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Pinela E, Schnürer A, Neubeck A, Moestedt J, Westerholm M. Impact of additives on syntrophic propionate and acetate enrichments under high-ammonia conditions. Appl Microbiol Biotechnol 2024; 108:433. [PMID: 39110235 PMCID: PMC11306274 DOI: 10.1007/s00253-024-13263-7] [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: 04/25/2024] [Revised: 07/17/2024] [Accepted: 07/20/2024] [Indexed: 08/10/2024]
Abstract
High ammonia concentrations in anaerobic degradation systems cause volatile fatty acid accumulation and reduced methane yield, which often derive from restricted activity of syntrophic acid-oxidising bacteria and hydrogenotrophic methanogens. Inclusion of additives that facilitate the electron transfer or increase cell proximity of syntrophic species by flocculation can be a suitable strategy to counteract these problems, but its actual impact on syntrophic interactions has yet to be determined. In this study, microbial cultivation and molecular and microscopic analysis were performed to evaluate the impact of conductive (graphene, iron oxide) and non-conductive (zeolite) additives on the degradation rate of acetate and propionate to methane by highly enriched ammonia-tolerant syntrophic cultures derived from a biogas process. All additives had a low impact on the lag phase but resulted in a higher rate of acetate (except graphene) and propionate degradation. The syntrophic bacteria 'Candidatus Syntrophopropionicum ammoniitolerans', Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen were found in higher relative abundance and higher gene copy numbers in flocculating communities than in planktonic communities in the cultures, indicating benefits to syntrophs of living in close proximity to their cooperating partner. Microscopy and element analysis showed precipitation of phosphates and biofilm formation in all batches except on the graphene batches, possibly enhancing the rate of acetate and propionate degradation. Overall, the concordance of responses observed in both acetate- and propionate-fed cultures highlight the suitability of the addition of iron oxide or zeolites to enhance acid conversion to methane in high-ammonia biogas processes. KEY POINTS: • All additives promoted acetate (except graphene) and propionate degradation. • A preference for floc formation by ammonia-tolerant syntrophs was revealed. • Microbes colonised the surfaces of iron oxide and zeolite, but not graphene.
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Affiliation(s)
- Eduardo Pinela
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Anna Neubeck
- Department of Earth Sciences, Uppsala University, 752 36, Uppsala, Sweden
| | - Jan Moestedt
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
- Department of Biogas R & D, Tekniska Verken I Linköping AB (Publ.), Box 1500, 581 15, Linköping, Sweden
- Department of Thematic Studies - Environmental Change, Linköping University, 581 83, Linköping, Sweden
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
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2
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Yan X, Peng P, Zhou X, Li X, Chen L, Zhao F. Fulvic acid-mediated efficient anaerobic digestion for kitchen wastewater: Electrochemical and biochemical mechanisms. WATER RESEARCH 2024; 256:121603. [PMID: 38631242 DOI: 10.1016/j.watres.2024.121603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Fulvic acid, prevalent in humus derived from the anaerobic digestion of kitchen wastewater, is crucial in organic matter transformation. However, its effects and underlying mechanisms remain unclear. In this study, the fate of anaerobic digestion of artificial and kitchen wastewater with different fulvic acid contents was investigated. The results showed that 125 mg/L fulvic acid resulted in a 64.02 and 51.72 % increase in methane production in synthetic and kitchen wastewater, respectively. Fulvic acid acted as an electron mediator and increased substrate oxidation by boosting NAD and ATP levels, thereby increasing microbial metabolic rates and ensuring an adequate substrate for methane generation. Isotope analysis suggested that fulvic acid boosts the conversion of volatile fatty acids to methane via the interspecies electron transfer pathway. Gene expression analysis revealed that cytochrome c, FAD, and other electron transport coenzymes were upregulated by fulvic acid, thereby enhancing substrate utilisation and biogas quality. Fulvic acid presented a dual stimulatory and inhibitory effect on anaerobic digestion, with concentrations over 125 mg/L diminishing its positive impact. This dual effect may stem from the properties and concentrations of fulvic acid. This study revealed the effect mechanism of fulvic acid and provided insights into the humus performance in anaerobic digestion.
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Affiliation(s)
- Xinyu Yan
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Science, 1799 Jimei Road, Xiamen 361021, Fujian, China; University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Pin Peng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Science, 1799 Jimei Road, Xiamen 361021, Fujian, China; University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Xudong Zhou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Science, 1799 Jimei Road, Xiamen 361021, Fujian, China
| | - Xiang Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Science, 1799 Jimei Road, Xiamen 361021, Fujian, China; University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Lixiang Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Science, 1799 Jimei Road, Xiamen 361021, Fujian, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Science, 1799 Jimei Road, Xiamen 361021, Fujian, China.
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3
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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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4
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Xu J, Shi Z, Xu L, Zheng X, Zong Y, Luo G, Zhang C, Liu M, Xie L. Recovery capability of anaerobic digestion from ammonia stress: Metabolic activity, energy generation, and genome-centric metagenomics. BIORESOURCE TECHNOLOGY 2024; 394:130203. [PMID: 38109977 DOI: 10.1016/j.biortech.2023.130203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Excessive ammonia stresses anaerobic digestion (AD) significantly. Although there has been progress in understanding AD under ammonia exposure, investigations on AD liberated from ammonia exposure are limited. Here, the recovery capability of AD from ammonia stress was evaluated, by examining specific methanogenic activity, energy-conserving capability, microbial community succession, and metabolic pathway reconstruction. The findings demonstrated that ammonia stress relief resulted in < 50% methane recovery, with propionate conversion identified as the critical impediment to AD reactivation. Energy generation could not recovered either. Efforts to mitigate ammonia stress failed to restore acetoclastic methanogens, e.g., Methanothrix soehngenii, and proved futile in awakening propionate oxidizers, e.g., Desulfobulbus. Interestingly, a symbiotic metabolism emerged, prevailing in stress-relieved AD due to its energy-conserving advantage. This study underscores the importance of targeted interventions, including stimulating acetoclastic methanogenesis, propionate oxidation, and energy generation, as priorities for AD recovery following ammonia stress, rather than focusing solely on ammonia level management.
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Affiliation(s)
- Jun Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China
| | - Ling Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xiaomei Zheng
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Yang Zong
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Chen Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co., LTD., Shanghai 200092, PR China
| | - Mingxian Liu
- Shanghai Key Lab of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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5
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Zhang X, Wang Y, Jiao P, Zhang M, Deng Y, Jiang C, Liu XW, Lou L, Li Y, Zhang XX, Ma L. Microbiome-functionality in anaerobic digesters: A critical review. WATER RESEARCH 2024; 249:120891. [PMID: 38016221 DOI: 10.1016/j.watres.2023.120891] [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: 06/25/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023]
Abstract
Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.
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Affiliation(s)
- Xingxing Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yiwei Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Pengbo Jiao
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ming Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xian-Wei Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Liping Ma
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai 200062, PR China.
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6
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Menezes CAD, Almeida PDS, Camargo FP, Delforno TP, Oliveira VMD, Sakamoto IK, Varesche MBA, Silva EL. One versus two-stage codigestion of sugarcane vinasse and glycerol: Assessing combinations at mesophilic and (hyper) thermophilic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166294. [PMID: 37586502 DOI: 10.1016/j.scitotenv.2023.166294] [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: 05/12/2023] [Revised: 07/16/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Sugarcane vinasse exits the distillation process at high temperatures, which may differ from the optimal temperatures for dark fermentation and anaerobic digestion. A 15 °C temperature increase, for example, stops sugarcane vinasse methane generation, making distillery vinasse digestion complicated. Conversely, in other aspects, co-digesting vinasse and glycerol has been proven to stabilize methane production from vinasse because of sulfate dilution. However, glycerol has not been tested to stabilize vinasse digestion under temperature changes. Thus, this study compared the effects of different temperature settings on the co-digestion of 10 g COD L-1 of vinasse and glycerol (50 %:50 % on a COD basis) in anaerobic fluidized bed reactors (AFBR), i.e., an acidogenic and a methanogenic one-stage AFBRs operated at 55, 60, and 65 °C, and two methanogenic AFBRs fed both with acidogenic effluent (one operated at room temperature (25 °C) and the other at 55, 60, and 65 °C). The co-digestion provided steady methane generation at all AFBRs, with methane production rates ranging from 2.27 to 2.93 L CH4 d-1 L-1, whether in one or two stages. A feature of this research was to unravel the black box of the role of sulfate in the digestion of sugarcane vinasse, which was rarely studied. Desulfovibrio was the primary genus degrading 1,3-propanediol into 3-hydroxypropanoate after genome sequencing. Phosphate acetyltransferase (EC: 2.3.1.8, K00625) and acetate kinase (EC: 2.7.2.1, K00925) genes were also found, suggesting propionate was metabolized. In practical aspects, regarding the two-stage systems, the thermophilic-mesophilic (acidogenic-methanogenic) configuration is best for extracting additional value-added products because 1,3-propanediol may be recovered at high yields with steady methane production at reduced energy expenditure in a reactor operated at room temperature. However, the one-stage design is best for methane generation per system volume since it remained stable with rising temperatures, and all systems presented similar methane production rates.
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Affiliation(s)
- Camila Aparecida de Menezes
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100, Jd. Santa Angelina, CEP 13563-120 São Carlos, SP, Brazil
| | - Priscilla de Souza Almeida
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luis, km 235, CEP 13565-905 São Carlos, SP, Brazil
| | - Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100, Jd. Santa Angelina, CEP 13563-120 São Carlos, SP, Brazil
| | - Tiago Palladino Delforno
- SENAI Innovation Institute for Biotechnology, Rua Anhaia, 1321, Bom Retiro - São Paulo, 01130-000 São Paulo, SP, Brazil
| | - Valeria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University, Campinas, SP CEP 13081-970, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100, Jd. Santa Angelina, CEP 13563-120 São Carlos, SP, Brazil
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100, Jd. Santa Angelina, CEP 13563-120 São Carlos, SP, Brazil
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luis, km 235, CEP 13565-905 São Carlos, SP, Brazil.
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7
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McDaniel EA, Scarborough M, Mulat DG, Lin X, Sampara PS, Olson HM, Young RP, Eder EK, Attah IK, Markillie LM, Hoyt DW, Lipton MS, Hallam SJ, Ziels RM. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. THE ISME JOURNAL 2023; 17:2326-2339. [PMID: 37880541 PMCID: PMC10689502 DOI: 10.1038/s41396-023-01542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Matthew Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, USA
| | - Daniel Girma Mulat
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Xuan Lin
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Pranav S Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Heather M Olson
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert P Young
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Elizabeth K Eder
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Isaac K Attah
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lye Meng Markillie
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David W Hoyt
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, The University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, The University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada.
- Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada.
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8
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Poulsen JS, Macêdo WV, Bonde T, Nielsen JL. Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:183. [PMID: 38017526 PMCID: PMC10685487 DOI: 10.1186/s13068-023-02432-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
The biogas produced through anaerobic digestion (AD) of renewable feedstocks is one of the promising alternatives to replace fossil-derived energy. Even though lignocellulosic biomass is the most abundant biomass on earth, only a small fraction is being used towards resources recovery, leaving a great potential unexploited. In this study, the combination of state-of-art genomic techniques and engineered systems were used to further advance the knowledge on biogas production from lignocellulosic-rich residues and the microbiome involved in the anaerobic digestion hereof. A long-term adapted anaerobic microbiome capable of degrading wheat straw as the sole substrate was investigated using protein stable isotope probing (protein-SIP). The results indicated that a diverse microbial community, primarily composed of Firmicutes and Methanogens, played crucial roles in cellulose degradation and methane production. Notably, Defluviitoga tunisiensis, Syntrophothermus lipocalidus, and Pelobacter carbinolicus were identified as direct metabolizers of cellulose, while Dehalobacterium assimilated labelled carbon through cross-feeding. This study provides direct evidence of primary cellulose degraders and sheds light on their genomic composition. By harnessing the potential of lignocellulosic biomass and understanding the microbial communities involved, we can promote sustainable biogas production, contributing to energy security and environmental preservation.
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Affiliation(s)
- Jan Struckmann Poulsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg E, Denmark
| | - Williane Vieira Macêdo
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg E, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej, 10 D, 8000, Aarhus C, Denmark
| | - Torben Bonde
- Biofuel Technology A/S, Bredkær Parkvej 58, 8250, Egå, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg E, Denmark.
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9
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Wu Z, Nguyen D, Shrestha S, Raskin L, Khanal SK, Lee PH. Evaluation of Nanaerobic Digestion as a Mechanism to Explain Surplus Methane Production in Animal Rumina and Engineered Digesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12302-12314. [PMID: 37565790 PMCID: PMC10448717 DOI: 10.1021/acs.est.2c07813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 07/02/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Nanaerobes are a newly described class of microorganisms that use a unique cytochrome bd oxidase to achieve nanaerobic respiration at <2 μM dissolved oxygen (∼1% of atmospheric oxygen) but are not viable above this value due to the lack of other terminal oxidases. Although sharing an overlapping ecological niche with methanogenic archaea, the role of nanaerobes in methanogenic systems has not been studied so far. To explore their occurrence and significance, we re-analyzed published meta-omic datasets from animal rumina and waste-to-energy digesters, including conventional anaerobic digesters and anaerobic digesters with ultra-low oxygenation. Results show that animal rumina share broad similarities in the microbial community and system performance with oxygenated digesters, rather than with conventional anaerobic digesters, implying that trace levels of oxygen drive the efficient digestion in ruminants. The rumen system serves as an ideal model for the newly named nanaerobic digestion, as it relies on the synergistic co-occurrence of nanaerobes and methanogens for methane yield enhancement. The most abundant ruminal bacterial family Prevotellaceae contains many nanaerobes, which perform not only anaerobic fermentation but also nanaerobic respiration using cytochrome bd oxidase. These nanaerobes generally accompany hydrogenotrophic methanogens to constitute a thermodynamically and physiologically consistent framework for efficient methane generation. Our findings provide new insights into ruminal methane emissions and strategies to enhance methane generation from biomass.
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Affiliation(s)
- Zhuoying Wu
- Department
of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United
Kingdom
- Shanghai
Shaanxi Coal Hi-tech Research Institute Co., Ltd., Shanghai 201613, China
| | - Duc Nguyen
- Department
of Molecular Biosciences and Bioengineering, University of Hawai’i at Ma̅noa, Honolulu 96822, Hawaii, United States
- The
Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Shilva Shrestha
- Department
of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor 48109, Michigan, United States
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lutgarde Raskin
- Department
of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor 48109, Michigan, United States
| | - Samir Kumar Khanal
- Department
of Molecular Biosciences and Bioengineering, University of Hawai’i at Ma̅noa, Honolulu 96822, Hawaii, United States
| | - Po-Heng Lee
- Department
of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United
Kingdom
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10
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Struckmann Poulsen J, Trueba Santiso A, Lema JM, Gregersen Echers S, Wimmer R, Lund Nielsen J. Assessing labelled carbon assimilation from poly butylene adipate-co-terephthalate (PBAT) monomers during thermophilic anaerobic digestion. BIORESOURCE TECHNOLOGY 2023:129430. [PMID: 37399952 DOI: 10.1016/j.biortech.2023.129430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
PBAT (poly butylene adipate-co-terephthalate) is a widely used biodegradable plastic, but the knowledge about its metabolization in anaerobic environments is very limited. In this study, the anaerobic digester sludge from a municipal wastewater treatment plant was used as inoculum to investigate the biodegradability of PBAT monomers in thermophilic conditions. The research employs a combination of 13C-labelled monomers and proteogenomics to track the labelled carbon and identify the microorganisms involved. A total of 122 labelled peptides of interest were identified for adipic acid (AA) and 1,4-butanedio (BD). Through the time-dependent isotopic enrichment and isotopic profile distributions, Bacteroides, Ichthyobacterium, and Methanosarcina were proven to be directly involved in the metabolization of at least one monomer. This study provides a first insight into the identity and genomic potential of microorganisms responsible for biodegradability of PBAT monomers during anaerobic digestion under thermophilic conditions.
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Affiliation(s)
- Jan Struckmann Poulsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark
| | - Alba Trueba Santiso
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark; CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Juan M Lema
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Simon Gregersen Echers
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark.
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11
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Jin Y, Lu Y. Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments. Appl Environ Microbiol 2023; 89:e0038423. [PMID: 37097179 PMCID: PMC10231205 DOI: 10.1128/aem.00384-23] [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] [Indexed: 04/26/2023] Open
Abstract
Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.
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Affiliation(s)
- Yidan Jin
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
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12
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Sun Z, He J, Yu N, Chen Y, Chen Y, Tang Y, Kida K. Biomethane production and microbial strategies corresponding to high organic loading treatment for molasses wastewater in an upflow anaerobic filter reactor. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02882-5. [PMID: 37209175 DOI: 10.1007/s00449-023-02882-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/10/2023] [Indexed: 05/22/2023]
Abstract
Molasses wastewater contains high levels of organic compounds, cations, and anions, causing operational problems for anaerobic biological treatment. In this study, an upflow anaerobic filter (UAF) reactor was employed to establish a high organic loading treatment system for molasses wastewater and further investigated the microbial community dynamics in response to this stressful operation. The biogas production increased with an increase in total organic carbon (TOC) loading rate from 1.0 to 14 g/L/day, and then it decreased with further TOC loading rate addition until 16 g/L/day. The UAF reactor achieved a maximum biogas production of 6800 mL/L/day with a TOC removal efficiency of 66.5% at a TOC loading rate of 14 g/L/day. Further microbial analyses revealed that both the bacterial and archaeal communities developed multiple strategies to maintain stable operation of the reactor at high organic loading (e.g., Proteiniphilum and Defluviitoga maintained high abundances throughout the operation; Tissierella temporarily dominated the bacterial community at TOC loading rates of 8.0 to 14 g/L/day; and multi-trophic Methanosarcina shifted as the dominant methanogen at the TOC loading rates of 8.0 to 16 g/L/day). This study presents insights into a high organic loading molasses wastewater treatment system and the microbial flexibility in methane fermentation in response to process disturbances.
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Affiliation(s)
- Zhaoyong Sun
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jinting He
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Na Yu
- School of Environmental and Planning, Liaocheng University, Liaocheng, 252000, China
| | - Yuwei Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yating Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China.
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China.
| | - Yueqin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
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13
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Prem EM, Schwarzenberger A, Markt R, Wagner AO. Effects of phenyl acids on different degradation phases during thermophilic anaerobic digestion. Front Microbiol 2023; 14:1087043. [PMID: 37089573 PMCID: PMC10113666 DOI: 10.3389/fmicb.2023.1087043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Aromatic compounds like phenyl acids (PA) can accumulate during anaerobic digestion (AD) of organic wastes due to an increased entry of lignocellulose, secondary plant metabolites or proteins, and thermodynamic challenges in degrading the benzene ring. The effects of aromatic compounds can be various – from being highly toxic to be stimulating for methanogenesis – depending on many parameters like inoculum or molecular characteristics of the aromatic compound. To contribute to a better understanding of the consequences of PA exposure during AD, the aim was to evaluate the effects of 10 mM PA on microbial communities degrading different, degradation phase–specific substrates in thermophilic batch reactors within 28 days: Microcrystalline cellulose (MCC, promoting hydrolytic to methanogenic microorganisms), butyrate or propionate (promoting syntrophic volatile fatty acid (VFA) oxidisers to methanogens), or acetate (promoting syntrophic acetate oxidisers to methanogens). Methane production, VFA concentrations and pH were evaluated, and microbial communities and extracellular polymeric substances (EPS) were assessed. The toxicity of PA depended on the type of substrate which in turn determined the (i) microbial diversity and composition and (ii) EPS quantity and quality. Compared with the respective controls, methane production in MCC reactors was less impaired by PA than in butyrate, propionate and acetate reactors which showed reductions in methane production of up to 93%. In contrast to the controls, acetate concentrations were high in all PA reactors at the end of incubation thus acetate was a bottle-neck intermediate in those reactors. Considerable differences in EPS quantity and quality could be found among substrates but not among PA variants of each substrate. Methanosarcina spp. was the dominant methanogen in VFA reactors without PA exposure and was inhibited when PA were present. VFA oxidisers and Methanothermobacter spp. were abundant in VFA assays with PA exposure as well as in all MCC reactors. As MCC assays showed higher methane yields, a higher microbial diversity and a higher EPS quantity and quality than VFA reactors when exposed to PA, we conclude that EPS in MCC reactors might have been beneficial for absorbing/neutralising phenyl acids and keeping (more susceptible) microorganisms shielded in granules or biofilms.
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Affiliation(s)
- Eva Maria Prem
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
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14
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Microbial Behavior and Influencing Factors in the Anaerobic Digestion of Distiller: A Comprehensive Review. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Anaerobic digestion technology is regarded as the most ideal technology for the treatment of a distiller in terms of environmental protection, resource utilization, and cost. However, there are some limitations to this process, the most prominent of which is microbial activity. The purpose of this paper is to provide a critical review of the microorganisms involved in the anaerobic digestion process of a distiller, with emphasis on the archaea community. The effects of operating parameters on microbial activity and process, such as pH, temperature, TAN, etc., are discussed. By understanding the activity of microorganisms, the anaerobic treatment technology of a distiller can be more mature. Aiming at the problem that anaerobic treatment of a distiller alone is not effective, the synergistic effect of different substrates is briefly discussed. In addition, the recent literature on the use of microorganisms to purify a distiller was collected in order to better purify the distiller and reduce harm. In the future, more studies are needed to elucidate the interactions between microorganisms and establish the mechanisms of microbial interactions in different environments.
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15
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Khesali Aghtaei H, Püttker S, Maus I, Heyer R, Huang L, Sczyrba A, Reichl U, Benndorf D. Adaptation of a microbial community to demand-oriented biological methanation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:125. [PMID: 36384582 PMCID: PMC9670408 DOI: 10.1186/s13068-022-02207-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Biological conversion of the surplus of renewable electricity and carbon dioxide (CO2) from biogas plants to biomethane (CH4) could support energy storage and strengthen the power grid. Biological methanation (BM) is linked closely to the activity of biogas-producing Bacteria and methanogenic Archaea. During reactor operations, the microbiome is often subject to various changes, e.g., substrate limitation or pH-shifts, whereby the microorganisms are challenged to adapt to the new conditions. In this study, various process parameters including pH value, CH4 production rate, conversion yields and final gas composition were monitored for a hydrogenotrophic-adapted microbial community cultivated in a laboratory-scale BM reactor. To investigate the robustness of the BM process regarding power oscillations, the biogas microbiome was exposed to five hydrogen (H2)-feeding regimes lasting several days. RESULTS Applying various "on-off" H2-feeding regimes, the CH4 production rate recovered quickly, demonstrating a significant resilience of the microbial community. Analyses of the taxonomic composition of the microbiome revealed a high abundance of the bacterial phyla Firmicutes, Bacteroidota and Thermotogota followed by hydrogenotrophic Archaea of the phylum Methanobacteriota. Homo-acetogenic and heterotrophic fermenting Bacteria formed a complex food web with methanogens. The abundance of the methanogenic Archaea roughly doubled during discontinuous H2-feeding, which was related mainly to an increase in acetoclastic Methanothrix species. Results also suggested that Bacteria feeding on methanogens could reduce overall CH4 production. On the other hand, using inactive biomass as a substrate could support the growth of methanogenic Archaea. During the BM process, the additional production of H2 by fermenting Bacteria seemed to support the maintenance of hydrogenotrophic methanogens at non-H2-feeding phases. Besides the elusive role of Methanothrix during the H2-feeding phases, acetate consumption and pH maintenance at the non-feeding phase can be assigned to this species. CONCLUSIONS Taken together, the high adaptive potential of microbial communities contributes to the robustness of BM processes during discontinuous H2-feeding and supports the commercial use of BM processes for energy storage. Discontinuous feeding strategies could be used to enrich methanogenic Archaea during the establishment of a microbial community for BM. Both findings could contribute to design and improve BM processes from lab to pilot scale.
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Affiliation(s)
- Hoda Khesali Aghtaei
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Sebastian Püttker
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Robert Heyer
- Database and Software Engineering Group, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
- Multidimensional Omics Analyses group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - Liren Huang
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alexander Sczyrba
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany.
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany.
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366, Köthen, Germany.
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16
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Syntrophic Acetate-Oxidizing Microbial Consortia Enriched from Full-Scale Mesophilic Food Waste Anaerobic Digesters Showing High Biodiversity and Functional Redundancy. mSystems 2022; 7:e0033922. [PMID: 36073802 PMCID: PMC9600251 DOI: 10.1128/msystems.00339-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis (HM) plays a vital role in the anaerobic digestion of protein-rich feedstocks such as food wastes. However, current knowledge of the biodiversity and genetic potential of the involved microbial participants, especially syntrophic acetate-oxidizing bacteria (SAOB), is limited due to the low abundance of these microorganisms and challenges in their isolation. The intent of this study was to enrich and identify potential SAOB. Therefore, we conducted continuous acetate feeding under high ammonia concentrations using two separate inoculum consortia of microorganisms that originated from full-scale mesophilic food waste digesters, which lasted for more than 200 days. Using 16S rRNA gene amplicon and metagenomic analyses, we observed a convergence of the experimental microbial communities during the enrichment regarding taxonomic composition and metabolic functional composition. Stable carbon isotope analyses of biogas indicated that SAO-HM was the dominant methanogenic pathway during the enrichment process. The hydrogenotrophic methanogen Methanoculleus dominated the archaeal community. The enriched SAO community featured high biodiversity and metabolic functional redundancy. By analyzing the metagenome-assembled genomes, the known SAOB Syntrophaceticus schinkii and six uncultured populations were identified to have the genetic potential to perform SAO through the conventional reversed Wood-Ljungdahl pathway, while another six bacteria were found to encode the reversed Wood-Ljungdahl pathway combined with a glycine cleavage system as novel SAOB candidates. These results showed that the food waste anaerobic digesters harbor diverse SAOB and highlighted the importance of the glycine cleavage system for acetate oxidation. IMPORTANCE Syntrophic acetate oxidation to CO2 and H2, together with hydrogenotrophic methanogenesis, contributes to much of the carbon flux in the anaerobic digestion of organic wastes, especially at high ammonia concentrations. A deep understanding of the biodiversity, metabolic genetic potential, and ecology of the SAO community can help to improve biomethane production from wastes for clean energy production. Here, we enriched the SAO-HM functional guild obtained from full-scale food waste anaerobic digesters and recorded dynamic changes in community taxonomic composition and functional profiles. By reconstructing the metabolic pathways, diverse known and novel bacterial members were found to have SAO potential via the reversed Wood-Ljungdahl (WL) pathway alone, or via the reversed WL pathway with a glycine cleavage system (WLP-GCS), and those catalyzing WLP-GCS showed higher microbial abundance. This study revealed the biodiversity and metabolic functional redundancy of SAOB in full-scale anaerobic digester systems and provided inspiration for further genome-centric studies.
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17
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Macêdo WV, Poulsen JS, Zaiat M, Nielsen JL. Proteogenomics identification of TBBPA degraders in anaerobic bioreactor. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119786. [PMID: 35872283 DOI: 10.1016/j.envpol.2022.119786] [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: 03/12/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified 13C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.
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Affiliation(s)
- Williane Vieira Macêdo
- Laboratory of Biological Processes, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, Zip Code 13563-120, São Carlos, SP, Brazil; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Jan Struckmann Poulsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Marcelo Zaiat
- Laboratory of Biological Processes, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, Zip Code 13563-120, São Carlos, SP, Brazil
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark.
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18
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Wang C, Yang Y, Wang Y, Wang D, Xu X, Wang Y, Li L, Yang C, Zhang T. Absolute quantification and genome-centric analyses elucidate the dynamics of microbial populations in anaerobic digesters. WATER RESEARCH 2022; 224:119049. [PMID: 36108398 DOI: 10.1016/j.watres.2022.119049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/25/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion (AD) relies on myriads of functions performed by complex microbial communities in customized settings, thus, a comprehensive investigation on the AD microbiome is central to the fine-tuned control. Most current AD microbiome studies are based on relative abundance, which hinders the interpretation of microbes' dynamics and inter-sample comparisons. Here, we developed an absolute quantification (AQ) approach that integrated cellular spike-ins with metagenomic sequencing to elucidate microbial community variations and population dynamics in four anaerobic digesters. Using this method, 253 microbes were defined as decaying populations with decay rates ranging from -0.05 to -5.85 d-1, wherein, a population from Flavobacteriaceae family decayed at the highest rates of -3.87 to -5.85 d-1 in four digesters. Meanwhile, 25 microbes demonstrated the growing trend in the AD processes with growth rates ranging from 0.11 to 1.77 d-1, and genome-centric analysis assigned some of the populations to the functional niches of hydrolysis, short-chain fatty acids metabolism, and methane generation. Additionally, we observed that the specific activity of methanogens was lower in the prolonged digestion stage, and redundancy analysis revealed that the feedstock composition and the digestion duration were the two key parameters in governing the AD microbial compositions.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
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19
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Azizan NAZ, Kamyab H, Yuzir A, Abdullah N, Vasseghian Y, Ali IH, Elboughdiri N, Sohrabi M. The selectivity of electron acceptors for the removal of caffeine, gliclazide, and prazosin in an up-flow anaerobic sludge blanket (UASB) reactor. CHEMOSPHERE 2022; 303:134828. [PMID: 35526684 DOI: 10.1016/j.chemosphere.2022.134828] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/17/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
This study attempts to investigate the relationship between the dominance of reducing conditions and the biotransformation of pharmaceutical compounds, which has been scarcely reported in a continuous anaerobic treatment process. Previous batch experiments have discovered the possible implications of different reducing conditions on the biotransformation process, but have failed to reflect actual removal performance due to substrate limitations and other operational factors. Continuously operating reactors commonly receive wastewater stream containing a wide range of electron acceptors that diversify the growth of microorganisms in anaerobic treatment. The alteration of the dominance of reducing conditions in a continuous anaerobic reactor may result in the improvement of biotransformation performance compared to a single reducing condition in a substrate-limited batch experiment. The removal of psychostimulant caffeine (CAF), anti-diabetic drug gliclazide (GCZ), and anti-hypertensive drug prazosin (PRZ) were examined through the operation of an up-flow anaerobic sludge blanket (UASB) reactor under predominant methanogenic condition (Phase I) and simultaneous reducing conditions provided by a nitrate supplement (Phase II). The results revealed high biotransformation performance for all three compounds (73-> 99%) in both Phase I and Phase II experiments and fitted the pseudo-first-order model. The biotransformation rate of CAF and PRZ were relatively lower by 25% and 29%, while the GCZ rate improvement doubled in Phase II compared to Phase I. The outcome from 16s rRNA sequencing suggested that the biotransformation of the compounds may be driven by Firmicutes and Bacteroidota in both phases, and Burkhorderiales and sulfate-reducing bacteria species in Phase II. This study proved preferential of reducing conditions does not negatively affect the biotransformation performance of each pharmaceutical compound in a continuous anaerobic reactor, but they led to varying biotransformation rate, hence shifting the microbial diversity.
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Affiliation(s)
- Nur Alyaa Zahida Azizan
- Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Hesam Kamyab
- Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India.
| | - Ali Yuzir
- Department of Chemical and Environmental Engineering (ChEE), Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia.
| | - Norhayati Abdullah
- Department of Chemical and Environmental Engineering (ChEE), Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Yasser Vasseghian
- Department of Chemistry, Soongsil University, Seoul, 06978, South Korea; The University of Johannesburg, Department of Chemical Engineering, P.O. Box 17011, Doornfontein, 2088, South Africa
| | - Ismat H Ali
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il, 81441, Saudi Arabia
| | - Mohsen Sohrabi
- Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
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20
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Rossi A, Morlino MS, Gaspari M, Basile A, Kougias P, Treu L, Campanaro S. Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. MICROBIOME 2022; 10:125. [PMID: 35965344 PMCID: PMC9377139 DOI: 10.1186/s40168-022-01316-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. RESULTS The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. CONCLUSIONS Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.
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Affiliation(s)
- Alessandro Rossi
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Gaspari
- Department of Hydraulics, Soil Science and Agricultural Engineering, Faculty of Agriculture, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Panagiotis Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organisation Demeter, Thermi, 57001, Thessaloniki, Greece
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
- CRIBI biotechnology center, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
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21
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De Bernardini N, Basile A, Zampieri G, Kovalovszki A, De Diego Diaz B, Offer E, Wongfaed N, Angelidaki I, Kougias PG, Campanaro S, Treu L. Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO 2 methanation. MICROBIOME 2022; 10:117. [PMID: 35918706 PMCID: PMC9347119 DOI: 10.1186/s40168-022-01311-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/30/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental biological system operating biogas upgrading and is paramount in power-to-gas conversion. Carbon dioxide (CO2) methanation is frequently performed by microbiota attached to solid supports generating biofilms. Despite the apparent simplicity of the microbial community involved in biogas upgrading, the dynamics behind most of the interspecies interaction remain obscure. To understand the role of the microbial species in CO2 fixation, the biofilm generated during the biogas upgrading process has been selected as a case study. The present work investigates via genome-centric metagenomics, based on a hybrid Nanopore-Illumina approach the biofilm developed on the diffusion devices of four ex situ biogas upgrading reactors. Moreover, genome-guided metabolic reconstruction and flux balance analysis were used to propose a biological role for the dominant microbes. RESULTS The combined microbiome was composed of 59 species, with five being dominant (> 70% of total abundance); the metagenome-assembled genomes representing these species were refined to reach a high level of completeness. Genome-guided metabolic analysis appointed Firmicutes sp. GSMM966 as the main responsible for biofilm formation. Additionally, species interactions were investigated considering their co-occurrence in 134 samples, and in terms of metabolic exchanges through flux balance simulation in a simplified medium. Some of the most abundant species (e.g., Limnochordia sp. GSMM975) were widespread (~ 67% of tested experiments), while others (e.g., Methanothermobacter wolfeii GSMM957) had a scattered distribution. Genome-scale metabolic models of the microbial community were built with boundary conditions taken from the biochemical data and showed the presence of a flexible interaction network mainly based on hydrogen and carbon dioxide uptake and formate exchange. CONCLUSIONS Our work investigated the interplay between five dominant species within the biofilm and showed their importance in a large spectrum of anaerobic biogas reactor samples. Flux balance analysis provided a deeper insight into the potential syntrophic interaction between species, especially Limnochordia sp. GSMM975 and Methanothermobacter wolfeii GSMM957. Finally, it suggested species interactions to be based on formate and amino acids exchanges. Video Abstract.
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Affiliation(s)
- Nicola De Bernardini
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Arianna Basile
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Guido Zampieri
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Adam Kovalovszki
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | | | - Elisabetta Offer
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Nantharat Wongfaed
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs, DK-2800, Lyngby, Denmark
| | - Panagiotis G Kougias
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi, Thessaloniki, Greece.
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy.
- CRIBI Biotechnology Center, University of Padova, 35131, Padova, Italy.
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
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22
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Wang C, Wang Y, Wang Y, Liu L, Wang D, Ju F, Xia Y, Zhang T. Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters. WATER RESEARCH 2022; 219:118590. [PMID: 35597218 DOI: 10.1016/j.watres.2022.118590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/18/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
| | - Yubo Wang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Yu Xia
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
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23
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Microbial Communities in Underground Gas Reservoirs Offer Promising Biotechnological Potential. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Securing new sources of renewable energy and achieving national self-sufficiency in natural gas have become increasingly important in recent times. The study described in this paper focuses on three geologically diverse underground gas reservoirs (UGS) that are the natural habitat of methane-producing archaea, as well as other microorganisms with which methanogens have various ecological relationships. The objective of this research was to describe the microbial metabolism of methane in these specific anoxic environments during the year. DNA sequencing analyses revealed the presence of different methanogenic communities and their metabolic potential in all sites studied. Hydrogenotrophic Methanobacterium sp. prevailed in Lobodice UGS, members of the hydrogenotrophic order Methanomicrobiales predominated in Dolní Dunajovice UGS and thermophilic hydrogenotrophic members of the Methanothermobacter sp. were prevalent in Tvrdonice UGS. Gas composition and isotope analyses were performed simultaneously. The results suggest that the biotechnological potential of UGS for biomethane production cannot be neglected.
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24
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Struckmann Poulsen J, de Jonge N, Vieira Macêdo W, Rask Dalby F, Feilberg A, Lund Nielsen J. Characterisation of cellulose-degrading organisms in an anaerobic digester. BIORESOURCE TECHNOLOGY 2022; 351:126933. [PMID: 35247567 DOI: 10.1016/j.biortech.2022.126933] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The recalcitrant nature of lignocellulosic biomass hinders efficient exploitation of this fraction for energy production. A better understanding of the microorganisms able to convert plant-based feedstocks is needed to improve anaerobic digestion of lignocellulosic biomass. In this study, active thermophilic cellulose-degrading microorganisms were identified from a full-scale anaerobic digester fed with maize by using metagenome-resolved protein stable isotope probing (protein-SIP). 13C-cellulose was converted into 13C-methane with a 13/12C isotope ratio of 0.127 after two days of incubation. Metagenomic analysis revealed 238 different genes coding for carbohydrate-active enzymes (CAZymes), six of which were directly associated with cellulose degradation. The protein-SIP analysis identified twenty heavily labelled peptides deriving from microorganisms actively assimilating labelled carbon from the degradation of 13C-cellulose, highlighting several members of the order Clostridiales. Corynebacterium was identified through CAZyme screening, amplicon analysis, and in the metagenome giving a strong identification of being a cellulose degrader.
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Affiliation(s)
- Jan Struckmann Poulsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark
| | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark
| | - Williane Vieira Macêdo
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark
| | - Frederik Rask Dalby
- Department of Biological and Chemical Engineering, Aarhus University, Finlandsgade 12, 8200 Aarhus N, Denmark
| | - Anders Feilberg
- Department of Biological and Chemical Engineering, Aarhus University, Finlandsgade 12, 8200 Aarhus N, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg E, Denmark.
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25
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The Measurement, Application and Effect of Oxygen in Microbial Fermentations: Focusing on Methane and Carboxylate Production. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8040138] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Oxygen is considered detrimental to anaerobic fermentation processes by many practitioners. However, deliberate oxygen sparging has been used successfully for decades to remove H2S in anaerobic digestion (AD) systems. Moreover, microaeration techniques during AD have shown that small doses of oxygen may enhance process performance and promote the in situ degradation of recalcitrant compounds. However, existing oxygen dosing techniques are imprecise, which has led to inconsistent results between studies. At the same time, real-time oxygen fluxes cannot be reliably quantified due to the complexity of most bioreactor systems. Thus, there is a pressing need for robust monitoring and process control in applications where oxygen serves as an operating parameter or an experimental variable. This review summarizes and evaluates the available methodologies for oxygen measurement and dosing as they pertain to anaerobic microbiomes. The historical use of (micro-)aeration in anaerobic digestion and its potential role in other anaerobic fermentation processes are critiqued in detail. This critique also provides insights into the effects of oxygen on these microbiomes. Our assessment suggests that oxygen dosing, when implemented in a controlled and quantifiable manner, could serve as an effective tool for bioprocess engineers to further manipulate anaerobic microbiomes for either bioenergy or biochemical production.
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26
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Cardona L, Mazéas L, Chapleur O. Deterministic processes drive the microbial assembly during the recovery of an anaerobic digester after a severe ammonia shock. BIORESOURCE TECHNOLOGY 2022; 347:126432. [PMID: 34838975 DOI: 10.1016/j.biortech.2021.126432] [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: 09/30/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion allows to produce sustainable energy but the microbial community involved in this process is highly sensitive to perturbations. In this study, a longitudinal experiment was performed in two sets of triplicate bioreactors to evaluate the influence of ammonia addition on AD microbiome and its recovery. Zeolite was added in three reactors to mitigate the inhibition. Microbial dynamics were monitored with 16S rRNA sequencing at 15 time points. Dominant methanogenic pathways were determined with gas isotopic signature analysis. Zeolite addition did not enable to reduce ammonia inhibition or improve the process under the conditions tested. In all the bioreactors, ammonia inhibition sharply decreased the methane production but the process could restart thanks to the increase of hydrogenotrophic archaea and syntrophic bacteria. Interestingly, similar behaviour was observed in the six reactors. Neutral modelling and null model were used and showed that a deterministic process governed the recovery of AD microbiome after failure.
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Affiliation(s)
- Laëtitia Cardona
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France.
| | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France.
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France.
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27
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Comparative Metagenomics of Anaerobic Digester Communities Reveals Sulfidogenic and Methanogenic Microbial Subgroups in Conventional and Plug Flow Residential Septic Tank Systems. Processes (Basel) 2022. [DOI: 10.3390/pr10030436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
On-site wastewater treatment systems (OWTS) are primarily monitored using physiochemical factors, including chemical oxygen demand (COD) and residual total suspended solids (TSS), which are indirect measures of the microbial action during the anaerobic digestion process. Changes in anaerobic digester microbial communities can alter the digester performance, but this information cannot be directly obtained from traditional physicochemical indicators. The potential of metagenomic DNA sequencing as a tool for taxonomic and functional profiling of microbial communities was examined in both common conventional and plug flow-type anaerobic digesters (single-pass and recirculating). Compared to conventional digesters, plug flow-type digesters had higher relative levels of sulfate-reducing bacteria (Desulfovibrio spp.) and hydrogenotrophic methanogens (Methanospirillum spp.). In contrast, recirculating anaerobic digesters were enriched with denitrifier bacteria and hydrogenotrophic methanogens, and both were significantly correlated with physicochemical factors such as COD and TSS. Stratification of microbial communities was observed along the digester treatment process according to hydrolytic, acidogenic, acetogenic, and methanogenic subgroups. These results indicate that the high-throughput DNA sequencing may be useful as a monitoring tool to characterize the changes in bacterial communities and the functional profile due to differences in digester design in on-site systems.
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28
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de Jonge N, Poulsen JS, Vechi NT, Kofoed MVW, Nielsen JL. Wood-Ljungdahl pathway utilisation during in situ H 2 biomethanation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151254. [PMID: 34710425 DOI: 10.1016/j.scitotenv.2021.151254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Biogas production from organic waste is a waste-to-energy technology with the potential to contribute significantly to sustainable energy production. Upgrading of biogas using in situ biomethanation with hydrogen has the potential for surplus electricity storage, and delivery of biogas with a methane content of >90%, allowing for easier integration into the natural gas grid, as well as conversion to other products. Microbial communities in biomethanation reactors undergo changes, however, these changes are largely unexplored. In the present study, metagenome-resolved protein stable isotope probing (Protein-SIP) was applied to laboratory scale batch incubations operating under anaerobic digestion, and (pre-adapted) biomethanation conditions, fed with 13C-labelled bicarbonate, in order to gain insight into the microbial activities during CO2-reduction. The strongest and most microbially diverse isotopic incorporation was observed in the pre-adapted biomethanation incubation. Furthermore, divergent incorporation of 13C-labelled bicarbonate was also observed in the Wood-Ljungdahl pathway, with the anaerobic digester incubations primarily showing labelled proteins in the peripheral pathways leading toward production of energy and biomass. The pre-adapted biomethanation incubations consumed H2 and CO2, but did not convert it to CH4, suggesting the production of acetate in these incubations, which was supported by heavy labelling of key enzymes in the Wood-Ljungdahl pathway. Twelve (ten high quality) metagenome-assembled genomes (MAGs) coding for 13C-incorporated proteins were extracted from the metagenome, eight of which contained one or more of the key genes in the Wood-Ljungdahl pathway, one of which was affiliated to Methanosarcina. Together, the findings in the present study deepen our knowledge surrounding microbial communities in biomethanation systems, and contribute to the development of better strategies for implementation of biogas upgrading and microbial management.
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Affiliation(s)
- Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg E, Denmark.
| | - Jan Struckmann Poulsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg E, Denmark.
| | - Nathalia Thygesen Vechi
- Department of Biological and Chemical Engineering, Aarhus University, Hangøvej 2, DK-8200 Aarhus N, Denmark.
| | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg E, Denmark.
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29
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Wang Y, Mairinger W, Raj SJ, Yakubu H, Siesel C, Green J, Durry S, Joseph G, Rahman M, Amin N, Hassan MZ, Wicken J, Dourng D, Larbi E, Adomako LAB, Senayah AK, Doe B, Buamah R, Tetteh-Nortey JNN, Kang G, Karthikeyan A, Roy S, Brown J, Muneme B, Sene SO, Tuffuor B, Mugambe RK, Bateganya NL, Surridge T, Ndashe GM, Ndashe K, Ban R, Schrecongost A, Moe CL. Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 763:143007. [PMID: 34718001 DOI: 10.1016/j.scitotenv.2020.143007] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal. OBJECTIVE Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities. METHODS In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods. RESULTS Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities). CONCLUSIONS Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.
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Affiliation(s)
- Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Wolfgang Mairinger
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Suraja J Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Habib Yakubu
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Casey Siesel
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jamie Green
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sarah Durry
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - George Joseph
- Water Global Practice, The World Bank, Washington, DC, USA
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | - Eugene Larbi
- Training Research and Networking for Development (TREND), Accra, Ghana
| | | | | | - Benjamin Doe
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard Buamah
- Department of Civil Engineering, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Gagandeep Kang
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Arun Karthikeyan
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Sheela Roy
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bacelar Muneme
- Water Supply and Mapping, WE Consult, Maputo, Mozambique
| | - Seydina O Sene
- Initiative Prospective Agricole et Rurale (IPAR), Dakar, Senegal
| | - Benedict Tuffuor
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard K Mugambe
- Department of Disease Control and Environmental Health, Makerere University School of Public Health, Kampala, Uganda
| | - Najib Lukooya Bateganya
- Department of Environment and Public Health, Kampala Capital City Authority, Kampala, Uganda
| | - Trevor Surridge
- Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH, Lusaka, Zambia
| | | | - Kunda Ndashe
- Department of Environmental Health, Faculty of Health Science, Lusaka Apex Medical University, Lusaka, Zambia
| | - Radu Ban
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Impact of Granular Activated Carbon on Anaerobic Process and Microbial Community Structure during Mesophilic and Thermophilic Anaerobic Digestion of Chicken Manure. SUSTAINABILITY 2022. [DOI: 10.3390/su14010447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this work, the impact of granular activated carbon (GAC) on the mesophilic and thermophilic anaerobic digestion of chicken manure and the structure of microbial communities was investigated. These results demonstrated that GAC supplementation effectively enhanced the consumption of produced organic acids in the mesophilic and thermophilic batch tests, accompanied by faster biomethane production in the presence of GAC than from reactors without GAC. However, since the free ammonia level was 3–6 times higher in the thermophilic reactors, this led to the instability of the anaerobic digestion process of the nitrogen-rich substrate at thermophilic temperatures. Bacteroidia and Clostridia were the two main bacterial classes in the mesophilic reactors, whereas the class Clostridia had a competitive advantage over other groups in the thermophilic systems. The archaeal communities in the mesophilic reactors were mainly represented by representatives of the genera Methanosarcina, Methanobacterium, and Methanotrix, whereas the archaeal communities in the thermophilic reactors were mainly represented by members of the genera Methanosarcina, Methanoculleus, and Methanothermobacter. New data obtained in this research will help control and manage biogas reactors in the presence of GAC at different temperatures.
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McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
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32
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Rahman MS, Hoque MN, Puspo JA, Islam MR, Das N, Siddique MA, Hossain MA, Sultana M. Microbiome signature and diversity regulates the level of energy production under anaerobic condition. Sci Rep 2021; 11:19777. [PMID: 34611238 PMCID: PMC8492712 DOI: 10.1038/s41598-021-99104-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH4%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH4, respectively. The physicochemical analysis revealed that level of energy production (CH4%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O2 level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH4 concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH4 concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.
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Affiliation(s)
- M. Shaminur Rahman
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Nazmul Hoque
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706 Bangladesh
| | - Joynob Akter Puspo
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Rafiul Islam
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Niloy Das
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Surge Engineering (www.surgeengineering.com), Dhaka, 1205 Bangladesh
| | - Mohammad Anwar Siddique
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Anwar Hossain
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Present Address: Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Munawar Sultana
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
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Hao L, Fan L, Chapleur O, Guenne A, Bize A, Bureau C, Lü F, He P, Bouchez T, Mazéas L. Gradual development of ammonia-induced syntrophic acetate-oxidizing activities under mesophilic and thermophilic conditions quantitatively tracked using multiple isotopic approaches. WATER RESEARCH 2021; 204:117586. [PMID: 34474248 DOI: 10.1016/j.watres.2021.117586] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Insights into microbiota adaptation to increased ammonia stress, and identification of indicator microorganisms can help to optimize the operation of anaerobic digesters. To identify microbial indicators and investigate their metabolic contribution to acetoclastic methanogenesis (AM), syntrophic acetate oxidation (SAO) or hydrogenotrophic methanogenesis (HM), 40 anaerobic batch reactors fed with acetate of 110 mmol/L were set up at NH4+-N concentrations of 0.14 g/L, 5.00 g/L or 7.00 g/L, inoculated with thermophilic or mesophilic microbiota with or without pre-exposure to ammonia stress. Four stable carbon isotope probing approaches were applied in parallel, with [1,2-13C]-CH3COOH, [2-13C]-CH3COOH, [13C]NaHCO3 or non-labeled CH3COOH used individually. The last three approaches were used to quantify the methanogenic pathways by tracking labeled 13C or natural 13C signatures in the resulting CH4 and CO2, and consistently detected the dynamic transition of dominant pathways from AM to SAO-HM under ammonia stress. Results of quantitative PCR and fluorescence in-situ hybridization illustrated the procedure, acetotrophic methanogens being outcompeted by acetate-oxidizing syntrophs. The first and last isotope-labeling approaches were designed to probe the active acetate-mineralizing microbes with DNA-SIP. Known acetate-oxidizing bacteria like Syntrophaceticus and Tepidanaerobacter, as well as novel members of Pseudomonas, Bacillus and Symbiobacteraceae were detected, with Methanoculleus as the predominant H2/CO2-utilizing partner. Using NanoSIMS, some bacterial cells were observed to be fixing CO2 from [13C]NaHCO3. In this study, Methanosaeta was only active with ammonia < 200 mg-N/L; the syntrophs catalyzing SAO-HM started to compete with AM-conducting Methanosarcina at intermediate concentrations of ammonia, i.e. 200-500 mg-N/L, and outcompeted the acetotrophic methanogens with ammonia > 500 mg-N/L. Under ammonia stress, diverse known and novel microbial taxa were involved in acetate mineralization, comparable with those identified in previous studies.
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Affiliation(s)
- Liping Hao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Lu Fan
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Angéline Guenne
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Chrystelle Bureau
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Fan Lü
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China.
| | - Théodore Bouchez
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France.
| | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France.
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Duan H, He P, Shao L, Lü F. Functional genome-centric view of the CO-driven anaerobic microbiome. THE ISME JOURNAL 2021; 15:2906-2919. [PMID: 33911204 PMCID: PMC8443622 DOI: 10.1038/s41396-021-00983-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 02/02/2023]
Abstract
CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.
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Affiliation(s)
- Haowen Duan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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35
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Dębowski M, Korzeniewska E, Kazimierowicz J, Zieliński M. Efficiency of sweet whey fermentation with psychrophilic methanogens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:49314-49323. [PMID: 33934309 PMCID: PMC8410717 DOI: 10.1007/s11356-021-14095-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Sweet whey is a waste product from the dairy industry that is difficult to manage. High hopes are fostered regarding its neutralization in the methane fermentation. An economically viable alternative to a typical mesophilic fermentation seems to be the process involving psychrophilic bacteria isolated from the natural environment. This study aimed to determine the feasibility of exploiting psychrophilic microorganisms in methane fermentation of sweet whey. The experiments were carried out under dynamic conditions using Bio Flo 310 type flow-through anaerobic bioreactors. The temperature inside the reactors was 10 ± 1 °C. The HRT was 20 days and the OLR was 0.2 g COD/dm3/day. The study yielded 132.7 ± 13.8 mL biogas/gCODremoved. The CH4 concentration in the biogas was 32.7 ± 1.6%, that of H2 was 8.7 ± 4.7%, whereas that of CO2 reached 58.42 ± 2.47%. Other gases were also determined, though in lower concentrations. The COD and BOD5 removal efficiency reached 21.4 ± 0.6% and 17.6 ± 1.0%, respectively.
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Affiliation(s)
- Marcin Dębowski
- Department of Environment Engineering, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, 10-720, Olsztyn, Poland
| | - Joanna Kazimierowicz
- Department of Water Supply and Sewage Systems, Faculty of Civil Engineering and Environmental Sciences, Bialystok University of Technology, 15-351, Bialystok, Poland.
| | - Marcin Zieliński
- Department of Environment Engineering, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, 10-720, Olsztyn, Poland
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Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021; 23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Yiyi Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Madeline Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Bryce Connors
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Jensen MB, de Jonge N, Dolriis MD, Kragelund C, Fischer CH, Eskesen MR, Noer K, Møller HB, Ottosen LDM, Nielsen JL, Kofoed MVW. Cellulolytic and Xylanolytic Microbial Communities Associated With Lignocellulose-Rich Wheat Straw Degradation in Anaerobic Digestion. Front Microbiol 2021; 12:645174. [PMID: 34113323 PMCID: PMC8186499 DOI: 10.3389/fmicb.2021.645174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
The enzymatic hydrolysis of lignocellulosic polymers is generally considered the rate-limiting step to methane production in anaerobic digestion of lignocellulosic biomass. The present study aimed to investigate how the hydrolytic microbial communities of three different types of anaerobic digesters adapted to lignocellulose-rich wheat straw in continuous stirred tank reactors operated for 134 days. Cellulase and xylanase activities were monitored weekly using fluorescently-labeled model substrates and the enzymatic profiles were correlated with changes in microbial community compositions based on 16S rRNA gene amplicon sequencing to identify key species involved in lignocellulose degradation. The enzymatic activity profiles and microbial community changes revealed reactor-specific adaption of phylogenetically different hydrolytic communities. The enzymatic activities correlated significantly with changes in specific taxonomic groups, including representatives of Ruminiclostridium, Caldicoprobacter, Ruminofilibacter, Ruminococcaceae, Treponema, and Clostridia order MBA03, all of which have been linked to cellulolytic and xylanolytic activity in the literature. By identifying microorganisms with similar development as the cellulase and xylanase activities, the proposed correlation method constitutes a promising approach for deciphering essential cellulolytic and xylanolytic microbial groups for anaerobic digestion of lignocellulosic biomass.
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Affiliation(s)
- Mads Borgbjerg Jensen
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- NIRAS A/S, Aalborg, Denmark
| | - Maja Duus Dolriis
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | | | | | | | - Karoline Noer
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Henrik Bjarne Møller
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Pan X, Zhao L, Li C, Angelidaki I, Lv N, Ning J, Cai G, Zhu G. Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis. WATER RESEARCH 2021; 190:116774. [PMID: 33387947 DOI: 10.1016/j.watres.2020.116774] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.
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Affiliation(s)
- Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing100081, China
| | - Chunxing Li
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China.
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Ma S, Jiang F, Huang Y, Zhang Y, Wang S, Fan H, Liu B, Li Q, Yin L, Wang H, Liu H, Ren Y, Li S, Cheng L, Fan W, Deng Y. A microbial gene catalog of anaerobic digestion from full-scale biogas plants. Gigascience 2021; 10:giaa164. [PMID: 33506264 PMCID: PMC7842101 DOI: 10.1093/gigascience/giaa164] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/10/2020] [Accepted: 12/18/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood. FINDINGS In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination. CONCLUSIONS This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.
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Affiliation(s)
- Shichun Ma
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120,China
| | - Yan Huang
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hui Fan
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Bo Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Qiang Li
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Lijuan Yin
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Yuwei Ren
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Shuqu Li
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Lei Cheng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Yu Deng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
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de Jonge N, Davidsson Å, la Cour Jansen J, Nielsen JL. Characterisation of microbial communities for improved management of anaerobic digestion of food waste. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 117:124-135. [PMID: 32823077 DOI: 10.1016/j.wasman.2020.07.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Anaerobic digestion of food waste is an attractive and increasingly popular technology within waste management and energy recovery. A better understanding of the microbiology associated with anaerobic digestion of food waste will provide new insight into the operational conditions required for optimizing this process, as well as its potential for utilisation in co-digestion systems. Eighteen full-scale reactors processing varying proportions of food waste under diverse operational configurations were subjected to microbial community analysis by amplicon sequencing of the 16S rRNA and mcrA genes to capture the bacterial and methanogenic populations. Statistical correlations between microbial populations, plant design and operating conditions revealed that the microbial communities were shaped by operational parameters such as the primary substrate type and operational temperature, while the methanogenic communities showed a more reactor specific distribution. The distribution of microbes based on the waste processed in the surveyed digesters was explored, as well as the presence of specialist populations such as syntrophs and methanogens. Food waste digester communities were not associated with a strong microbial fingerprint compared to other waste types (wastewater and manure) but contained greater abundance and unique syntrophic acetate oxidising populations, suggesting that co-digestion with food waste may improve the functional diversity of anaerobic digesters.
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Affiliation(s)
- Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg E, Denmark.
| | - Åsa Davidsson
- Water and Environmental Engineering at Department of Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Jes la Cour Jansen
- Water and Environmental Engineering at Department of Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg E, Denmark.
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Basile A, Campanaro S, Kovalovszki A, Zampieri G, Rossi A, Angelidaki I, Valle G, Treu L. Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis. Metab Eng 2020; 62:138-149. [PMID: 32905861 DOI: 10.1016/j.ymben.2020.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Anaerobic digestion is a key biological process for renewable energy, yet the mechanistic knowledge on its hidden microbial dynamics is still limited. The present work charted the interaction network in the anaerobic digestion microbiome via the full characterization of pairwise interactions and the associated metabolite exchanges. To this goal, a novel collection of 836 genome-scale metabolic models was built to represent the functional capabilities of bacteria and archaea species derived from genome-centric metagenomics. Dominant microbes were shown to prefer mutualistic, parasitic and commensalistic interactions over neutralism, amensalism and competition, and are more likely to behave as metabolite importers and profiteers of the coexistence. Additionally, external hydrogen injection positively influences microbiome dynamics by promoting commensalism over amensalism. Finally, exchanges of glucogenic amino acids were shown to overcome auxotrophies caused by an incomplete tricarboxylic acid cycle. Our novel strategy predicted the most favourable growth conditions for the microbes, overall suggesting strategies to increasing the biogas production efficiency. In principle, this approach could also be applied to microbial populations of biomedical importance, such as the gut microbiome, to allow a broad inspection of the microbial interplays.
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Affiliation(s)
- Arianna Basile
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy; CRIBI Biotechnology Center, University of Padova, 35131, Padua, Italy.
| | - Adam Kovalovszki
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Guido Zampieri
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy; Department of Computer Science and Information Systems, Teesside University, Middlesbrough, United Kingdom
| | - Alessandro Rossi
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Giorgio Valle
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padua, Italy
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Wang C, Wang Y, Wang Y, Cheung KK, Ju F, Xia Y, Zhang T. Genome-centric microbiome analysis reveals solid retention time (SRT)-shaped species interactions and niche differentiation in food waste and sludge co-digesters. WATER RESEARCH 2020; 181:115858. [PMID: 32505886 DOI: 10.1016/j.watres.2020.115858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Co-digestion of food waste with sewage sludge is widely applied for waste stabilization and energy recovery around the world. However, the effect of solid retention time (SRT) on the microbial population dynamics, metabolism and interspecies interaction have not been fully elucidated. Here, the influence of SRTs (5-25 days) on the performance of the co-digestion system was investigated and state-of-the-art genome-centric metagenomic analysis was employed to uncover the dynamics and metabolic network of the key players underlying the well-functioned and poorly-functioned co-digestion microbial communities. The results of the microbial analyses indicated that SRT largely shaped microbial community structure by enriching the syntrophic specialist Syntrophomonas and CO2/H2 ( formate)-using methanogen Methanocorpusculum in the well-functioned co-digester operated at SRT of 25 days, while selecting acid-tolerant populations Lactobacillus at SRT of 5 days. The metagenome assembled genomes (MAGs) of key players, such as Syntrophomonadaceae, Methanocorpusculum, and Mesotoga, were retrieved, additionally, the syntrophic acetate oxidation plus hydrogenotrophic methanogenesis (SAO-HM) were proposed as the dominant pathway for methane production. The metabolic interaction in the co-digestion microbial consortia was profiled by assigning MAGs into functional guilds. Functional redundancy was found in the bacterial groups in hydrolysis step, and the members in these groups reduced the direct competition by niche differentiation.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | | | - Feng Ju
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Yu Xia
- State Environmental Protection Key Laboratory of Integrated Surface Water- Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Dyksma S, Jansen L, Gallert C. Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste. MICROBIOME 2020; 8:105. [PMID: 32620171 PMCID: PMC7334858 DOI: 10.1186/s40168-020-00862-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate oxidation is an important pathway for methane production, knowledge about the SAOB is still very limited. RESULTS A metabolic reconstruction of metagenome-assembled genomes (MAGs) from a thermophilic solid state biowaste digester covered the basic functions of the biogas microbial community. Firmicutes was the most abundant phylum in the metagenome (53%) harboring species that take place in various functions ranging from the hydrolysis of polymers to syntrophic acetate oxidation. The Wood-Ljungdahl pathway for syntrophic acetate oxidation and corresponding genes for energy conservation were identified in a Dethiobacteraceae MAG that is phylogenetically related to known SAOB. 16S rRNA gene amplicon sequencing and enrichment cultivation consistently identified the uncultured Dethiobacteraceae together with Syntrophaceticus, Tepidanaerobacter, and unclassified Clostridia as members of a potential acetate-oxidizing core community in nine full-scare digesters, whereas acetoclastic methanogens were barely detected. CONCLUSIONS Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.
| | - Lukas Jansen
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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Aoyagi T, Inaba T, Aizawa H, Mayumi D, Sakata S, Charfi A, Suh C, Lee JH, Sato Y, Ogata A, Habe H, Hori T. Unexpected diversity of acetate degraders in anaerobic membrane bioreactor treating organic solid waste revealed by high-sensitivity stable isotope probing. WATER RESEARCH 2020; 176:115750. [PMID: 32272322 DOI: 10.1016/j.watres.2020.115750] [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: 09/17/2019] [Revised: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
In anaerobic membrane bioreactor (AnMBR) treating organic solid waste, acetate is one of the most important precursors to CH4. However, the identity and diversity of anaerobic acetate degraders are largely unknown, possibly due to their slow growth rates and low abundances. Here, we identified acetate-degrading microorganisms in the AnMBR sludges by high-sensitivity stable isotope probing. Degradation of the amended 13C-acetate coincided with production of 13CH4 and 13CO2 during the sludge incubation. High-throughput sequencing of RNA density fractions indicated that the aceticlastic and hydrogenotrophic methanogens, i.e., Methanosaeta sp. (acetate dissimilator) and Methanolinea sp. (acetate assimilator), incorporated 13C-acetate significantly. Remarkably, 22 bacterial species incorporating 13C-acetate were identified, whereas their majority was distantly related to the cultured representatives. Only two of them were the class Deltaproteobacteria-affiliated lineages with syntrophic volatile fatty acid oxidation activities. Phylogenetic tree analysis and population dynamics tracing revealed that novel species of the hydrolyzing and/or fermenting taxa, such as the phyla Bacteroidetes, Chloroflexi and Lentisphaerae, exhibited low relative abundances comparable to that of Methanolinea sp. (0.00011%) during the AnMBR operation, suggesting that these bacteria were involved in anaerobic acetate assimilation. Meanwhile, novel species of the phyla Firmicutes, Synergistetes and Caldiserica, the candidate phyla Aminicenantes and Atribacteria and the candidate division GOUTA4-related clade, as well as the known Deltaproteobacteria members, existed at relatively high abundances (0.00031%-0.31121%) in the reactor, suggesting that these bacterial species participated in anaerobic dissimilation of acetate, e.g., syntrophic acetate oxidation. The results of this study demonstrated the unexpected diversity and ecophysiological features of the anaerobic acetate degraders in the AnMBR treating organic solid waste.
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Affiliation(s)
- Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan
| | - Hidenobu Aizawa
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Amine Charfi
- LG-Hitachi Water Solutions Co., Ltd., Gasan R&D Campus, 51, Gasan Digital 1-ro, Geumcheon-gu, Seoul, 08592, South Korea
| | - Changwon Suh
- LG-Hitachi Water Solutions Co., Ltd., Gasan R&D Campus, 51, Gasan Digital 1-ro, Geumcheon-gu, Seoul, 08592, South Korea
| | - Jong Hoon Lee
- LG-Hitachi Water Solutions Co., Ltd., Gasan R&D Campus, 51, Gasan Digital 1-ro, Geumcheon-gu, Seoul, 08592, South Korea
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, 395-8569, Japan.
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Logroño W, Popp D, Kleinsteuber S, Sträuber H, Harms H, Nikolausz M. Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH. Microorganisms 2020; 8:microorganisms8040614. [PMID: 32344539 PMCID: PMC7232305 DOI: 10.3390/microorganisms8040614] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Biomethanation is a promising solution to convert H2 (produced from surplus electricity) and CO2 to CH4 by using hydrogenotrophic methanogens. In ex situ biomethanation with mixed cultures, homoacetogens and methanogens compete for H2/CO2. We enriched a hydrogenotrophic microbiota on CO2 and H2 as sole carbon and energy sources, respectively, to investigate these competing reactions. The microbial community structure and dynamics of bacteria and methanogenic archaea were evaluated through 16S rRNA and mcrA gene amplicon sequencing, respectively. Hydrogenotrophic methanogens and homoacetogens were enriched, as acetate was concomitantly produced alongside CH4. By controlling the media composition, especially changing the reducing agent, the formation of acetate was lowered and grid quality CH4 (≥97%) was obtained. Formate was identified as an intermediate that was produced and consumed during the bioprocess. Stirring intensities ≥ 1000 rpm were detrimental, probably due to shear force stress. The predominating methanogens belonged to the genera Methanobacterium and Methanoculleus. The bacterial community was dominated by Lutispora. The methanogenic community was stable, whereas the bacterial community was more dynamic. Our results suggest that hydrogenotrophic communities can be steered towards the selective production of CH4 from H2/CO2 by adapting the media composition, the reducing agent and the stirring intensity.
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Steinke L, Slysz GW, Lipton MS, Klatt C, Moran JJ, Romine MF, Wood JM, Anderson G, Bryant DA, Ward DM. Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat. Appl Environ Microbiol 2020; 86:e01829-19. [PMID: 31953342 PMCID: PMC7082580 DOI: 10.1128/aem.01829-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/12/2020] [Indexed: 11/20/2022] Open
Abstract
The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation.IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.
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Affiliation(s)
- Laurey Steinke
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gordon W Slysz
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christian Klatt
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - James J Moran
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Margie F Romine
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Gordon Anderson
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, Pennsylvania, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
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Awhangbo L, Bendoula R, Roger JM, Béline F. Detection of early imbalances in semi-continuous anaerobic co-digestion process based on instantaneous biogas production rate. WATER RESEARCH 2020; 171:115444. [PMID: 31918387 DOI: 10.1016/j.watres.2019.115444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to investigate the use of biogas production rate kinetics for the monitoring of anaerobic co-digestion. Recent extensive studies of degradation pathways showed that acetoclastic methanogenesis is not always the main pathway. Hydrogenotrophic methanogenesis and syntrophic acetate oxidation can also dominate, mostly for operating conditions with high concentrations of ammonia or volatile fatty acids … These conditions are also known to cause instability in the digester's operation especially in co-digestion due to substrate variability. Therefore, co-digestion experiments were conducted with several co-substrates using a continuously stirred 35-L tank reactor. Degradation pathways and their potential shifts were identified by monitoring variations in biogas production rate kinetics using a principal component analysis model. The shifts in the degradation pathways were used to monitor the process. These shift points were found to provide early warnings of instabilities in the anaerobic co-digestion process.
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Affiliation(s)
- L Awhangbo
- Irstea, UR OPAALE, 17 av. de Cucillé, CS 64427, F-35044, Rennes, France; Univ. Bretagne Loire, France.
| | - R Bendoula
- Irstea, UMR ITAP, 361, rue J.F. Breton, BP 5095, F-34196, Montpellier, France.
| | - J M Roger
- Irstea, UMR ITAP, 361, rue J.F. Breton, BP 5095, F-34196, Montpellier, France.
| | - F Béline
- Irstea, UR OPAALE, 17 av. de Cucillé, CS 64427, F-35044, Rennes, France.
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Zhu X, Campanaro S, Treu L, Seshadri R, Ivanova N, Kougias PG, Kyrpides N, Angelidaki I. Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem. MICROBIOME 2020; 8:22. [PMID: 32061251 PMCID: PMC7024554 DOI: 10.1186/s40168-019-0780-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/27/2019] [Indexed: 05/03/2023]
Abstract
Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.
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Affiliation(s)
- Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121, Padua, Italy
- CRIBI Biotechnology Center, University of Padua, 35131, Padua, Italy
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark.
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121, Padua, Italy.
| | - Rekha Seshadri
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark.
- Soil and Water Resources Institute, Hellenic Organisation-DEMETER, 57001, Thermi-, Thessaloniki, Greece.
| | - Nikos Kyrpides
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark
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Jiang Y, Chu N, Qian DK, Jianxiong Zeng R. Microbial electrochemical stimulation of caproate production from ethanol and carbon dioxide. BIORESOURCE TECHNOLOGY 2020; 295:122266. [PMID: 31669871 DOI: 10.1016/j.biortech.2019.122266] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/08/2019] [Accepted: 10/12/2019] [Indexed: 06/10/2023]
Abstract
The production of value added chemicals from CO2 is of critical importance for the practical application of microbial electrosynthesis (MES). Here, a binary electron donor (ED) design (using electrode and ethanol) was introduced to provide an efficient caproate production with the bioconversion of both CO2 and ethanol. A maximum caproate production rate of 2.41 ± 0.69 g L-1 d-1, and a final concentration of 7.66 ± 1.38 g L-1 was achieved. Caproate production selectivity based on the substrate increased to 91.47 ± 0.58% (Binary EDs) from 32.22 ± 32.58% (open circuit Electrode ED). An observed amount of 23.43 ± 0.69% of carbon within the final binary ED products originated from the CO2. This work proves for the first time the potential of caproate production from CO2 utilization and ethanol upgrading using solid electrodes to regulate the chain elongation process.
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Affiliation(s)
- Yong Jiang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Na Chu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ding-Kang Qian
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Raymond Jianxiong Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Abstract
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
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