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Wang S, Wu Q, Han Y, Du R, Wang X, Nie Y, Du X, Xu Y. Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data. mSystems 2021; 6:e00964-20. [PMID: 33436513 PMCID: PMC7901480 DOI: 10.1128/msystems.00964-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/03/2020] [Indexed: 11/20/2022] Open
Abstract
High-throughput amplicon sequencing is a critical tool for studying microbiota; however, it results only in relative abundance data. Thus, changes in absolute abundance of microbiota cannot be determined, which hinders further microbiology research. We have therefore established a gradient internal standard absolute quantification (GIS-AQ) method to overcome this issue, which can simultaneously obtain the absolute abundances of bacteria and fungi. Deviations from the quantitative equations of microbes and internal standards were eliminated through calibration. Compared with traditional quantitative real-time PCR and microscopy quantifications, this method is reliable (R 2 average = 0.998; P < 0.001) and accurate (P internals versus microscopy > 0.05). The GIS-AQ method can be adapted to any amplicon primer choice (e.g., 336F/806R and ITS3/ITS4), rendering it applicable to ecosystem studies including food, soil, and water samples. Crucially, when using solid-state fermentation samples from various temporal dimensions, the results obtained from the relative and absolute abundance are different. The absolute abundance can be used to study the difference in communities between different samples, and the GIS-AQ method allows this to be done rapidly. Therefore, combining the absolute abundance with relative abundance can accurately reflect the microbiota composition.IMPORTANCE To solve the problem of amplicon sequencing cannot discern the microbiota absolute abundance, we proposed a gradient internal standard absolute quantification method. We used Chinese liquor fermentation as a model system to demonstrate the reliability and accuracy of the method. By comparing the relative and absolute abundances of microbiota in various temporal dimensions, we found dynamic changes in the absolute abundance of communities under various temporal dimensions from the relative abundance. Based on its design principle, this method can be widely applied to different ecosystems. Therefore, we believe that the GIS-AQ method can play an immeasurably useful role in microbiological research.
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Affiliation(s)
- Shilei Wang
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qun Wu
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Ying Han
- Technical Center, Xinghuacun Fenjiu Distillery Co. Ltd., Fenyang, Shanxi, China
| | - Rubing Du
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaoyong Wang
- Technical Center, Xinghuacun Fenjiu Distillery Co. Ltd., Fenyang, Shanxi, China
| | - Yao Nie
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Du
- Technical Center, Xinghuacun Fenjiu Distillery Co. Ltd., Fenyang, Shanxi, China
| | - Yan Xu
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Ravindran B, Karmegam N, Yuvaraj A, Thangaraj R, Chang SW, Zhang Z, Kumar Awasthi M. Cleaner production of agriculturally valuable benignant materials from industry generated bio-wastes: A review. BIORESOURCE TECHNOLOGY 2021; 320:124281. [PMID: 33099155 DOI: 10.1016/j.biortech.2020.124281] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Bio-wastes from different agro-based industries are increasing at a rapid rate with the growing human population's demand for the products. The industries procure raw materials largely from agriculture, finish it with the required major product, and produce huge bio-wastes which are mostly disposed unscientifically. This creates serious environmental problems and loss of resources and nutrients. Traditional bio-wastes disposal possess several demerits which again return with negative impact over the eco-system. Anaerobic digestion, composting, co-composting, and vermicomposting are now-a-days given importance due to the improved and modified methods with enhanced transformation of bio-wastes into suitable soil amendments. The advanced and modified methods like biochar assisted composting and vermicomposting is highlighted with the updated knowledge in the field. Hence, the present study has been carried to compile the effective and efficient methods of utilizing industry generated bio-wastes for circularity between agriculture - industrial sectors to promote sustainability.
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Affiliation(s)
- Balasubramani Ravindran
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Department of Environmental Energy and Engineering, Kyonggi University, Youngtong - Gu, Suwon 16227, South Korea
| | - Natchimuthu Karmegam
- Department of Botany, Government Arts College (Autonomous), Salem 636 007, Tamil Nadu, India
| | - Ananthanarayanan Yuvaraj
- Vermitechnology and Ecotoxicology Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Ramasundaram Thangaraj
- Vermitechnology and Ecotoxicology Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem 636 011, Tamil Nadu, India
| | - S W Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong - Gu, Suwon 16227, South Korea
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, China.
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Yuvaraj A, Thangaraj R, Ravindran B, Chang SW, Karmegam N. Centrality of cattle solid wastes in vermicomposting technology - A cleaner resource recovery and biowaste recycling option for agricultural and environmental sustainability. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115688. [PMID: 33039975 DOI: 10.1016/j.envpol.2020.115688] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 05/09/2023]
Abstract
The current review reports the importance and significance of cattle solid waste in vermicomposting technology concerning biowaste pollution in the environment. Needy increasing population evokes livestock production resulting in the massive generation of livestock wastes, especially cattle dung. Improper disposal and handling of biowastes originating from agriculture, industries, forests, rural and urban areas lead to nutrient loss, environmental pollution and health risks. Among the organic waste disposal methods available, vermicomposting is regarded as an environmentally friendly technology for bioconversion of agricultural, industrial, rural and urban generated organic solid wastes which are serving as reservoirs of environmental pollution. In vermicomposting of organic wastes, cattle dung plays a central role in mineralization, nutrient recovery, earthworm and microbial activity leading to vermifertilizer production. Even though the vermicomposting studies use cattle dung invariably as an amendment material, its importance has not been reviewed to highlight its central role. Hence, the present review mainly emphasizes the key role played by cattle dung in vermicomposting. Vermiconversion of cattle dung alone and in combination with other biowaste materials of environmental concern, mechanisms involved and benefits of vermicompost in sustainable agriculture are the major objectives addressed in the present review. The analysis reveals that cattle dung is indispensable amendment material for vermicomposting technology to ensure agricultural and environmental sustainability by reducing pollution risks associated with biowastes on one hand, and nutrient-rich benign vermifertilizer production on the other hand.
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Affiliation(s)
- Ananthanarayanan Yuvaraj
- Vermitechnology and Ecotoxicology Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Ramasundaram Thangaraj
- Vermitechnology and Ecotoxicology Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Balasubramani Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong - Gu, Gyeonggi - Do, 16227, South Korea
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong - Gu, Gyeonggi - Do, 16227, South Korea
| | - Natchimuthu Karmegam
- Department of Botany, Government Arts College (Autonomous), Salem, 636 007, Tamil Nadu, India.
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Khoshnevisan B, Duan N, Tsapekos P, Awasthi MK, Liu Z, Mohammadi A, Angelidaki I, Tsang DCW, Zhang Z, Pan J, Ma L, Aghbashlo M, Tabatabaei M, Liu H. A critical review on livestock manure biorefinery technologies: Sustainability, challenges, and future perspectives. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2021; 135:110033. [DOI: 10.1016/j.rser.2020.110033] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
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Zhao Y, Li W, Chen L, Meng L, Zheng Z. Effect of enriched thermotolerant nitrifying bacteria inoculation on reducing nitrogen loss during sewage sludge composting. BIORESOURCE TECHNOLOGY 2020; 311:123461. [PMID: 32417656 DOI: 10.1016/j.biortech.2020.123461] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
In the study, enriched thermotolerant nitrifying bacteria (TNB) was acquired from compost samples by domesticated cultivation under high temperature, and was inoculated into sewage sludge composting. The effect of inoculation on physical-chemical parameters, nitrogen loss and bacterial population involved in nitrogen transformation were determined. The results revealed that inoculation with enriched TNB improved the compost quality in terms of temperature, pH, organic matter degradation, C/N ratio and germination index. Compared to the control treatment, inoculation also decreased 29.7% of ammonia emission and reduced nitrogen loss by converting more NH4+-N into NO3--N in composting. In addition, inoculation increased the population of nitrifying bacteria and was not capable of inhibiting the growth of indigenous ammonifying bacteria as well. The results suggested that inoculation with enriched TNB was a feasible way to reduce nitrogen loss and promote maturity in sewage sludge composting.
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Affiliation(s)
- Yi Zhao
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Weiguang Li
- School of Environment, Harbin Institute of Technology, Harbin 150090, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Li Chen
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Liqiang Meng
- Institute of Microbiology, Heilongjiang Academy of Science, Harbin 150010, China
| | - Zejia Zheng
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
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The Prevention of Bio-Organic Fertilizer Fermented from Cow Manure Compost by Bacillus sp. XG-1 on Watermelon Continuous Cropping Barrier. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17165714. [PMID: 32784764 PMCID: PMC7459639 DOI: 10.3390/ijerph17165714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 01/01/2023]
Abstract
The continuous cropping barrier is an important factor leading to the decline of watermelon quality and yield. In this study, we focused on a bio-organic fertilizer prepared with one bacterial strain, Bacillus sp. XG-1, to prevent the occurrence of the continuous cropping barrier. The strain XG-1 was isolated from watermelon rhizosphere soil, and promoted the growth of watermelon by producing phytase (0.19 U/mL), indole-3-acetic acid (IAA, 7.31 mg/L), and gibberellins (GA3, 2.47 mg/L). In addition, the strain also possessed a strong antagonistic effect against the pathogen Fusarium oxysporum f. sp. niveum (Fon) by inhibiting conidia germination with an inhibition ratio of 85.3% and mycelium growth. The bio-organic fertilizer fermented by XG-1, based on cow manure compost and rapeseed meal (85:15, w/w) under optimal conditions, was mixed in soil (watermelon had been planted for two consecutive years). After the cultivation of watermelon for 50 d, a higher density of XG-1 (9.79 × 105 colony-forming units (CFU)/g) and one order of magnitude lower of Fon (1.29 × 103 copies/g) were detected in the rhizosphere soil compared with soils without bio-organic fertilizer (7.59 × 104 copies/g for Fon), leading to an 86.4% control efficiency of watermelon caused by Fusarium wilt. The application of bio-organic fertilizer enriched soil nutrients, including the organic matter (13.2%), total nitrogen (13.9%), total phosphorus (20.5%), and total potassium (3.77%), adjusted the soil pH from 6.69 to 7.01, and significantly improved the watermelon growth in terms of the seedling height, root length, fresh weight of seedling and root with increase of 78.8%, 72.2%, 84.6%, and 96.4%, respectively. This study regarded the watermelon continuous cropping soil as the research point, and focused on inhibiting Fon, regulating soil properties and enhancing watermelon growth to eliminate the continuous cropping barrier through a combination of compost and functional strains, demonstrating the potential application value in watermelon production.
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Duan M, Zhang Y, Zhou B, Qin Z, Wu J, Wang Q, Yin Y. Effects of Bacillus subtilis on carbon components and microbial functional metabolism during cow manure-straw composting. BIORESOURCE TECHNOLOGY 2020; 303:122868. [PMID: 32032936 DOI: 10.1016/j.biortech.2020.122868] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/14/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
This study is the first to investigate the changes in the composting process and carbon conversion in a cow manure-straw compost matrix with Bacillus subtilis added at four different levels (0, 0.5%, 1%, and 2% w/w compost), and to explain the mechanism responsible for carbon conversion through microbial functional metabolism. Inoculation with Bacillus subtilis at 2% had the best effect on fermentation among all treatments, but it inhibited the synthesis of total organic carbon and humus. Bacillus subtilis at 0.5% reduced mineralization in the cooling and maturity stages of composting, and enhanced the humification of carbon. The total organic carbon and humic sequence contents were significantly higher with Bacillus subtilis at 0.5% (12.5% and 20.2%, respectively) than Bacillus subtilis at 2% (P < 0.05). Redundancy analysis demonstrated that the pH and microbial functional metabolism were closely related to carbon sequestration during composting.
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Affiliation(s)
- Manli Duan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Yuhua Zhang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Beibei Zhou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China.
| | - Zhenlun Qin
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Junhu Wu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Quanjiu Wang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Yanan Yin
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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