China.
Collapse
Affiliation(s)
- Na Sun
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Liying Wang
- Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yanxin Sun
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hong Li
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shangqiang Liao
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jianli Ding
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guoliang Wang
- Institute of Biotechnology, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Linna Suo
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanmei Li
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guoyuan Zou
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shaowen Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
11
|
Meng L, Xu C, Wu F. Microbial co-occurrence networks driven by low-abundance microbial taxa during composting dominate lignocellulose degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157197. [PMID: 35839876 DOI: 10.1016/j.scitotenv.2022.157197] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulose, which contains cellulose, hemicellulose and lignin, is one of the most important factors determining the rate and quality of compost decomposition, and the microbial community composition affects the rate of lignocellulose decomposition. Interactions between microbial taxa contribute significantly to ecosystem energy flow and material cycling. However, it is not clear how interactions between microbial taxa affect the degradation of lignocellulose during the composting process. For this reason we carried out aerobic co-composting experiments with maize straw and cattle manure to explore the contribution of microbial community diversity and the interaction between taxa to lignocellulosic degradation. The results showed that moisture and temperature had the greatest effect on microbial communities during composting and that lignocellulose degradation was dominated by microbial co-occurrence networks rather than microbial community diversity. Overall co-occurrence network and bacterial-fungal interactions explained 23.9-84.1 % of lignocellulosic degradation, whereas microbial diversity only accounted for 24.6-31.5 %. Interestingly, keystone taxa analysis of the microbial co-occurrence networks revealed that low-abundance taxa influenced microbial interactions driving lignocellulose degradation. Our results provide a new perspective for understanding lignocellulose degradation during composting, offering insights into important microbial interaction mechanisms for improving compost quality and efficiency.
Collapse
Affiliation(s)
- Lingxu Meng
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010000, China
| | - Chunxue Xu
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010000, China
| | - Fanlin Wu
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010000, China
| |
Collapse
|
12
|
Pot S, Tender CD, Ommeslag S, Delcour I, Ceusters J, Vandecasteele B, Debode J, Vancampenhout K. Elucidating the microbiome of the sustainable peat replacers composts and nature management residues. Front Microbiol 2022; 13:983855. [PMID: 36246232 PMCID: PMC9555241 DOI: 10.3389/fmicb.2022.983855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Sustainable peat alternatives, such as composts and management residues, are considered to have beneficial microbiological characteristics compared to peat-based substrates. Studies comparing microbiological characteristics of these three types of biomass are, however, lacking. This study examined if and how microbiological characteristics of subtypes of composts and management residues differ from peat-based substrates, and how feedstock and (bio)chemical characteristics drive these characteristics. In addition, microbiome characteristics were evaluated that may contribute to plant growth and health. These characteristics include: genera associated with known beneficial or harmful microorganisms, microbial diversity, functional diversity/activity, microbial biomass, fungal to bacterial ratio and inoculation efficiency with the biocontrol fungus Trichoderma harzianum. Bacterial and fungal communities were studied using 16S rRNA and ITS2 gene metabarcoding, community-level physiological profiling (Biolog EcoPlates) and PLFA analysis. Inoculation with T. harzianum was assessed using qPCR. Samples of feedstock-based subtypes of composts and peat-based substrates showed similar microbial community compositions, while subtypes based on management residues were more variable in their microbial community composition. For management residues, a classification based on pH and hemicellulose content may be relevant for bacterial and fungal communities, respectively. Green composts, vegetable, fruit and garden composts and woody composts show the most potential to enhance plant growth or to suppress pathogens for non-acidophilic plants, while grass clippings, chopped heath and woody fractions of compost show the most potential for blends for calcifuge plants. Fungal biomass was a suitable predictor for inoculation efficiency of composts and management residues.
Collapse
Affiliation(s)
- Steffi Pot
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Geel, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- *Correspondence: Steffi Pot,
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Zwijnaarde, Belgium
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Ilse Delcour
- PCS Ornamental Plant Research, Destelbergen, Belgium
| | - Johan Ceusters
- Division of Crop Biotechnics, Department of Biosystems, Research Group for Sustainable Crop Production & Protection, KU Leuven, Geel, Belgium
- Centre for Environmental Sciences, Environmental Biology, UHasselt, Diepenbeek, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Karen Vancampenhout
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Geel, Belgium
| |
Collapse
|
13
|
Qiu W, Kang J, Ding H, Sun R, Yang Z, Ge J. Aerobic composting of chicken manure with amoxicillin: Alpha diversity is closely related to lipid metabolism, and two-component systems mediating their relationship. BIORESOURCE TECHNOLOGY 2022; 360:127543. [PMID: 35777649 DOI: 10.1016/j.biortech.2022.127543] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Composting is a technology that can use various functional microorganisms to degrade antibiotics. However, antibiotics will cause a coercion for the growth of most microorganisms. Microorganism can survive different environments, thanks to the development of different adaptive responses. Often, two-component systems sense changes in the environment and trigger a cellular response and adaptation. Therefore, the main purpose of this study was to explore how the two-component system modulates the corresponding metabolic functions to affect alpha diversity during composting. The results show that amoxicillin increases species diversity, reduces species richness. Lipid metabolism is an important metabolic pathway mediating changes in alpha diversity. Two-component system indirectly affects alpha diversity by regulating lipid metabolism. Firmicutes are important microbial communities mediating changes in alpha diversity This work presents an understanding of the impact of environmental information processing on microbial diversity, during composting.
Collapse
Affiliation(s)
- Wei Qiu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Hao Ding
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Rui Sun
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Zhichao Yang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China.
| |
Collapse
|
14
|
Wang Y, Chu L, Ma J, Chi G, Lu C, Chen X. Effects of multiple antibiotics residues in broiler manure on composting process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152808. [PMID: 34982991 DOI: 10.1016/j.scitotenv.2021.152808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
At present, the effect of multiple antibiotics on aerobic composting process and its mechanism are not clear. So in this study, broiler manure containing different doses of Doxycycline (DOX) and Gatifloxacin (GAT) were used as raw materials and mixed with rice hull for aerobic composting, and the effects of the combination of multiple antibiotics on the process parameters of broiler manure composting and the succession of bacterial and fungal community structures were systematically analyzed. Our results showed that at the initial period of composting, the combination of multiple antibiotics led to a delayed temperature and pH increase (T1: 57.0 °C, T2: 48.3 °C, T3: 45.5 °C on Day 3 for temperature and T1: 7.44, T2: 7.1, T3: 6.88 on Day 5 for pH), and a slow total nitrogen decrease (T1: 1.56%, T2: 1.82%, T3: 1.74% on Day 5). Although these effects decreased gradually with the degradation of antibiotics, the relative abundance of Actinobacteriota (T1: 13.29%, T2: 10.57%, T3: 8.99%) and Bacteroidota (T1:27.52%, T2:40.03%, T3:39.81%)) were still influenced by multiple antibiotic residuals until the end of composting period. Higher levels of antibiotics had more lasting effects on the bacterial community (T3 > T2). However, the combination of these two antibiotics did not significantly promote or inhibit the succession of the fungal community structure. The heatmaps showed that composting stage had a greater effect on the microbial community structures than antibiotics. The results provided a theoretical reference for composting broiler manure containing DOX and GAT.
Collapse
Affiliation(s)
- Yongcui Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lei Chu
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100039, China; Wellhope Foods Co., Ltd, Shenyang, Liaoning Province, PR China
| | - Jian Ma
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Guangyu Chi
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Caiyan Lu
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xin Chen
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| |
Collapse
|
15
|
Bello A, Ogundeji A, Yu S, Jiang X, Deng L, Zhao L, Jong C, Xu X. Dynamics of fungal species related to nitrogen transformation and their network patterns during cattle manure-corn straw with biochar composting. Arch Microbiol 2022; 204:236. [PMID: 35362815 DOI: 10.1007/s00203-022-02848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 11/02/2022]
Abstract
Fungi are reputed to play a significant role in the composting matrix as decomposers of recalcitrant organic materials like cellulose and lignin. However, information on the fungi communities' roles in nitrogen transformation under a compost-biochar mixture is scarce. This study investigated shifts in fungal species mediating N transformation and their network patterns in cattle manure-corn straw (CMCS) and CMCS plus biochar (CMCB) composting using high-throughput sequencing data. The results revealed that the addition of biochar altered fungal richness and diversity and significantly influenced their compositions during composting. Biochar also altered the compost fungal network patterns; CMCS had a more complex network with higher positive links than CMCB, suggesting stable niche overlap. The consistent agreement of multivariate analyses (redundancy, network, regression, Mantel and path analyses) indicated that Ciliophora_sp in CMCS and unclassified_norank_Pleosporales in CMCB were the key fungal species mediating total N transformation, whereas Scedosporium_prolificans in CMCS and unclassified_Microascaceae in CMCB were identified as major predictive indices determining NO3--N transformation. Also, Coprinopsis cinerea and Penicillium oxalicum were the predictive factors for NH4+-N transformation in CMCS and CMCB during composting. These results indicated that the effects of biochar on N conversions in composting could be unraveled using multivariate analyses on fungi community evolution, network patterns, and metabolism.
Collapse
Affiliation(s)
- Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.,College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Abiola Ogundeji
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Sun Yu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liyan Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Chol Jong
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.,College of Agriculture, Kimjewon Agricultural University, Haeju City, Hwanghae South Province, 999093, Republic of Korea
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
16
|
Ubani O, Atagana HI, Selvarajan R, Ogola HJO. Unravelling the genetic and functional diversity of dominant bacterial communities involved in manure co-composting bioremediation of complex crude oil waste sludge. Heliyon 2022; 8:e08945. [PMID: 35243067 PMCID: PMC8857465 DOI: 10.1016/j.heliyon.2022.e08945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/07/2022] [Accepted: 02/09/2022] [Indexed: 01/07/2023] Open
Abstract
The present study aimed to characterize the bacterial community and functional diversity in co-composting microcosms of crude oil waste sludge amended with different animal manures, and to evaluate the scope for biostimulation based in situ bioremediation. Gas chromatography–mass spectrometry (GC–MS) analyses revealed enhanced attenuation (>90%) of the total polyaromatic hydrocarbons (PAHs); the manure amendments significantly enhancing (up to 30%) the degradation of high molecular weight (HMW) PAHs. Microbial community analysis showed the dominance (>99% of total sequences) of sequences affiliated to phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The core genera enriched were related to hydrocarbon metabolism (Pseudomonas, Delftia, Methylobacterium, Dietzia, Bacillus, Propionibacterium, Bradyrhizobium, Streptomyces, Achromobacter, Microbacterium and Sphingomonas). However, manure-treated samples exhibited high number and heterogeneity of unique operational taxonomic units (OTUs) with enrichment of additional hydrocarbon-degrading bacterial taxa (Proteiniphilum, unclassified Micrococcales, unclassified Lachnospiraceae, Sphingobium and Stenotrophomonas). Thirty-three culturable hydrocarbon-degrading microbes were isolated from the co-composting microcosms and mainly classified into Burkholderia, Sanguibacter, Pseudomonas, Bacillus, Rhodococcus, Lysinibacillus, Microbacterium, Brevibacterium, Geobacillus, Micrococcus, Arthrobacter, Cellulimicrobacterium, Streptomyces Dietzia,etc,. that was additionally affirmed with the presence of catechol 2,3-dioxygenase gene. Finally, enhanced in situ degradation of total (49%), LMW (>75%) and HMW PAHs (>35%) was achieved with an enriched bacterial consortium of these microbes. Overall, these findings suggests that co-composting treatment of crude oil sludge with animal manures selects for intrinsically diverse bacterial community, that could be a driving force behind accelerated bioremediation, and can be exploited for engineered remediation processes.
Collapse
Affiliation(s)
- Onyedikachi Ubani
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
- Corresponding author.
| | - Harrison I. Atagana
- Institute of Nanotechnology & Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, 572000, Hainan Province, PR China
- PG Research Department of Microbiology, J.J College of Arts and Science (Autonomous), Sivapuram, Pudukkottai, 622 422, Tamil Nadu, India
| | - Henry JO. Ogola
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, P.O Box 210-40601, Kenya
| |
Collapse
|
17
|
Tondello A, Fasolo A, Marcato S, Treu L, Bonato T, Zanardi W, Concheri G, Squartini A, Baldan B. Characterization of bacterial communities isolated from municipal waste compost and screening of their plant-interactive phenotypes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150592. [PMID: 34592304 DOI: 10.1016/j.scitotenv.2021.150592] [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: 04/21/2021] [Revised: 07/26/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Four batches of commercial compost obtained from the organic fraction of municipal solid waste were analyzed from chemical and microbiological standpoints. The working hypothesis was that, being this type of compost derived partly from plant waste, it could contain plant-growth promoting bacterial endophytes, prone to be active again upon its usual delivery as fertilizer. Culturable bacteria were isolated at different temperatures, quantified by colony morphology, identified taxonomically by 16S sequencing and screened for plant-growth promoting phenotypes including auxin and siderophore production, phosphate solubilization and peptide mineralization to ammonia. In parallel, the total community was assessed by culture independent DNA metabarcoding. The capability of plants to select, uptake and internally multiply bacteria from these compost samples was analyzed using grapevine in-vitro rooting cuttings from which acquired bacteria were reisolated, quantified and their identities determined as above. Major differences in compost bacterial composition were observed as function of the season, with the winter sample being rather distinct from the summer ones. Bacillales and Actinomycetales dominated the culturable communities while Alteromonadales, Oceanospirillales and Flavobacteriales prevailed in the total community. In spite of the challenging composting cycle conditions, the plant nature of the main input substrates appeared determinant in guaranteeing that 82% of the culturable bacteria were found endowed with one or more of the plant growth-promoting phenotypes tested. Beside its fertilization role, compost proved to be also a potential inoculant carrier for the in-soil delivery of plant beneficial microorganisms. Furthermore, upon an in vitro passage through grapevine plants under axenic conditions, the subsequently recoverable endophyte community yielded also members of the Rhizobiales order which had not been detectable when culturing directly from compost. This observation further suggests that compost-borne plant-interacting taxa could be also rescued from non-culturable states and/or enriched above detectability levels by a contact with their potential host plants.
Collapse
Affiliation(s)
- Alessandra Tondello
- Department of Biology, UniPD, Padova, Italy; Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), UniPD, Legnaro, PD, Italy
| | | | | | - Laura Treu
- Department of Biology, UniPD, Padova, Italy
| | - Tiziano Bonato
- Società Estense Servizi Ambientali S.E.S.A., Este, PD, Italy
| | - Werner Zanardi
- Società Estense Servizi Ambientali S.E.S.A., Este, PD, Italy
| | - Giuseppe Concheri
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), UniPD, Legnaro, PD, Italy
| | - Andrea Squartini
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), UniPD, Legnaro, PD, Italy
| | - Barbara Baldan
- Department of Biology, UniPD, Padova, Italy; Botanical Garden, UniPD, Padova, Italy.
| |
Collapse
|
18
|
Wen X, Wang R, Jiang Y, Deng X, Wei S, Liu X, Wang Y. Diversity and Composition of Rhizosphere Fungal Community in Pure and Mixed Forests of South China. POLISH JOURNAL OF ECOLOGY 2021. [DOI: 10.3161/15052249pje2020.69.2.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xinmiao Wen
- Hunan international economics university, 822 Fenglin 3rd Road, Yuelu District, Changsha, Hunan, 410000, China
| | - Renjie Wang
- Guangxi Key Laboratory of Superior Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530000, China
| | - Yi Jiang
- Guangxi Key Laboratory of Superior Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530000, China
| | - Xiaojun Deng
- Guangxi Key Laboratory of Superior Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530000, China
| | - Shuoxin Wei
- Guangxi Key Laboratory of Superior Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530000, China
| | - Xiongsheng Liu
- Guangxi Key Laboratory of Superior Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530000, China
| | - Yong Wang
- Guangxi Key Laboratory of Superior Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530000, China
| |
Collapse
|
19
|
Ye Z, Ding H, Yin Z, Ping W, Ge J. Evaluation of humic acid conversion during composting under amoxicillin stress: Emphasizes the driving role of core microbial communities. BIORESOURCE TECHNOLOGY 2021; 337:125483. [PMID: 34320763 DOI: 10.1016/j.biortech.2021.125483] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
This study aimed to investigate the effects of various amoxicillin (AMX) concentrations on humic acid (HA) formation and the bacterial community structure (BCS) during chicken manure aerobic composting. The findings showed that AMX caused a rise in pH and a shortening of the thermophilic cycle during the thermophilic period. Moreover, a high concentration of AMX (150 mg/kg) inhibited community succession and humification at maturity. In addition to influencing environmental factors, AMX increased the relative abundance (RA) of the dominant bacteria in the thermophilic phase (Firmicutes) and decreased the RA of the dominant bacteria in the mature phase (Proteobacteria). From carbon conversion, AMX promoted fulvic acid (FA) anabolism in the early period and inhibited HA accumulation in the later period. As a result, the primary impact of AMX on HA transformation was the alteration of the BCS, ultimately affecting the quality of compost.
Collapse
Affiliation(s)
- Zeming Ye
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Hao Ding
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Ziliang Yin
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Wenxiang Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China.
| |
Collapse
|
20
|
Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review. Microorganisms 2021; 9:microorganisms9061165. [PMID: 34071426 PMCID: PMC8227910 DOI: 10.3390/microorganisms9061165] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil.
Collapse
|
21
|
Ferguson RMW, Neath CEE, Nasir ZA, Garcia-Alcega S, Tyrrel S, Coulon F, Dumbrell AJ, Colbeck I, Whitby C. Size fractionation of bioaerosol emissions from green-waste composting. ENVIRONMENT INTERNATIONAL 2021; 147:106327. [PMID: 33387881 DOI: 10.1016/j.envint.2020.106327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Particle size is a significant factor in determining the dispersal and inhalation risk from bioaerosols. Green-waste composting is a significant source of bioaerosols (including pathogens), but little is known about the distribution of specific taxa across size fractions. To characterise size fractionated bioaerosol emissions from a compost facility, we used a Spectral Intensity Bioaerosol Sensor (SIBS) to quantify total bioaerosols and qPCR and metabarcoding to quantify microbial bioaerosols. Overall, sub-micron bioaerosols predominated, but molecular analysis showed that most (>75%) of the airborne microorganisms were associated with the larger size fractions (>3.3 µm da). The microbial taxa varied significantly by size, with Bacilli dominating the larger, and Actinobacteria the smaller, size fractions. The human pathogen Aspergillus fumigatus dominated the intermediate size fractions (>50% da 1.1-4.7 µm), indicating that it has the potential to disperse widely and once inhaled may penetrate deep into the respiratory system. The abundance of Actinobacteria (>60% at da < 2.1 µm) and other sub-micron bioaerosols suggest that the main health effects from composting bioaerosols may come from allergenic respiratory sensitisation rather than directly via infection. These results emphasise the need to better understand the size distributions of bioaerosols across all taxa in order to model their dispersal and to inform risk assessments of human health related to composting facilities.
Collapse
Affiliation(s)
- Robert M W Ferguson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Charlotte E E Neath
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; School of Applied Sciences, University of South Wales, Cemetery Road, Glyntaff, Pontypridd CF37 4BD, UK
| | - Zaheer A Nasir
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Sonia Garcia-Alcega
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Sean Tyrrel
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Frederic Coulon
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Ian Colbeck
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Corinne Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
| |
Collapse
|
22
|
Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil. Int J Mol Sci 2020; 21:ijms21176008. [PMID: 32825476 PMCID: PMC7504009 DOI: 10.3390/ijms21176008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 12/23/2022] Open
Abstract
Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant–pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil.
Collapse
|
23
|
Meng Q, Han Y, Zhu H, Yang W, Bello A, Deng L, Jiang X, Wu X, Sheng S, Xu Y, Xu X. Differences in distribution of functional microorganism at DNA and cDNA levels in cow manure composting. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110161. [PMID: 31954219 DOI: 10.1016/j.ecoenv.2019.110161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Denitrification and nitrification processes are the two prominent pathways of nitrogen (N) transformation in composting matrix. This study explored the dynamics of denitrifying and nitrifying bacteria at different composting stages of cow manure and corn straw using functional gene sequencing at DNA and cDNA levels. Corresponding agreement among OTUs, NMDS, mental test and network analyses revealed that functional bacteria community compositions and responses to physicochemical factors were different at DNA and cDNA levels. Specifically, some OTUs were detected at the DNA level but were not observed at cDNA level, differences were also found in the distribution patterns of nitrifying and denitrifying bacteria communities at both levels. Furthermore, co-occurrence network analysis indicated that Pseudomonas, Paracoccus and Nitrosomonas were identified as the keystone OTUs at the DNA level, while Paracoccus, Agrobacterium and Nitrosospira were keystone OTUs at the cDNA level. Mantel test revealed that TN, C/N and moisture content significantly influenced both the denitrifying bacteria and ammonia-oxidizing bacteria (AOB) communities at the DNA level. NO3--N, NH4+-N, TN, C/N, and moisture content only registered significant correlation with the nosZ-type denitrifiers and ammonia-oxidizing bacteria (AOB) communities at the cDNA level. Structural equation model (SEM) showed that TN, NH4+-N, and pH were direct and significantly influenced the gene abundance of denitrifying bacteria. Howbeit, TN, NH4+-N, and NO3--N had significant direct effects on amoA gene abundance.
Collapse
Affiliation(s)
- Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Haifeng Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaotong Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Siyuan Sheng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yingying Xu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
24
|
Wu X, Sun Y, Deng L, Meng Q, Jiang X, Bello A, Sheng S, Han Y, Zhu H, Xu X. Insight to key diazotrophic community during composting of dairy manure with biochar and its role in nitrogen transformation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 105:190-197. [PMID: 32078983 DOI: 10.1016/j.wasman.2020.02.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/14/2020] [Accepted: 02/10/2020] [Indexed: 05/26/2023]
Abstract
Analyzing diazotrophic community may help to understand nitrogen transformation in composting and improves the final compost quality. In this study, diazotrophic community dynamics were investigated in terms of nifH gene during dairy manure and corn straw composting with biochar addition using high-throughput sequencing. Biochar decreased the diversity of diazotrophic community and altered diazotroph community structure during composting. At phylum level, Proteobacteria, Actinobacteria and Firmicutes were dominant diazotrophic communities throughout composting process. Biochar addition registered higher correlation coefficient (R) between physicochemical factors (temperature, ammonium (NH4+-N) and nitrate (NO3--N)) and diazotroph community composition. Rhodopseudomonas and Pseudoxanthomonas was the key diazotrophic communities influencing NH4+-N transformation in control (CK) and biochar compost (BC), respectively, while for NO3--N transformation Clostridium and Bradyrhizobium in CK, Azospira and Methylocystis in BC served as predominant factors. These results indicated that addition of biochar altered the key diazotroph communities influencing nitrogen transformation. Furthermore, some diazotrophs (e.g. Rhodopseudomonas, Bradyrhizobium and Azospira) affecting NH4+-N and NO3--N transformation were also observed to be mediating total nitrogen (TN). Interestingly, interactions between diazotrophic communities were observed and these interactions could also influence nitrogen transformation.
Collapse
Affiliation(s)
- Xiaotong Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Siyuan Sheng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Haifeng Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
| |
Collapse
|
25
|
Jiang X, Deng L, Meng Q, Sun Y, Han Y, Wu X, Sheng S, Zhu H, Ayodeji B, Egbeagu UU, Xu X. Fungal community succession under influence of biochar in cow manure composting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:9658-9668. [PMID: 31925688 DOI: 10.1007/s11356-019-07529-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/25/2019] [Indexed: 06/10/2023]
Abstract
This study examined the influence of biochar addition on fungal community during composting of cow manure using high-throughput sequencing. Two treatments were set up, including compost of cow manure plus 10% biochar (BC) and cow manure compost without biochar (CK). Fungal community composition varied obviously during composting in both treatments, and main fungi included Aspergillus, Myriococcum, Thermomyces, Mycothermus, Scedosporium, Cladosporium, and unclassified Microascaceae. Fungal community composition was altered by biochar during composting, especially during the thermophilic and the cooling phase, promoting Aspergillus and Myriococcum while inhibiting unclassified Microascaceae and Thermomyces. Based on linear discriminant analysis effect size analysis, common indicator groups were detected in both composts; however, specific indicator groups were also found in BC treatment, including Clavicipitaceae, Tremellales, Gibberella, and Coprinopsis. Canonical correspondence analysis (CCA) indicated that moisture content, organic matter, C/N, and pH had significant correlation (p < 0.05) with fungal composition in both treatments. However, in compost added with biochar, temperature was not an important factor affecting fungal community (p > 0.05).
Collapse
Affiliation(s)
- Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaotong Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Siyuan Sheng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Haifeng Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Bello Ayodeji
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ugochi Uzoamaka Egbeagu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
26
|
Sun L, Han X, Li J, Zhao Z, Liu Y, Xi Q, Guo X, Gun S. Microbial Community and Its Association With Physicochemical Factors During Compost Bedding for Dairy Cows. Front Microbiol 2020; 11:254. [PMID: 32153538 PMCID: PMC7047772 DOI: 10.3389/fmicb.2020.00254] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/03/2020] [Indexed: 11/27/2022] Open
Abstract
Overproduction of livestock manure can cause significant environmental challenges. Compost bedding (CB) is considered an effective approach for recycling the agricultural byproducts and improving the welfare of dairy cattle. During the CB preparing, the composition of microbial communities is usually altered; however, the patterns and drivers of CB microbial communities remains to be investigated. The current study aimed to explore the dynamics of bacterial and fungal communities during the various padded stages, using high throughput sequencing technology and qPCR. The relationships across physicochemical parameters, microbial community composition, and abundance were also evaluated. Sequencing results revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes of bacteria, and Ascomycota of fungi as the major phyla found in CB. qPCR results showed a significant increase in the number of bacterial genome copies from 1.20 × 107 to 3.35 × 107 copies/gram of dry soil, while the number of fungal genome copies significantly increased from 8.43 × 104 to 7.02 × 106 copies/gram of dry soil. Linear discriminant analysis effect size (LEfSe) showed that Actinobacteria was the primary indicator in raw materials while the phylum Bacteroidetes was in the other padded stages. Dothideomycetes was significantly enriched in the initial stage of fungi, whereas Sordariomycetes, including a pathogen Scedosporium prolificans, was the major indicator in CB after 9 days of padding. Mantel test showed that pH significantly influenced bacterial community composition while temperature and total organic carbon (TOC) had a significant effect on fungal community structure. Redundancy analysis indicated that TOC, temperature, and water content had a significant effect on bacterial abundance while total nitrogen, water content, and pH significantly affected fungal abundance. Our finding contributed to the understanding of microbial community succession in CB across different padded stages, and suggests CB management by changing the bedding material every 7 days.
Collapse
Affiliation(s)
- Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Gansu Provincial Engineering Research Center for Animal Waste Utilization, Gansu Agricultural University, Lanzhou, China
| | - Xiangmin Han
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Jianshu Li
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Zhidong Zhao
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Yuzhen Liu
- Grassland Science College of Gansu Agricultural University, Lanzhou, China
| | - Qiming Xi
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Xinyu Guo
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
27
|
Tortosa G, Torralbo F, Maza-Márquez P, Aranda E, Calvo C, González-Murua C, Bedmar EJ. Assessment of the diversity and abundance of the total and active fungal population and its correlation with humification during two-phase olive mill waste (''alperujo") composting. BIORESOURCE TECHNOLOGY 2020; 295:122267. [PMID: 31648128 DOI: 10.1016/j.biortech.2019.122267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/10/2019] [Accepted: 10/12/2019] [Indexed: 05/22/2023]
Abstract
Metagenomic and transcriptomic techniques applied to composting could increase our understanding of the overall microbial ecology and could help us to optimise operational conditions which are directly related with economic interest. In this study, the fungal diversity and abundance of two-phase olive mill waste ("alperujo") composting was studied using Illumina MiSeq sequencing and quantitative PCR, respectively. The results showed an increase of the fungal diversity during the process, with Ascomycota being the predominant phylum. Penicillium was the main genera identified at the mesophilic and maturation phases, with Debaryomyces and Sarocladium at the thermophilic phase, respectively. The fungal abundance was increased during composting, which confirms their important role during thermophilic and maturation phases. Some Basidiomycota showed an increased during the process, which showed a positive correlation with the humification parameters. According to that, the genus Cystofilobasidium could be used as a potential fungal biomarker to assess alperujo compost maturation.
Collapse
Affiliation(s)
- Germán Tortosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), Agencia Estatal CSIC, c/Profesor Albareda, 1, 18008 Granada, Spain
| | - Fernando Torralbo
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, 48940 Leioa, Bizkaia, Spain
| | - Paula Maza-Márquez
- Institute of Water Research, University of Granada, Edificio Fray Luis, c/Ramón y Cajal, 4, 18071 Granada, Spain; Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain
| | - Elisabet Aranda
- Institute of Water Research, University of Granada, Edificio Fray Luis, c/Ramón y Cajal, 4, 18071 Granada, Spain; Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain.
| | - Concepción Calvo
- Institute of Water Research, University of Granada, Edificio Fray Luis, c/Ramón y Cajal, 4, 18071 Granada, Spain; Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, 48940 Leioa, Bizkaia, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), Agencia Estatal CSIC, c/Profesor Albareda, 1, 18008 Granada, Spain
| |
Collapse
|
28
|
Exploring the long-term effect of plastic on compost microbiome. PLoS One 2019; 14:e0214376. [PMID: 30908552 PMCID: PMC6433246 DOI: 10.1371/journal.pone.0214376] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/12/2019] [Indexed: 11/29/2022] Open
Abstract
Little is known about the ecology of microbial plastic degradation. In this study, we employed next generation amplicon sequencing to assess the effect of low-density polyethylene (LDPE) films on the structure of bacterial and fungal communities in four mature compost piles with age ranging between 2 and 10 years. While, bacterial Proteobacteria, Bacteroidetes, Actinobacteria and fungi Ascomycota were most abundant across all facilities, our data indicated significant differences in compost microbiomes between compost facilities, which might be related to compost chemical parameters, age of piles and characteristics of the feedstock. In addition, a substantial shift in the interaction pattern within microbial communities from bulk and plastic-associated (PA) compost was detected. For example, cooperation between Firmicutes Bacillaceae and Thermoactinomycetaceae was detected only in PA compost. However, based on the analysis of the diversity indices and the relative abundances of microbial taxa we can conclude that the presence of plastics in compost had no significant effect on the structure of microbial community.
Collapse
|
29
|
Meng Q, Yang W, Men M, Bello A, Xu X, Xu B, Deng L, Jiang X, Sheng S, Wu X, Han Y, Zhu H. Microbial Community Succession and Response to Environmental Variables During Cow Manure and Corn Straw Composting. Front Microbiol 2019; 10:529. [PMID: 30936861 PMCID: PMC6431636 DOI: 10.3389/fmicb.2019.00529] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
In composting system, the composition of microbial communities is determined by the constant change in the physicochemical parameters. This study explored the dynamics of bacterial and fungal communities during cow manure and corn straw composting using high throughput sequencing technology. The relationships between physicochemical parameters and microbial community composition and abundance were also evaluated. The sequencing results revealed the major phyla included Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Actinobacteria, Ascomycota, and Basidiomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Actinomycetales and Sordariomycetes were the indicators of bacteria and fungi in the maturation phase, respectively. Mantel test showed that NO3 --N, NH4 +-N, TN, C/N, temperature and moisture content significantly influenced bacterial community composition while only TN and moisture content had a significant effect on fungal community structure. Structural equation model (SEM) indicated that TN, NH4 +-N, NO3 --N and pH had a significant effect on fungal abundance while TN and temperature significantly affected bacterial abundance. Our finding increases the understanding of microbial community succession in cow manure and corn straw composting under natural conditions.
Collapse
Affiliation(s)
| | | | | | | | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Liu T, He J, Cui C, Tang J. Exploiting community structure, interactions and functional characteristics of fungi involved in the biodrying of storage sludge and beer lees. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 232:321-329. [PMID: 30496961 DOI: 10.1016/j.jenvman.2018.11.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/09/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
In this study, the dynamic changes in fungal biodiversity, community structure, fungal associations and functional characteristics were investigated in the biodrying of storage sludge and beer lees by using high throughput sequencing, network and correlation matrix analyses, and FUNGuild database. Additionally, a hypothetical model was provided to better understand the biodrying system. The results showed that fungal diversity decreased after biodrying, while community richness increased in the mesophilic stage and decreased as biodrying progressed. Fungal communities differed in different stages of the biodrying process. Ascomycota and Basidiomycota were the dominant phyla throughout the biodrying process, while Pichia was the dominant genus in the thermophilic stage. Network and correlation matrix analyses provided useful tools for insight into the fungal interactions, allowing us to propose a conceptual model of how succession in fungal associations regulates the dynamics of biodrying systems. Biodrying treatment had a significant effect on fungal trophic modes, with most pathogenic fungi fading away over the process, illustrating that biodrying is an effective bio-treatment method to eliminate pathogenic fungi. These findings provide information that elucidates the fungal interactions and functional characteristics during the biodrying process.
Collapse
Affiliation(s)
- Tiantian Liu
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Junguo He
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
| | - Chongwei Cui
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Jian Tang
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| |
Collapse
|
31
|
Liu Y, Wang W, Xu J, Xue H, Stanford K, McAllister TA, Xu W. Evaluation of compost, vegetable and food waste as amendments to improve the composting of NaOH/NaClO-contaminated poultry manure. PLoS One 2018; 13:e0205112. [PMID: 30307982 PMCID: PMC6181338 DOI: 10.1371/journal.pone.0205112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/19/2018] [Indexed: 11/20/2022] Open
Abstract
Regular usage of NaOH/NaClO disinfectants results in high sodium salt and alkalinity of poultry manure. This study compared three amendments: vegetable waste (V), food waste (F) and mature compost (C) for their ability to improve the composting of NaOH/NaClO-contaminated poultry manure. C compost resulted in the highest compost temperatures (p<0.001) and greatest reduction in OM, TC, TN and NH4-N (p<0.05). C and V composts were more efficient at lowering extractable-Na (ext-Na) and electrical conductivity (EC) than F (p<0.05). Maturity was primarily indicated by NH4-N, EC and ext-Na. Bacterial dynamics was profoundly influenced by NH4-N, EC and TC, with the decrease leading to discriminate genera shift from Sinibacillus and Thiopseudomonas to Brevbacterium, Brachybacterium, and Microbacterium. These findings suggest that mature compost was more desirable amendment than vegetable and food waste in the composting of NaOH/NaClO-contaminated poultry manure, and the decrease of ext-Na indicated compost maturity but did not influence bacterial dynamics.
Collapse
Affiliation(s)
- Yuting Liu
- School of Food and Environment, Dalian University of Technology, Panjin campus, Panjin, China
| | - Wenxia Wang
- School of Food and Environment, Dalian University of Technology, Panjin campus, Panjin, China
| | - Jianqiang Xu
- School of Life Science and Medicine, Dalian University of Technology, Panjin campus, Panjin, China
- Panjin Industrial Technology Institute of Dalian University of Technology, Panjin, China
| | - Hongyu Xue
- School of Life Science and Medicine, Dalian University of Technology, Panjin campus, Panjin, China
| | - Kim Stanford
- Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, Alberta, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Weiping Xu
- School of Food and Environment, Dalian University of Technology, Panjin campus, Panjin, China
- Panjin Industrial Technology Institute of Dalian University of Technology, Panjin, China
- * E-mail:
| |
Collapse
|
32
|
Huhe, Jiang C, Wu Y, Cheng Y. Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting. Microbiologyopen 2017; 6. [PMID: 28736905 PMCID: PMC5727367 DOI: 10.1002/mbo3.518] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/06/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022] Open
Abstract
During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high‐throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed. Bacterial and fungal community diversity and relative abundance varied significantly, and inversely, over time. Relationships between physicochemical factors and microbial community compositions were evaluated by redundancy analysis. The variation in bacterial community composition was significantly related to water‐soluble organic carbon (WSOC), and pile temperature and moisture (p < .05), while the largest portions of variation in fungal community composition were explained by pile temperature, WSOC, and C/N (p < .05). These findings indicated that those parameters are the most likely ones to influence, or be influenced by the bacterial and fungal communities. Variation partitioning analyses indicated that WSOC and pile temperature had predominant effects on bacterial and fungal community composition, respectively. Our findings will be useful for improving the quality of cattle farm waste composts.
Collapse
Affiliation(s)
- Huhe
- Soil Fertilizer and Water-Saving Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China.,The Ministry of Agriculture in Gansu Province Cultivated Land Conservation and Agricultural Environmental Science Observation Experiment Stations, Wuwei, Gansu, China
| | - Chao Jiang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, Inner Mongolia, China
| | - Yanpei Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Yunxiang Cheng
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| |
Collapse
|