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Liu C, Wen S, Li S, Tian Y, Wang L, Zhu L, Wang J, Kim YM, Wang J. Enhanced remediation of chlorpyrifos-contaminated soil by immobilized strain Bacillus H27. J Environ Sci (China) 2024; 144:172-184. [PMID: 38802229 DOI: 10.1016/j.jes.2023.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 05/29/2024]
Abstract
Chlorpyrifos is a pesticide widely used in agricultural production with a relatively long residual half-life in soil. Addressing the problem of residual chlorpyrifos is of universal concern. In this study, rice hull biochar was used as an immobilized carrier to prepare the immobilized strain H27 for the remediation of chlorpyrifos-contamination soil. Soil microorganisms after remediation were investigated by ecotoxicological methods. The immobilized strain H27 had the highest removal rate of chlorpyrifos when 10% bacterial solution was added to the liquid medium containing 0.075-0.109 mm diameter biochar cultured for 22 hr. This study on the removal of chlorpyrifos by immobilized strain H27 showed that the initial concentration of chlorpyrifos in solution was 25 mg/L, and the removal rate reached 97.4% after 7 days of culture. In the soil, the removal rate of the immobilized bacteria group increased throughout the experiment, which was significantly higher than that of the free bacteria and biochar treatment groups. The Biolog-ECO test, T-RFLP and RT-RCR were used to study the effects of the soil microbial community and nitrogen cycling functional genes during chlorpyrifos degradation. It was found that ICP group had the highest diversity index among the four treatment groups. The microflora of segment containing 114 bp was the dominant bacterial community, and the dominant microflora of the immobilized bacteria group was more evenly distributed. The influence of each treatment group on ammonia-oxidizing bacteria (AOB) was greater than on ammonia-oxidizing archaea (AOA). This study offers a sound scientific basis for the practical application of immobilized bacteria to reduce residual soil pesticides.
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Affiliation(s)
- Changrui Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Shengfang Wen
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Shuhan Li
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Yu Tian
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Lanjun Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Lusheng Zhu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Jun Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Korea
| | - Jinhua Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China.
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Zeng Y, Zheng D, Li LP, Wang M, Gou M, Kamagata Y, Chen YT, Nobu MK, Tang YQ. Metabolism of novel potential syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats. Appl Environ Microbiol 2024; 90:e0109023. [PMID: 38259075 PMCID: PMC10880629 DOI: 10.1128/aem.01090-23] [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: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH4. In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized. In this study, the in situ activity and metabolic characteristics of potential SAOB and their interactions with methanogens were elucidated through metagenomics and metatranscriptomics. In addition to the reported SAOB classified in the genera Tepidanaerobacter, Desulfotomaculum, and Thermodesulfovibrio, we identified a number of potential SAOB that are affiliated with Clostridia, Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. The potential SAOB possessing the glycine-mediated acetate oxidation pathway dominates SAOB communities. Moreover, formate appeared to be the main product of the acetate degradation by the most active potential SAOB. We identified the methanogen partner of these potential SAOB in the acetate-fed chemostat as Methanosarcina thermophila. The dominated potential SAOB in each chemostat had similar metabolic characteristics, even though they were in different fatty-acid-fed chemostats. These novel syntrophic lineages are prevalent and may play critical roles in thermophilic methanogenic reactors. This study expands our understanding of the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders and presents novel insights into how they interact with methanogens.IMPORTANCECombining reactor operation with omics provides insights into novel uncultured syntrophic acetate degraders and how they perform in thermophilic anaerobic digesters. This improves our understanding of syntrophic acetate degradation and contributes to the background knowledge necessary to better control and optimize anaerobic digestion processes.
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Affiliation(s)
- Yan Zeng
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chengdu, Sichuan, China
| | - Dan Zheng
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Lan-Peng Li
- Sinopec (Dalian) Research Institute of Petroleum and Petrochemicals Co. Ltd., Dalian, Liaoning, China
| | - Miaoxiao Wang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ya-Ting Chen
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Masaru Konishi Nobu
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yue-Qin Tang
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chengdu, Sichuan, China
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Engineering Research Centre of Alternative Energy Materials and Devices, Ministry of Education, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorisation, Chengdu, Sichuan, China
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3
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Liu C, Zhao C, Wang L, Du X, Zhu L, Wang J, Mo Kim Y, Wang J. Biodegradation mechanism of chlorpyrifos by Bacillus sp. H27: Degradation enzymes, products, pathways and whole genome sequencing analysis. ENVIRONMENTAL RESEARCH 2023; 239:117315. [PMID: 37805180 DOI: 10.1016/j.envres.2023.117315] [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: 07/24/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Chlorpyrifos (CP) is a pesticide widely used in agricultural production. However, excessive use of CP is risky for human health and the ecological environment. Microbial remediation has become a research hotspot of environmental pollution control. In this study, the effective CP-degrading strain H27 (Bacillus cereus) was screened from farmland soil, and the degradation ratio was more than 80%. Then, the degradation mechanism was discussed in terms of enzymes, pathways, products and genes, and the mechanism was improved in terms of cell motility, secretory transport system and biofilm formation. The key CP-degrading enzymes were mainly intracellular enzymes (IE), and the degradation ratio reached 49.6% within 30 min. The optimal pH for IE was 7.0, and the optimal temperature was 25 °C. Using DFT and HPLC‒MS analysis, it was found that degradation mainly involved oxidation, hydrolysis and other reactions, and 3 degradation pathways and 14 products were identified, among which TCP (3,5,6-trichloro-2-pyridinol) was the main primary degradation product in addition to small molecules such as CO2 and H2O. Finally, the whole genome of strain H27 was sequenced, and the related degrading genes and enzymes were investigated to improve the metabolic pathways. Strain H27 had perfect genes related to flagellar assembly and chemotaxis and tended to tolerate CP. Moreover, it can secrete esterase, phosphatase and other substances, which can form biofilms and degrade CP in the environment. In addition, CP enters the cell under the action of permeases or transporters, and it is metabolized by IE. The degradation mechanism of CP by strain H27 is speculated in this study, which provided a theoretical basis for enriching CP-degrading bacteria resources, improving degradation metabolic pathways and mechanisms, and applying strain H27 to environmental pollution remediation.
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Affiliation(s)
- Changrui Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Changyu Zhao
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Lanjun Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Xiaomin Du
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Lusheng Zhu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jun Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Jinhua Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
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He K, Li W, Tang L, Li W, Lv S, Xing D. Suppressing Methane Production to Boost High-Purity Hydrogen Production in Microbial Electrolysis Cells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11931-11951. [PMID: 35969804 DOI: 10.1021/acs.est.2c02371] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hydrogen gas (H2) is an attractive fuel carrier due to its high specific enthalpy; moreover, it is a clean source of energy because in the combustion reaction with oxygen (O2) it produces water as the only byproduct. The microbial electrolysis cell (MEC) is a promising technology for producing H2 from simple or complex organics present in wastewater and solid wastes. Methanogens and non-archaeal methane (CH4)-producing microorganisms (NAMPMs) often grow in the MECs and lead to rapid conversion of produced H2 to CH4. Moreover, non-archaeal methane production (NAMP) catalyzed by nitrogenase of photosynthetic bacteria was always overlooked. Thus, suppression of CH4 production is required to enhance H2 yield and production rate. This review comprehensively addresses the principles and current state-of-the-art technologies for suppressing methanogenesis and NAMP in MECs. Noteworthy, specific strategies aimed at the inhibition of methanogenic enzymes and nitrogenase could be a more direct approach than physical and chemical strategies for repressing the growth of methanogenic archaea. In-depth studies on the multiomics of CH4 metabolism can possibly provide insights into sustainable and efficient approaches for suppressing metabolic pathways of methanogenesis and NAMP. The main objective of this review is to highlight key concepts, directions, and challenges related to boosting H2 generation by suppressing CH4 production in MECs. Finally, perspectives are briefly outlined to guide and advance the future direction of MECs for production of high-purity H2 based on genetic and metabolic engineering and on the interspecific interactions.
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Affiliation(s)
- Kuanchang He
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Wei Li
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Longxiang Tang
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Wei Li
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Sihao Lv
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Sánchez-Sánchez C, Aranda-Medina M, Rodríguez A, Hernández A, Córdoba MG, Cuadros-Blázquez F, Ruiz-Moyano S. Development of real-time PCR methods for the quantification of Methanoculleus, Methanosarcina and Methanobacterium in anaerobic digestion. J Microbiol Methods 2022; 199:106529. [PMID: 35772572 DOI: 10.1016/j.mimet.2022.106529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/27/2022]
Abstract
Anaerobic digestion is a growing technology to manage organic waste and produce bioenergy. To promote this technology, it is essential to know, at the molecular level, the dynamics of microbial communities, specifically the methanogenic community. In the present study, three primer pairs were selected from seven primer pairs which were designed and tested with different concentrations and conditions to detect Methanosarcina, Methanoculleus and Methanobacterium by real-time PCR based on the SYBR Green System. The functionality of the developed methods was demonstrated by the high linear relationship of the standard curves, and the specificity of each primer was empirically verified by testing DNA isolated from methane-producing and non-producing strains. These assays also exhibited good repeatability and reproducibility, which indicates the robustness of the methods. The described primers were successfully used to investigate the methanogenic communities of 10 samples from an anaerobic co-digestion. The genus Methanosarcina was the dominant methanogenic group.
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Affiliation(s)
- Consolación Sánchez-Sánchez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Mercedes Aranda-Medina
- Expresión Gráfica, Escuela de Ingenierías Industriales, Campus Universitario, Avda de Elvas sn, 06006 Badajoz, Spain
| | - Alicia Rodríguez
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain.
| | - Alejandro Hernández
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - María G Córdoba
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - Francisco Cuadros-Blázquez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Santiago Ruiz-Moyano
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
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6
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Thanarasu A, Periyasamy K, Subramanian S. An integrated anaerobic digestion and microbial electrolysis system for the enhancement of methane production from organic waste: Fundamentals, innovative design and scale-up deliberation. CHEMOSPHERE 2022; 287:131886. [PMID: 34523450 DOI: 10.1016/j.chemosphere.2021.131886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/19/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
In the foreseeable future, renewable energy generation from electromethanogenesis to be more cost-effective energy. Electromethanogenesis system is a recent and efficient CO2 to methane technology to upgrade biogas to 100% methane for power generation. And this can be attained through by integrating anaerobic digestion with microbial electrolysis system. Microbial electrolysis system can able to support carbon reduction on cathode and oxidation on anode by CO2 capture thereby provides more CH4 production from an integrated anaerobic digestion system. Scale-up the recent advance technique of microbial electrolysis system in the anaerobic digestion process for 100% methane production for power generation is need of the hour. The overall objective of this review is to facilitate the recent technology of microbial electrolysis system in the anaerobic digestion process. At first, the function of electromethanogenesis system and innovative integrated design method are outlined. Secondly, different external parameters such as applied voltage, operating temperature, pH etc are examined for the significance on process optimization. Eventually, electrode selections, electrode spacing, surface chemistry and surface area are critically reviewed for the scale-up considerations of integration process.
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Affiliation(s)
- Amudha Thanarasu
- Department of Applied Science & Technology, AC Tech Campus, Anna University, Chennai, India
| | - Karthik Periyasamy
- Department of Applied Science & Technology, AC Tech Campus, Anna University, Chennai, India
| | - Sivanesan Subramanian
- Department of Applied Science & Technology, AC Tech Campus, Anna University, Chennai, India.
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Fernández-Palacios E, Zhou X, Mora M, Gabriel D. Microbial Diversity Dynamics in a Methanogenic-Sulfidogenic UASB Reactor. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18031305. [PMID: 33535604 PMCID: PMC7908407 DOI: 10.3390/ijerph18031305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 11/16/2022]
Abstract
In this study, the long-term performance and microbial dynamics of an Upflow Anaerobic Sludge Blanket (UASB) reactor targeting sulfate reduction in a SOx emissions treatment system were assessed using crude glycerol as organic carbon source and electron donor under constant S and C loading rates. The reactor was inoculated with granular sludge obtained from a pulp and paper industry and fed at a constant inlet sulfate concentration of 250 mg S-SO42−L−1 and a constant C/S ratio of 1.5 ± 0.3 g Cg−1 S for over 500 days. Apart from the regular analysis of chemical species, Illumina analyses of the 16S rRNA gene were used to study the dynamics of the bacterial community along with the whole operation. The reactor was sampled along the operation to monitor its diversity and the changes in targeted species to gain insight into the performance of the sulfidogenic UASB. Moreover, studies on the stratification of the sludge bed were performed by sampling at different reactor heights. Shifts in the UASB performance correlated well with the main shifts in microbial communities of interest. A progressive loss of the methanogenic capacity towards a fully sulfidogenic UASB was explained by a progressive wash-out of methanogenic Archaea, which were outcompeted by sulfate-reducing bacteria. Desulfovibrio was found as the main sulfate-reducing genus in the reactor along time. A progressive reduction in the sulfidogenic capacity of the UASB was found in the long run due to the accumulation of a slime-like substance in the UASB.
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Shamurad B, Gray N, Petropoulos E, Dolfing J, Quintela-Baluja M, Bashiri R, Tabraiz S, Sallis P. Low-Temperature Pretreatment of Organic Feedstocks with Selected Mineral Wastes Sustains Anaerobic Digestion Stability through Trace Metal Release. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9095-9105. [PMID: 32551555 DOI: 10.1021/acs.est.0c01732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A low-cost approach for enhancing mesophilic (37 °C) anaerobic digestion (AD) of organic waste using a low-temperature (37 °C) pretreatment with different mineral wastes (MW) was investigated. A higher and stable methane production rate, in comparison to MW-free controls, was achieved for 80 days at organic loading rates of 1-2 g VS/L·d, using a feed substrate pretreated with incinerator bottom ash (IBA). The boiler ash and cement-based waste pretreatments also produced high methane production rates but with some process instability. In contrast, an incinerator fly ash pretreatment showed a progressive decrease in methane production rates and poor process stability, leading to reactor failure after 40 days. To avoid process instability and/or reactor failure, two metrics had to be met: (a) a methanogenesis to fermentation ratio higher than 0.6 and (b) a cell-specific methanogenic activity to cell-specific fermentation activity ratio of >1000. The prevalence of Methanofastidiosum together with a mixed community of acetoclastic (Methanosaeta) and hydrogenotrophic (Methanobacterium) methanogens in the stable IBA treatment indicated the importance of Methanofastidiosum as a potential indicator of a healthy and stable reactor.
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Affiliation(s)
- Burhan Shamurad
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Neil Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | | | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | | | - Reihaneh Bashiri
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Shamas Tabraiz
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Paul Sallis
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
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Chen YT, Zeng Y, Wang HZ, Zheng D, Kamagata Y, Narihiro T, Nobu MK, Tang YQ. Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats. MICROBIAL ECOLOGY 2020; 80:120-132. [PMID: 31982930 DOI: 10.1007/s00248-020-01485-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Propionate is one of the major intermediates in anaerobic digestion of organic waste to CO2 and CH4. In methanogenic environments, propionate is degraded through a mutualistic interaction between symbiotic propionate oxidizers and methanogens. Although temperature heavily influences the microbial ecology and performance of methanogenic processes, its effect on syntrophic interaction during propionate degradation remains poorly understood. In this study, metagenomics and metatranscriptomics were employed to compare mesophilic and thermophilic propionate degradation communities. Mesophilic propionate degradation involved multiple syntrophic organisms (Syntrophobacter, Smithella, and Syntrophomonas), pathways, interactions, and preference toward formate-based electron transfer to methanogenic partners (i.e., Methanoculleus). In thermophilic propionate degradation, one syntrophic organism predominated (Pelotomaculum), interspecies H2 transfer played a major role, and phylogenetically and metabolically diverse H2-oxidizing methanogens were present (i.e., Methanoculleus, Methanothermobacter, and Methanomassiliicoccus). This study showed that microbial interactions, metabolic pathways, and niche diversity are distinct between mesophilic and thermophilic microbial communities responsible for syntrophic propionate degradation.
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Affiliation(s)
- Ya-Ting Chen
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yan Zeng
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Dan Zheng
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Masaru Konishi Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
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Wang HZ, Li J, Yi Y, Nobu MK, Narihiro T, Tang YQ. Response to inhibitory conditions of acetate-degrading methanogenic microbial community. J Biosci Bioeng 2020; 129:476-485. [DOI: 10.1016/j.jbiosc.2019.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/23/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022]
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11
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Acclimation Improves Methane Production from Molasses Wastewater with High Salinity in an Upflow Anaerobic Filter Reactor: Performance and Microbial Community Dynamics. Appl Biochem Biotechnol 2020; 191:397-411. [DOI: 10.1007/s12010-020-03236-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/08/2020] [Indexed: 11/26/2022]
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12
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Yi Y, Wang H, Chen Y, Gou M, Xia Z, Hu B, Nie Y, Tang Y. Identification of Novel Butyrate- and Acetate-Oxidizing Bacteria in Butyrate-Fed Mesophilic Anaerobic Chemostats by DNA-Based Stable Isotope Probing. MICROBIAL ECOLOGY 2020; 79:285-298. [PMID: 31263981 DOI: 10.1007/s00248-019-01400-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results showed that, in addition to known SBOB, Syntrophomonas, other species of unclassified Syntrophomonadaceae were putative butyrate-oxidizing bacteria. Species of Mesotoga, Aminivibrio, Acetivibrio, Desulfovibrio, Petrimonas, Sedimentibacter, unclassified Anaerolineae, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria may contribute to acetate oxidation from butyrate metabolism. Among them, the ability of butyrate oxidation was unclear for species of Sedimentibacter, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria. These results suggested that more unknown species participated in the degradation of butyrate. However, the corresponding function and pathway for butyrate or acetate oxidization of these labeled species need to be further investigated.
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Affiliation(s)
- Yue Yi
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - HuiZhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - YaTing Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-The Hong Kong Polytechnic University, No. 122 Huanghe Middle Road Section 1, Shuangliu District, Chengdu, 610027, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
| | - ZiYuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bin Hu
- College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
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Li J, Wang HZ, Yi Y, Gou M, Nobu MK, Chen YT, Tang YQ. Response of Isovalerate-Degrading Methanogenic Microbial Community to Inhibitors. Appl Biochem Biotechnol 2020; 191:1010-1026. [PMID: 31950447 DOI: 10.1007/s12010-020-03234-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/08/2020] [Indexed: 10/25/2022]
Abstract
Isovalerate is one of the key intermediates during anaerobic digestion treating protein-containing waste/wastewater. Investigating the effect of different kinds of inhibitors on isovalerate-degrading microbial community is necessary to develop measures for improving the effectiveness of the treatment plants. In the present study, dynamic changes in the isovalerate-degrading microbial community in presence of inhibitors (ammonium, sulfide, mixed ammonium and sulfide, and chlortetracycline (CTC)) were investigated using high-throughput sequencing of 16S rRNA gene. Our observations showed that the isovalerate-degrading microbial community responded differently to different inhibitors and that the isovalerate degradation and gas production were strongly repressed by each inhibitor. We found that sulfide inhibited both isovalerate oxidation followed by methanogenesis, while ammonium, mixed ammonium and sulfide, and CTC mainly inhibited isovalerate oxidation. Genera classified into Proteobacteria and Chloroflexi were less sensitive to inhibitors. The two dominant genera, which are potential syntrophic isovalerate oxidizers, exhibited different responses to inhibitors that the unclassified_Peptococcaceae_3 was more sensitive to inhibitors than the unclassified_Syntrophaceae. Upon comparison to acetoclastic methanogen Methanosaeta, hydrogenotrophic methanogens Methanoculleus and Methanobacterium were less sensitive to inhibitors.
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Affiliation(s)
- Jie Li
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yue Yi
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Masaru Konishi Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Ya-Ting Chen
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
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14
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Gou M, Wang H, Li J, Sun Z, Nie Y, Nobu MK, Tang Y. Different inhibitory mechanisms of chlortetracycline and enrofloxacin on mesophilic anaerobic degradation of propionate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1406-1416. [PMID: 31745805 DOI: 10.1007/s11356-019-06705-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
In anaerobic digestion, propionate is a key intermediate whose degradation is thermodynamically challenging and accumulation is detrimental to the process. Many wastewater streams contain antibiotics due to its globally increasing use, and these compounds can inhibit methane production. However, the effect of antibiotics on propionate degradation in anaerobic digestion remains unclear. In this study, the influence of two antibiotics (chlortetracycline [CTC] and enrofloxacin [EFX]) on biogas production and mesophilic propionate-degrading microbial community was investigated. CTC strongly repressed propionate oxidation, acetate utilization, and methane production, while EFX only inhibited propionate oxidation and methane production to a lesser extent. Microbial community analyses showed that syntrophic propionate-oxidizing bacteria (SPOB) Syntrophobacter had strong tolerance to both CTC and EFX. CTC inhibition mainly acted on the activity of acetate-oxidizing bacteria (Mesotoga, Geovibrio, Tepidanaerobacter, unclassified Bacteroidetes, and unclassified Clostridia) and acetoclastic methanogen, while EFX inhibition applied to the SPOB Smithella and acetoclastic methanogen. Network analysis further indicated that more complicated correlation among bacterial genera occurred in CTC treatments. These results suggested that CTC and EFX inhibited propionate degradation via different mechanisms, which was the result of joint action by antibiotics and microbial interactions.
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Affiliation(s)
- Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - HuiZhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Jie Li
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - ZhaoYong Sun
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yong Nie
- College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - Masaru Konishi Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
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15
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Identification of novel potential acetate-oxidizing bacteria in thermophilic methanogenic chemostats by DNA stable isotope probing. Appl Microbiol Biotechnol 2019; 103:8631-8645. [DOI: 10.1007/s00253-019-10078-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/30/2019] [Accepted: 07/31/2019] [Indexed: 01/04/2023]
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16
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Wang HZ, Yan YC, Gou M, Yi Y, Xia ZY, Nobu MK, Narihiro T, Tang YQ. Response of Propionate-Degrading Methanogenic Microbial Communities to Inhibitory Conditions. Appl Biochem Biotechnol 2019; 189:233-248. [PMID: 30972704 DOI: 10.1007/s12010-019-03005-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
Propionate is a crucial intermediate during methane fermentation. Investigating the effects of different kinds of inhibitors on the propionate-degrading microbial community is necessary to develop countermeasures for improving process stability. In the present study, under inhibitory conditions (acetate, propionate, sulfide, and ammonium addition), the dynamic changes of the propionate-degrading microbial community from a mesophilic chemostat fed with propionate as the sole carbon source were investigated using high-throughput sequencing of 16S rRNA. Sulfide and/or ammonia inhibited specific species in the microbial community. Compared with Syntrophobacter, Smithella was more resistant to inhibition by sulfide and/or ammonia. However, Syntrophobacter demonstrated greater tolerance than Smithella under acid inhibition conditions. Some genera that had close phylogenetic relationships and similar functions showed similar responses to different inhibitors.
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Affiliation(s)
- Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Ying-Chun Yan
- Institute of New Energy and Low-Carbon Technology, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yue Yi
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
- Institute of New Energy and Low-Carbon Technology, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
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17
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Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities. Microorganisms 2018; 6:microorganisms6040103. [PMID: 30287755 PMCID: PMC6313629 DOI: 10.3390/microorganisms6040103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/29/2018] [Indexed: 12/19/2022] Open
Abstract
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived from engineered algae. The microbial community structure was measured on the single cell level using flow cytometry. Abiotic and operational reactor parameters were analyzed in parallel. The R-based tool flowCyBar facilitated visualization of community dynamics and indicated sub-communities involved in glycolate fermentation and methanogenesis. Cell sorting and amplicon sequencing of 16S rRNA and mcrA genes were used to identify the key organisms involved in the anaerobic conversion process. The microbial community allowed a constant fermentation, although it was sensitive to high glycolate concentrations in the feed. A linear correlation between glycolate loading rate and biogas amount was observed (R2 = 0.99) for glycolate loading rates up to 1.81 g L−1 day−1 with a maximum in biogas amount of 3635 mL day−1 encompassing 45% methane. The cytometric diversity remained high during the whole cultivation period. The dominating bacterial genera were Syntrophobotulus, Clostridia genus B55_F, Aminobacterium, and Petrimonas. Methanogenesis was almost exclusively performed by the hydrogenotrophic genus Methanobacterium.
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18
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Wang HZ, Gou M, Yi Y, Xia ZY, Tang YQ. Identification of novel potential acetate-oxidizing bacteria in an acetate-fed methanogenic chemostat based on DNA stable isotope probing. J GEN APPL MICROBIOL 2018; 64:221-231. [DOI: 10.2323/jgam.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University
| | - Min Gou
- College of Architecture and Environment, Sichuan University
| | - Yue Yi
- College of Architecture and Environment, Sichuan University
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University
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19
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Zhang Q, Yuan Y, Liao Z, Zhang W. Use of microbial indicators combined with environmental factors coupled with metrology tools for discrimination and classification ofLuzhou-flavoured pit muds. J Appl Microbiol 2017; 123:933-943. [DOI: 10.1111/jam.13544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/22/2017] [Accepted: 07/12/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Q.Y. Zhang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu Sichuan China
| | - Y.J. Yuan
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu Sichuan China
| | - Z.M. Liao
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu Sichuan China
| | - W.X. Zhang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu Sichuan China
- School of Liquor-Making Engineering; Sichuan University; Jinjiang College; Meishan Sichuan China
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20
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Biogas Production from Distilled Grain Waste by Thermophilic Dry Anaerobic Digestion: Pretreatment of Feedstock and Dynamics of Microbial Community. Appl Biochem Biotechnol 2017; 184:685-702. [DOI: 10.1007/s12010-017-2557-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/13/2017] [Indexed: 11/26/2022]
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21
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Assessment of hydrogen metabolism in commercial anaerobic digesters. Appl Microbiol Biotechnol 2016; 100:4699-710. [DOI: 10.1007/s00253-016-7436-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 01/13/2023]
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22
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Volume ratios between the thermophilic and the mesophilic digesters of a temperature-phased anaerobic digestion system affect their performance and microbial communities. N Biotechnol 2016; 33:245-54. [DOI: 10.1016/j.nbt.2015.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/24/2015] [Accepted: 07/16/2015] [Indexed: 11/20/2022]
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23
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Freetly HC, Lindholm-Perry AK, Hales KE, Brown-Brandl TM, Kim M, Myer PR, Wells JE. Methane production and methanogen levels in steers that differ in residual gain123. J Anim Sci 2015; 93:2375-81. [DOI: 10.2527/jas.2014-8721] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- H. C. Freetly
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
| | | | - K. E. Hales
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
| | | | - M. Kim
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - P. R. Myer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - J. E. Wells
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
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24
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Dynamics of the microbial community during continuous methane fermentation in continuously stirred tank reactors. J Biosci Bioeng 2015; 119:375-83. [DOI: 10.1016/j.jbiosc.2014.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 09/03/2014] [Accepted: 09/16/2014] [Indexed: 11/20/2022]
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25
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Primers: Functional Genes and 16S rRNA Genes for Methanogens. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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26
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Effect of sulfate addition on methane production and sulfate reduction in a mesophilic acetate-fed anaerobic reactor. Appl Microbiol Biotechnol 2014; 99:3269-77. [DOI: 10.1007/s00253-014-6235-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
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27
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Luo Q, Liu C, Wu Z, Wang H, Li W, Zhang K, Huang D, Zhang J, Zhang W. Monitoring of the prokaryotic diversity in pit mud from aLuzhou-flavourliquor distillery and evaluation of two predominant archaea using qPCR assays. JOURNAL OF THE INSTITUTE OF BREWING 2014. [DOI: 10.1002/jib.132] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qingchun Luo
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Chaolan Liu
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Zhengyun Wu
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Haiying Wang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Wenfang Li
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Kaizheng Zhang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
- College of Bioengineering; University of Sichuan Science and Engineering; Zigong 643000 China
| | - Dan Huang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Jing Zhang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
| | - Wenxue Zhang
- College of Light Industry; Textile and Food Engineering; Sichuan University; Chengdu 610065 China
- School of Liquor-Making Engineering; Sichuan University Jinjiang College; Meishan 620860 China
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28
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Li YF, Chen PH, Yu Z. Spatial and temporal variations of microbial community in a mixed plug-flow loop reactor fed with dairy manure. Microb Biotechnol 2014; 7:332-46. [PMID: 24690147 PMCID: PMC4241726 DOI: 10.1111/1751-7915.12125] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/02/2014] [Indexed: 02/01/2023] Open
Abstract
Mixed plug-flow loop reactor (MPFLR) has been widely adopted by the US dairy farms to convert cattle manure to biogas. However, the microbiome in MPFLR digesters remains unexplored. In this study, the microbiome in a MPFLR digester operated on a mega-dairy farm was examined thrice over a 2 month period. Within 23 days of retention time, 55-70% of total manure solid was digested. Except for a few minor volatile fatty acids (VFAs), total VFA concentration and pH remained similar along the course of the digester and over time. Metagenomic analysis showed that although with some temporal variations, the bacterial community was rather stable spatially in the digester. The methanogenic community was also stable both spatially and temporally in the digester. Among methanogens, genus Methanosaeta dominated in the digester. Quantitative polymerase chain reaction (qPCR) analysis and metagenomic analysis yielded different relative abundance of individual genera of methanogens, especially for Methanobacterium, which was predominant based on qPCR analysis but undetectable by metagenomics. Collectively, the results showed that only small microbial and chemical gradients existed within the digester, and the digestion process occurred similarly throughout the MPFLR digester. The findings of this study may help improve the operation and design of this type of manure digesters.
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Affiliation(s)
- Yueh-Fen Li
- Environmental Science Graduate Program, The Ohio State University, Columbus, OH, USA
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29
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Yilmaz V, Ince-Yilmaz E, Yilmazel YD, Duran M. Is aceticlastic methanogen composition in full-scale anaerobic processes related to acetate utilization capacity? Appl Microbiol Biotechnol 2014; 98:5217-26. [DOI: 10.1007/s00253-014-5597-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/24/2014] [Accepted: 02/04/2014] [Indexed: 11/24/2022]
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30
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Chen S, Zhu Z, Park J, Zhang Z, He Q. Development of Methanoculleus-specific real-time quantitative PCR assay for assessing methanogen communities in anaerobic digestion. J Appl Microbiol 2014; 116:1474-81. [PMID: 24521054 DOI: 10.1111/jam.12471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 12/08/2013] [Accepted: 02/03/2014] [Indexed: 12/01/2022]
Abstract
AIM To develop a Methanoculleus-specific real-time quantitative PCR (RT-qPCR) assay with high coverage and specificity for the analysis of methanogenic populations in anaerobic digestion. METHODS AND RESULTS A Methanoculleus-specific primer/probe set for RT-qPCR was designed in this study based on all Methanoculleus 16S rRNA gene sequences in Ribosomal Database Project (RDP) according to TaqMan chemistry. The newly designed primer/probe set was shown to have high coverage and specificity by both in silico and experimental analyses. Amplification efficiency of the Methanoculleus-specific primer/probe set was determined to be ideal for RT-qPCR applications. Subsequent field testing on anaerobic digesters showed that results from RT-qPCR were consistent with those from clone library analysis, validating the accuracy of the RT-qPCR assay. CONCLUSIONS The Methanoculleus-specific RT-qPCR assay designed in this study can serve as a rapid and effective tool for the quantification of Methanoculleus populations in anaerobic digestion. SIGNIFICANCE AND IMPACT OF THE STUDY Methanoculleus populations represent important members of archaeal communities in methanogenic processes, necessitating the need to develop effective tools to monitor Methanoculleus population abundance. The RT-qPCR developed in this study provides an essential tool for the quantification of Methanoculleus populations in anaerobic digestion and for the understanding of the functions of these methanogens in anaerobic biotransformation.
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Affiliation(s)
- S Chen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA
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31
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Microbial ecology of anaerobic digesters: the key players of anaerobiosis. ScientificWorldJournal 2014; 2014:183752. [PMID: 24701142 PMCID: PMC3950365 DOI: 10.1155/2014/183752] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 12/10/2013] [Indexed: 11/17/2022] Open
Abstract
Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.
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32
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A pilot scale two-stage anaerobic digester treating food waste leachate (FWL): Performance and microbial structure analysis using pyrosequencing. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.10.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kobayashi T, Tang Y, Urakami T, Morimura S, Kida K. Digestion performance and microbial community in full-scale methane fermentation of stillage from sweet potato-shochu production. J Environ Sci (China) 2014; 26:423-431. [PMID: 25076534 DOI: 10.1016/s1001-0742(13)60423-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Sweet potato shochu is a traditional Japanese spirit produced mainly in the South Kyushu area in Japan. The amount of stillage reaches approximately 8 x 10(5) tons per year. Wastewater mainly containing stillage from the production of sweet potato-shochu was treated thermophilically in a full-scale treatment plant using fixed-bed reactors (8 reactors x 283 m3). Following the addition of Ni2+ and Co2+, the reactors have been stably operated for six years at a high chemical oxygen demand (COD) loading rate of 14 kg/(m3 x day). Analysis of coenzyme content and microbial communities indicated that similar microbial communities were present in the liquid phase and on the fiber carriers installed in reactors. Bacteria in the phyla Firmicutes as well as Bacteroidetes were dominant bacteria, and Methanosarcina thermophila as well as Methanothermobacter crinale were dominant methanogens in the reactors. This study reveals that stillage from sweet potato-shochu production can be treated effectively in a full-scale fixed-bed reactor under thermophilic conditions with the help of Ni2+ and Co2+. The high diversity of bacterial community and the coexistence of both aceticlastic and hydrogenotrophic methanogens contributed to the excellent fermentation performance.
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Characterization of persistent virus-like particles in two acetate-fed methanogenic reactors. PLoS One 2013; 8:e81040. [PMID: 24278372 PMCID: PMC3838374 DOI: 10.1371/journal.pone.0081040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/18/2013] [Indexed: 11/26/2022] Open
Abstract
The objective of this study was to characterize the morphology, size-distribution, concentration and genome size of virus-like particles (VLPs) in two acetate-fed Methanosaeta-dominated reactors to better understand the possible correlation between viruses and archaeal hosts. The study reactors were dominated by a single genus of acetoclastic methanogen, Methanosaeta, which was present at 6 to 13 times higher than the combined bacterial populations consisting of Proteobacteria, Firmicutes, and Bacteroidetes. Epifluorescent microscopy showed VLPs concentration of 7.1 ± 1.5×107 VLPs/ml and 8.4 ± 4.3×107 VLPs/ml in the two laboratory reactors. Observations of no detectable import of VLPs with the reactor feed combined long operational time since the last inocula were introduced suggests that the VLP populations were actively propagating in the reactors. Transmission electron microscopy images showed VLPs with morphology consistent with Siphoviridae in both reactors, and VLPs with morphologies consistent with Myoviridae in one of the reactors. The morphology, size-distribution and genome size of VLPs were distinct between reactors suggesting that unique viral populations inhabited each reactor, though the hosts of these VLPs remain unclear.
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Lv W, Zhang W, Yu Z. Evaluation of system performances and microbial communities of two temperature-phased anaerobic digestion systems treating dairy manure. BIORESOURCE TECHNOLOGY 2013; 143:431-438. [PMID: 23819980 DOI: 10.1016/j.biortech.2013.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/03/2013] [Accepted: 06/05/2013] [Indexed: 06/02/2023]
Abstract
Two temperature-phased anaerobic digestion (TPAD) systems, with the thermophilic digesters acidified by acidogenesis products (AT-TPAD) or operated at neutral pH and balanced hydrolysis/acidogenesis and methanogenesis (NT-TPAD), were evaluated to treat high-strength dairy cattle manure. Despite similar methane productions (about 0.22 L/g VS fed), the NT-TPAD system removed significantly more VS (36%) than the AT-TPAD system (31%) and needed no pH adjustments. The thermophilic digester of the NT-TPAD system dominated the system performance and performed significantly better than that of the AT-TPAD system. The opposite held true for the mesophilic digesters. Differences of the thermophilic digesters between two TPAD systems affected the microbial communities of both local and downstream digesters. Each digester harbored distinctive microbial populations, some of which were significantly correlated with system performance. Methanosarcina was the most important methanogenic genus in both TPAD systems, while Methanosaeta only in the NT-TPAD system. Their populations were inversely related to VFA concentrations.
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Affiliation(s)
- Wen Lv
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
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Primer evaluation and adaption for cost-efficient SYBR Green-based qPCR and its applicability for specific quantification of methanogens. World J Microbiol Biotechnol 2013; 30:293-304. [PMID: 23918633 DOI: 10.1007/s11274-013-1450-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022]
Abstract
In the present study nine promising primer sets, targeting Archaea and methanogenic Archaea in particular, were evaluated in silico, in vitro and in situ concerning specificity, accuracy and applicability in end-point (ep-) and especially quantitative (q-)PCR research. The main goal was to adapt and evaluate already adapted primer sets, which were partially designed in combination with TaqMan probes, in substantially cheaper SYBR Green-based qPCR applications. An initial 16S rRNA gene bank-based in silico evaluation revealed high coverage potentials for all primers within targeted groups, ranging from 71 to 90%, except the Methanosaeta specific set showing a low potential of 37%. Mentionable cross-reacting potentials could be detected for the Methanothermobacter, Methanomicrobiales and Methanoculleus sets. The in vitro evaluation with selected reference organisms revealed a specific behavior for most primer sets, while the Methanosarcina and Methanothermobacter sets showed most problematic cross-reactions in epPCR application. We were able to show that primers for detecting the total archaeal community, methanogenic orders Methanosarcinales, Methanobacteriales, Methanococcales and the genus Methanoculleus performed in a highly specific way and allowed an accurate quantification of targeted organisms without the use of expensive TaqMan probes. However, primer pairs designed for detecting Methanomicrobiales, Methanothermobacter, Methanosarcina and Methanosaeta are not suitable for SYBR Green applications. The reliability of in situ quantifications was assessed for a typical methanogenic community, derived from a thermophilic fermenter, and confirmed via denaturing gradient gel band quantification and sequencing. Thereby, we revealed high abundances of methanogenic Archaea, mainly comprising Methanoculleus and Methanosarcinales, while Methanobacteriales only formed a minor fraction.
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Lv W, Zhang W, Yu Z. Evaluation of system performance and microbial communities of a temperature-phased anaerobic digestion system treating dairy manure: thermophilic digester operated at acidic pH. BIORESOURCE TECHNOLOGY 2013; 142:625-632. [PMID: 23771002 DOI: 10.1016/j.biortech.2013.05.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 06/02/2023]
Abstract
A temperature-phased anaerobic digestion system with the thermophilic digester acidified by acidogenesis products (referred to as AT-TPAD) was evaluated to treat high-strength dairy cattle manure at a 15-day retention time. Three temperatures (50, 55, and 60°C) were tested on the thermophilic digester, and 50°C was found to be the optimal temperature for overall performance of the AT-TPAD system, achieving 31% VS removal and 0.22 L methane/g VS fed. The mesophilic digester contributed significantly more to the overall system performance than the thermophilic digester. The thermophilic and the mesophilic digesters had different microbial communities under all conditions, and both microbial communities exhibited dynamic changes in response to different conditions. Certain microbial groups were found significantly correlated with the system performance. Methanosarcina was the most important methanogen genus of the AT-TPAD system and its population abundance was inversely correlated with high concentrations of volatile fatty acids (VFA).
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Affiliation(s)
- Wen Lv
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, United States
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Demirer SU, Taskin B, Demirer GN, Duran M. The effect of managing nutrients in the performance of anaerobic digesters of municipal wastewater treatment plants. Appl Microbiol Biotechnol 2012; 97:7899-907. [DOI: 10.1007/s00253-012-4499-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 11/30/2022]
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Anditalea andensis gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from extreme alkali–saline soil. Antonie van Leeuwenhoek 2012; 102:703-10. [DOI: 10.1007/s10482-012-9770-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 06/21/2012] [Indexed: 11/26/2022]
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40
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De Vrieze J, Hennebel T, Boon N, Verstraete W. Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. BIORESOURCE TECHNOLOGY 2012; 112:1-9. [PMID: 22418081 DOI: 10.1016/j.biortech.2012.02.079] [Citation(s) in RCA: 448] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 05/07/2023]
Abstract
Anaerobic digestion is an important technology in the framework of renewable energy production. The anaerobic digestion system is susceptible to perturbations due to the sensitivity of the methanogens towards environmental factors. Currently, technology is evolving from conventional waste treatment, i.e. the removal of pollutants, to very intensive biogas production from concentrated wastes, in the framework of bio-energy production. In the latter configuration Methanosarcina species appear to be of crucial importance. Methanosarcina sp. are, compared to other methanogens, quite robust towards different impairments. They are reported to be tolerant to total ammonium concentrations up to 7000 mg L(-1), salt concentrations up to 18,000 mg Na(+)L(-1), a pH shock of 0.8-1.0 units and acetate concentrations up to 15,000 mg CODL(-1). The possibilities of Methanosarcina sp. as key organisms in specific types of anaerobic digestion systems are demonstrated in this review.
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Affiliation(s)
- Jo De Vrieze
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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41
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Narihiro T, Sekiguchi Y. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea. Microb Biotechnol 2011; 4:585-602. [PMID: 21375721 PMCID: PMC3819009 DOI: 10.1111/j.1751-7915.2010.00239.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 11/12/2010] [Indexed: 11/28/2022] Open
Abstract
For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.
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Affiliation(s)
- Takashi Narihiro
- International Patent Organism Depositary (IPOD), Tsukuba, Ibaraki 305‐8566, Japan
| | - Yuji Sekiguchi
- Bio‐medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305‐8566, Japan
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Zhang J, Wei Y, Xiao W, Zhou Z, Yan X. Performance and spatial community succession of an anaerobic baffled reactor treating acetone-butanol-ethanol fermentation wastewater. BIORESOURCE TECHNOLOGY 2011; 102:7407-7414. [PMID: 21664129 DOI: 10.1016/j.biortech.2011.05.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 05/10/2011] [Accepted: 05/10/2011] [Indexed: 05/30/2023]
Abstract
An anaerobic baffled reactor with four compartments (C1-C4) was successfully used for treatment of acetone-butanol-ethanol fermentation wastewater and methane production. The chemical oxygen demand (COD) removal efficiency was 88.2% with a CH(4) yield of 0.25L/(g COD(removed)) when organic loading rate (OLR) was 5.4kg CODm(-3)d(-1). C1 played the most important role in solvents (acetone, butanol and ethanol) and COD removal. Community structure of C2 was similar to that in C1 at stage 3 with higher OLR, but was similar to those in C3 and C4 at stages 1-2 with lower OLR. This community variation in C2 was consistent with its increased role in COD and solvent removal at stage 3. During community succession from C1 to C4 at stage 3, abundance of Firmicutes (especially OTUs ABRB07 and ABRB10) and Methanoculleus decreased, while Bacteroidetes and Methanocorpusculum became dominant. Thus, ABRB07 coupled with Methanoculleus and/or acetogen (ABRB10) may be key species for solvents degradation.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd., Shanghai 200032, China
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43
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Feng XM, Karlsson A, Svensson BH, Bertilsson S. Impact of trace element addition on biogas production from food industrial waste - linking process to microbial communities. FEMS Microbiol Ecol 2010; 74:226-40. [DOI: 10.1111/j.1574-6941.2010.00932.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Kovacik WP, Scholten JCM, Culley D, Hickey R, Zhang W, Brockman FJ. Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed. Microbiology (Reading) 2010; 156:2418-2427. [DOI: 10.1099/mic.0.036715-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The upflow anaerobic sludge blanket (UASB) reactor is a microcosm for the methanogenic degradation of organic matter in anaerobic environments, and depends on the auto-formation of dense 3D biofilms of 1–3 mm in diameter, referred to as granular sludge (biogranules). Past research has shown that UASB and other methanogenic reactors are extremely stable functionally, but the underlying basis of the functional stability is not well understood. In this study, microbial dynamics in the communities residing in UASB biogranules were analysed to determine responses to short-term perturbations (change in reactor feed). The reactor was fed with simulated brewery wastewater (SBWW) for 1.5 months (phase 1), acetate/sulfate for 2 months (phase 2), acetate alone for 3 months (phase 3) and then a return to SBWW for 2 months (phase 4). Analysis of 16S rRNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB gene-based-clone libraries showed a relatively simple community composed mainly of the methanogenic archaea (Methanobacterium and Methanosaeta), members of the green non-sulfur (Chloroflexi) group of bacteria and Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related bacterial sequences. The mcrA clone libraries were dominated throughout by Methanobacterium- and Methanospirillum-related sequences. Although the reactor performance remained relatively stable throughout the experiment, community diversity levels generally decreased for all libraries in response to a change from SBWW to acetate alone feed. There was a large transitory increase noted in 16S diversity at the 2 month sampling on acetate alone, entirely related to an increase in bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels. Our results demonstrated that microbial communities, even highly structured ones such as in UASB biogranules, are very capable of responding to rapid and major changes in their environment.
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Affiliation(s)
- William P. Kovacik
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - David Culley
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Weiwen Zhang
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Fred J. Brockman
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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Adaptation of methanogenic communities to the cofermentation of cattle excreta and olive mill wastes at 37 degrees C and 55 degrees C. Appl Environ Microbiol 2010; 76:6564-71. [PMID: 20675446 DOI: 10.1128/aem.00961-10] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The acclimatization of methanogens to two-phase olive mill wastes (TPOMW) was investigated in pilot fermenters started up with cattle excreta (37°C) and after changing their feed to excreta plus TPOMW (37°C or 55°C) or TPOMW alone (37°C) until a steady state was reached (28 days). Methanogenic diversity was screened using a phylogenetic microarray (AnaeroChip), and positive targets were quantified by real-time PCR. Results revealed high phylogenetic richness, with representatives of three out of the four taxonomic orders found in digesters. Methanosarcina dominated in the starting excreta (>96% of total 16S rRNA gene copies; over 45 times more abundant than any other methanogen) at high acetate (0.21 g liter(-1)) and ammonia N concentrations (1.3 g liter(-1)). Codigestion at 37°C induced a 6-fold increase of Methanosarcina numbers, correlated with CH(4) production (r(Pearson) = 0.94; P = 0.02). At 55°C, the rise in temperature and H(2) partial pressure induced a burst of Methanobacterium, Methanoculleus, Methanothermobacter, and a group of uncultured archaea. The digestion of excreta alone resulted in low but constant biogas production despite certain oscillations in the methanogenic biomass. Unsuccessful digestion of TPOMW alone was attributed to high Cu levels inducing inhibition of methanogenic activity. In conclusion, the versatile Methanosarcina immediately adapted to the shift from excreta to excreta plus TPOMW and was responsible for the stimulated CH(4) production at 37°C. Higher temperatures (55°C) fostered methanogenic diversity by promoting some H(2) scavengers while yielding the highest CH(4) production. Further testing is needed to find out whether there is a link between increased methanogenic diversity and reactor productivity.
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Microbial community dynamics in anaerobic bioreactors and algal tanks treating piggery wastewater. Appl Microbiol Biotechnol 2010; 87:353-63. [DOI: 10.1007/s00253-010-2539-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 11/27/2022]
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Franke-Whittle IH, Goberna M, Insam H. Design and testing of real-time PCR primers for the quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of uncultured methanogens. Can J Microbiol 2009; 55:611-6. [PMID: 19483790 DOI: 10.1139/w08-157] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, 16S rRNA gene primers were designed to complement the suite of already available PCR primers for the detection of different methanogens involved in biogas production through anaerobic digestion by SYBR Green real-time PCR. Primers designed for use in TaqMan real-time PCR for the organisms Methanosaeta, Methanosarcina, and Methanoculleus have been described previously; however, we found that (i) the Methanoculleus primers were not specific to members of the genus and that (ii) the Methanosarcina primers did not work specifically with SYBR Green real-time PCR. Thus, we designed new primers for these and other methanogens, and we optimized SYBR Green real-time PCR assays. Primers were tested by end-point and real-time PCR, and they were found to work specifically and sensitively. Application of these primers will allow the detection and quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of yet uncultured archaea from anaerobic habitats.
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Affiliation(s)
- Ingrid H Franke-Whittle
- Leopold-Franzens-Universität, Institute for Microbiology, Technikerstrasse 25 d, Innsbruck, Austria.
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Wang H, Tolvanen K, Lehtomäki A, Puhakka J, Rintala J. Microbial community structure in anaerobic co-digestion of grass silage and cow manure in a laboratory continuously stirred tank reactor. Biodegradation 2009; 21:135-46. [PMID: 19642000 DOI: 10.1007/s10532-009-9288-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 07/17/2009] [Indexed: 11/24/2022]
Abstract
The impacts of feeding ratio and loading rate on the microbial community during co-digestion of grass silage with cow manure in an anaerobic laboratory continuously stirred tank reactor were investigated by 16S rRNA gene-based fingerprints. The microbial community remained stable when the reactor was fed with cow manure alone and with up to 20% of grass silage in feedstock at an organic loading rate (OLR) of 2 kg VS m(-3) day(-1). Large changes in the bacterial community were observed when the loading ratio of grass was increased to 40%, while there was little change in the archaeal community. During the increase in OLR from 2 to 4 kg VS m(-3) day(-1) the bacterial community structure showed few differences, whereas Archaea was undetectable. Sequencing of the major DGGE bands indicated that the phylum Bacteriodetes predominated in the bacterial community. Two unclassified bacteria with high abundance survived throughout the operation of the reactor.
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Affiliation(s)
- Hong Wang
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (NSC), 40014 University of Jyväskylä, Finland.
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Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor. Appl Environ Microbiol 2009; 75:2566-72. [PMID: 19218417 DOI: 10.1128/aem.02260-08] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Prokaryotic diversity was investigated near the inlet and outlet of a plug-flow reactor. After analyzing 800 clones, 50 bacterial and 3 archaeal phylogenetic groups were defined. Clostridia (>92%) dominated among bacteria and Methanoculleus (>90%) among archaea. Significant changes in pH and volatile fatty acids did not invoke a major shift in the phylogenetic groups. We suggest that the environmental filter imposed by the saline conditions (20 g liter(-1)) selected a stable community of halotolerant and halophilic prokaryotes.
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50
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Espinosa-Solares T, Valle-Guadarrama S, Bombardiere J, Domaschko M, Easter M. Effect of Heating Strategy on Power Consumption and Performance of a Pilot Plant Anaerobic Digester. Appl Biochem Biotechnol 2009; 156:35-44. [DOI: 10.1007/s12010-008-8487-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 12/10/2008] [Indexed: 10/21/2022]
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