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Niya B, Yaakoubi K, Beraich FZ, Arouch M, Meftah Kadmiri I. Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches. Heliyon 2024; 10:e28221. [PMID: 38560681 PMCID: PMC10979216 DOI: 10.1016/j.heliyon.2024.e28221] [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] [Received: 08/17/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.
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Affiliation(s)
- Btissam Niya
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Kaoutar Yaakoubi
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Fatima Zahra Beraich
- Biodome.sarl, Research and Development Design Office of Biogas Technology, Casablanca, Morocco
| | - Moha Arouch
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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2
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Nutaratat P, Arigul T, Srisuk N, Kruasuwan W. Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil. PLoS One 2024; 19:e0299251. [PMID: 38442103 PMCID: PMC10914256 DOI: 10.1371/journal.pone.0299251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Environmental variations have been observed to influence bacterial community composition, thereby impacting biological activities in the soil. Together, the information on bacterial functional groups in Phatthalung sago palm-growing soils remains limited. In this work, the core soil bacterial community in the Phatthalung sago palm-growing areas during both the summer and rainy seasons was examined using V3-V4 amplicon sequencing. Our findings demonstrated that the seasons had no significant effects on the alpha diversity, but the beta diversity of the community was influenced by seasonal variations. The bacteria in the phyla Acidobacteriota, Actinobacteriota, Chloroflexi, Methylomirabilota, Planctomycetota, and Proteobacteria were predominantly identified across the soil samples. Among these, 26 genera were classified as a core microbiome, mostly belonging to uncultured bacteria. Gene functions related to photorespiration and methanogenesis were enriched in both seasons. Genes related to aerobic chemoheterotrophy metabolisms and nitrogen fixation were more abundant in the rainy season soils, while, human pathogen pneumonia-related genes were overrepresented in the summer season. The investigation not only provides into the bacterial composition inherent to the sago palm-cultivated soil but also the gene functions during the shift in seasons.
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Affiliation(s)
- Pumin Nutaratat
- Department of Biology, Faculty of Science and Digital Innovation, Thaksin University, Pa Phayom, Phatthalung, Thailand
- Microbial Technology for Agriculture, Food and Environment Research Center, Faculty of Science and Digital Innovation, Thaksin University, Pa Phayom, Phatthalung, Thailand
| | - Tantip Arigul
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, Thailand
| | - Worarat Kruasuwan
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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3
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Peng G, Li-Xian L, Xi L, Shuang-Fei W, Jian Z. Roles of entrapped bubbles in methanogenic granules under oscillating pressure: Respiration and embolization for intra-granular transport. BIORESOURCE TECHNOLOGY 2024; 395:130356. [PMID: 38262541 DOI: 10.1016/j.biortech.2024.130356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
Anaerobic granular sludge plays a pivotal role in the treatment of concentrated organic wastewater. However, previous studies on intra- granular transport have generally overlooked lung-like respiration that expedites transport in response to fluctuating pressure. This study explored the activities of calcified and normal granules under simulated hydrostatic pressure oscillations. The results revealed a significant enhancement in the bioactivity of calcified granules under oscillating pressure, contrasting with the comparatively lower bioactivity observed in normal granules. The hypothesis posited that the gas pockets in calcified granules facilitated respiration as the functional structure. The presence of tiny bubbles exhibited a propensity for inducing clogging, thereby diminishing the capillary connectivity essential for substrate diffusion. The proposed respiration and embolization concepts decipher the distinct roles of entrapped bubbles in the granular bioactivity across diverse fluid states. This study offers valuable insights into the impact of fluidization on microscopic transport within granule-based bed reactors.
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Affiliation(s)
- Gan Peng
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Lu Li-Xian
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Liu Xi
- Guangxi Bossco Environment Co., Ltd, Nanning 530007, China
| | - Wang Shuang-Fei
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Zhang Jian
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China.
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4
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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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5
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Shi Z, Zhang C, Tan X, Xie L, Luo G. Syntrophic microbes involved in the oxidation of short-chain fatty acids in continuous-flow anaerobic digesters treating waste activated sludge with hydrochar. Appl Environ Microbiol 2024; 90:e0204723. [PMID: 38205997 PMCID: PMC10880590 DOI: 10.1128/aem.02047-23] [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: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
The rapid degradation of short-chain fatty acids (SCFAs) is an essential issue of anaerobic digestion (AD), in which SCFA oxidizers could generally metabolize in syntrophy with methanogens. The dynamic responses of active metagenome-assembled genomes to low concentrations of propionate and acetate were analyzed to identify specific syntrophic SCFA oxidizers and their metabolic characteristics in continuous-flow AD systems treating waste activated sludge with and without hydrochar. In this study, hydrochar increased methane production by 19%, possibly due to hydrochar enhancing acidification and methanogenesis processes. A putative syntrophic propionate oxidizer and two acetate oxidizers contributed substantially to the syntrophic degradation of SCFAs, and hydrochar positively regulated their functional gene expressions. A significant relationship was established between the replication rate of SCFA oxidizers and their stimulation-related transcriptional activity. Acetate was degraded in the hydrochar group, which might be mainly through the syntrophic acetate oxidizer from the genus Desulfallas and methanogens from the genus Methanosarcina.IMPORTANCEShort-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar.
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Affiliation(s)
- Zhijian Shi
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Chen Zhang
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Xuejun Tan
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Gang Luo
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
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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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Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK. Identification and cultivation of anaerobic bacterial scavengers of dead cells. THE ISME JOURNAL 2023; 17:2279-2289. [PMID: 37872273 PMCID: PMC10689501 DOI: 10.1038/s41396-023-01538-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
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Affiliation(s)
- Yuga Hirakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
| | - Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Taiki Katayama
- Geomicrobiology Research Group, Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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8
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Finn DR, Rohe L, Krause S, Guliyev J, Loewen A, Tebbe CC. Methanogenesis in biogas reactors under inhibitory ammonia concentration requires community-wide tolerance. Appl Microbiol Biotechnol 2023; 107:6717-6730. [PMID: 37672072 PMCID: PMC10567828 DOI: 10.1007/s00253-023-12752-5] [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: 06/05/2023] [Revised: 08/11/2023] [Accepted: 08/26/2023] [Indexed: 09/07/2023]
Abstract
Ammonia (NH3) inhibition represents a major limitation to methane production during anaerobic digestion of organic material in biogas reactors. This process relies on co-operative metabolic interactions between diverse taxa at the community-scale. Despite this, most investigations have focused singularly on how methanogenic Archaea respond to NH3 stress. With a high-NH3 pre-adapted and un-adapted community, this study investigated responses to NH3 inhibition both at the community-scale and down to individual taxa. The pre-adapted community performed methanogenesis under inhibitory NH3 concentrations better than the un-adapted. While many functionally important phyla were shared between the two communities, only taxa from the pre-adapted community were robust to NH3. Functionally important phyla were mostly comprised of sensitive taxa (≥ 50%), yet all groups, including methanogens, also possessed tolerant individuals (10-50%) suggesting that potential mechanisms for tolerance are non-specific and widespread. Hidden Markov Model-based phylogenetic analysis of methanogens confirmed that NH3 tolerance was not restricted to specific taxonomic groups, even at the genus level. By reconstructing covarying growth patterns via network analyses, methanogenesis by the pre-adapted community was best explained by continued metabolic interactions (edges) between tolerant methanogens and other tolerant taxa (nodes). However, under non-inhibitory conditions, sensitive taxa re-emerged to dominate the pre-adapted community, suggesting that mechanisms of NH3 tolerance can be disadvantageous to fitness without selection pressure. This study demonstrates that methanogenesis under NH3 inhibition depends on broad-scale tolerance throughout the prokaryotic community. Mechanisms for tolerance seem widespread and non-specific, which has practical significance for the development of robust methanogenic biogas communities. KEY POINTS: • Ammonia pre-adaptation allows for better methanogenesis under inhibitory conditions. • All functionally important prokaryote phyla have some ammonia tolerant individuals. • Methanogenesis was likely dependent on interactions between tolerant individuals.
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Affiliation(s)
- Damien R Finn
- Thünen Institute for Biodiversity, Johann Heinrich von Thünen Institute, 38116, Braunschweig, Germany.
| | - Lena Rohe
- Thünen Institute for Climate-Smart Agriculture, Johann Heinrich von Thünen Institute, 38116, Braunschweig, Germany
| | - Sascha Krause
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062, China
| | - Jabrayil Guliyev
- Faculty of Resource Management, University of Applied Sciences and Arts (HAWK), 37085, Göttingen, Germany
| | - Achim Loewen
- Faculty of Resource Management, University of Applied Sciences and Arts (HAWK), 37085, Göttingen, Germany
| | - Christoph C Tebbe
- Thünen Institute for Biodiversity, Johann Heinrich von Thünen Institute, 38116, Braunschweig, Germany
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9
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Dang H, Ewald JM, Mattes TE. Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16386-16398. [PMID: 37856784 PMCID: PMC10621002 DOI: 10.1021/acs.est.3c05439] [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: 07/10/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Jessica M. Ewald
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Timothy E. Mattes
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
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10
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Hong Dao NP, Nguyen TH, Watari T, Hatamoto M, Tan NM, Huong NL, Yamaguchi T. Investigate the anaerobic degradation of high-acetone latex wastewater with magnetite supplement. CHEMOSPHERE 2023; 339:139626. [PMID: 37487980 DOI: 10.1016/j.chemosphere.2023.139626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/24/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This study evaluated the effects of acetone on the anaerobic degradation of synthetic latex wastewater, which was simulated from the wastewater of the deproteinized natural rubber production process, including latex, acetate, propionate, and acetone as the main carbon sources, at a batch scale in 5 cycles of a total of 60 days. Fe3O4 was applied to accelerate the treatment performance from cycle 3. Acetone was added in concentration ranges of 0%, 0.05%, 0.1%, 0.15%-included latex, and 0.15%-free latex (w/v). In the Fe3O4-free cycles, for latex-added vials, soluble chemical oxygen demand (sCOD) was removed at 43.20%, 43.20%, and 12.65%, corresponding to the input acetone concentrations varying from 0.05% to 0.15%, indicating the interference of acetone for COD reduction. After adding Fe3O4, all flasks reported a significant increase in COD removal efficiency, especially for acetone-only and latex-only vials, from 36.9% to 14.30%-42.95% and 83.20%, respectively. Other highlighted results of COD balance showed that Fe3O4 involvement improved the degradation process of acetate, propionate, acetone, and the other COD parts, including the intermediate products of latex reduction. Besides, during the whole batch process, the order of reduction priority of the carbon sources in the synthetic wastewater was acetate, propionate and acetone. We also found that the acetate concentration appeared to be strongly related to reducing other carbon sources in natural rubber wastewater. Microbial community analysis revealed that protein-degrading bacteria Bacteroidetes vadinHA17 and Proteinniphilum and methylotrophic methanogens might play key roles in treating simulated deproteinized-natural-rubber wastewater.
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Affiliation(s)
- Nguyen Pham Hong Dao
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Thu Huong Nguyen
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan; School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam.
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Nguyen Minh Tan
- Institute for R&D of Natural Products, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam
| | - Nguyen Lan Huong
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan; Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan; School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, 11600, Viet Nam
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11
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George AB, Wang T, Maslov S. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. THE ISME JOURNAL 2023; 17:1482-1494. [PMID: 37380829 PMCID: PMC10432562 DOI: 10.1038/s41396-023-01455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
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Affiliation(s)
- Ashish B George
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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12
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Kuroda K, Tomita S, Kurashita H, Hatamoto M, Yamaguchi T, Hori T, Aoyagi T, Sato Y, Inaba T, Habe H, Tamaki H, Hagihara Y, Tamura T, Narihiro T. Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems. WATER RESEARCH X 2023; 20:100196. [PMID: 37662426 PMCID: PMC10469934 DOI: 10.1016/j.wroa.2023.100196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/03/2023] [Accepted: 08/12/2023] [Indexed: 09/05/2023]
Abstract
Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Shun Tomita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Hazuki Kurashita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Masashi Hatamoto
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Hideyuki Tamaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshihisa Hagihara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
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13
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Li J, Xu X, Chen C, Xu L, Du Z, Gu L, Xiang P, Shi D, Huangfu X, Liu F. Conductive materials enhance microbial salt-tolerance in anaerobic digestion of food waste: Microbial response and metagenomics analysis. ENVIRONMENTAL RESEARCH 2023; 227:115779. [PMID: 36967003 DOI: 10.1016/j.envres.2023.115779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 05/08/2023]
Abstract
Previous studies have shown that high salinity environments can inhibit anaerobic digestion (AD) of food waste (FW). Finding ways to alleviate salt inhibition is important for the disposal of the growing amount of FW. We selected three common conductive materials (powdered activated carbon, magnetite, and graphite) to understand their performance and individual mechanisms that relieve salinity inhibition. Digester performances and related enzyme parameters were compared. Our data revealed that under normal and low salinity stress conditions, the anaerobic digester ran steady without significant inhibitions. Further, the presence of conductive materials promoted conversion rate of methanogenesis. This promotion effect was highest from magnetite > powdered activated carbon (PAC) > graphite. At 1.5% salinity, PAC and magnetite are beneficial in maintaining high methane production efficiency while control and the graphite added digester acidified and failed rapidly. Additionally, metagenomics and binning were used to analyze the metabolic capacity of the microorganisms. Some species enriched by PAC and magnetite possessed higher cation transport capacities and were to accumulate compatible solutes. PAC and magnetite promoted direct interspecies electron transference (DIET) and syntrophic oxidation of butyrate and propionate. Also, the microorganisms had more energy available to cope with salt inhibition in the PAC and magnetite added digesters. Our data imply that the promotion of Na+/H+ antiporter, K+ uptake, and osmoprotectant synthesis or transport by conductive materials may be crucial for their proliferation in highly stressful environments. These findings will help to understand the mechanisms of alleviate salt inhibition by conductive materials and help to recover methane from high-salinity FW.
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Affiliation(s)
- Jianhao Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Xiaofeng Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Cong Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Linji Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Zexuan Du
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Li Gu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China.
| | - Ping Xiang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China.
| | - Dezhi Shi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Xiaoliu Huangfu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, 400045, PR China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
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14
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Wirth R, Bagi Z, Shetty P, Szuhaj M, Cheung TTS, Kovács KL, Maróti G. Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants. THE ISME JOURNAL 2023:10.1038/s41396-023-01448-3. [PMID: 37286740 DOI: 10.1038/s41396-023-01448-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.
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Affiliation(s)
- Roland Wirth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.
- Faculty of Water Sciences, University of Public Service, Baja, Hungary.
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15
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Hou Y, He M, Liu Y, Wang Q, Yang A, Yang F, Lei Z, Yi X, Huang W. Biological nitrogen removal mechanisms during anaerobic digestion of swine manure: Effects of biogas circulation and activated carbon addition. BIORESOURCE TECHNOLOGY 2023; 374:128766. [PMID: 36813051 DOI: 10.1016/j.biortech.2023.128766] [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: 01/03/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
This study investigated the biological nitrogen removal mechanisms during the anaerobic digestion of swine manure and the effects of biogas circulation and activated carbon (AC) addition. Biogas circulation, AC addition, and their combination increased the methane yield by 25.9%, 22.3%, and 44.1%, respectively, when compared to the control. Nitrogen species analysis and metagenomic results indicated that nitrification-denitrification was the dominant ammonia removal pathway in all digesters with little oxygen, while anammox did not occur. Biogas circulation could promote mass transfer and induce air infiltration to enrich nitrification- and denitrification-related bacteria and functional genes. And AC might act as an electron shuttle to facilitate ammonia removal. The combined strategies showed a synergetic effect on the enrichment of nitrification and denitrification bacteria and functional genes, significantly lowering the total ammonia nitrogen by 23.6%. A single digester with biogas circulation and AC addition could enhance methanogenesis and ammonia removal via nitrification and denitrification.
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Affiliation(s)
- Yaoqi Hou
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Mengqi He
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Yongjie Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Qian Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Aopan Yang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Fei Yang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Xuesong Yi
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Weiwei Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China.
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16
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Peng F, Zhang Z, Sun M, Shao Y, Feng Y. Evaluating performance of nano-Fe 3O 4 modified granular activated carbon assisted wastewater treatment in anaerobic fluidized membrane bioreactor. BIORESOURCE TECHNOLOGY 2023; 374:128737. [PMID: 36781146 DOI: 10.1016/j.biortech.2023.128737] [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: 12/24/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Magnetic granular activated carbon (MGAC), a nano-Fe3O4 modified granular activated carbon, was used as the carrier in an anaerobic fluidized-bed membrane bioreactor (AFMBR) to promote domestic wastewater treatment efficiency and alleviate membrane biofouling. Chemical oxygen demand (COD) removal reached 89 ± 2.6% with the effluent concentration of 20 ± 3.9 mg/L in the MGAC-AFMBR, while it was 28 ± 5.2 mg/L in AFMBR at hydraulic retention time (HRT) of 4 h. Total nitrogen (TN) removal was also enhanced by 4.0% with MGAC. An increased proportion of Chloroflexi and Bacteroidetes in the sludge may be responsible for improved treatment performance. MGAC reduced the protein and polysaccharide content in extracellular polymeric substances (EPS) by 9.8% and 8.1%, respectively. Besides, Bacteroidetes and Proteobacteria abundance decreased by 4.0% and 16.6% in the membrane cake layer with MGAC addition. Therefore, the high-quality effluent and low membrane biofouling of AFMBR was sustained by MGAC.
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Affiliation(s)
- Fangyue Peng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Zhaohan Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Muchen Sun
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Yuqiang Shao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090, China.
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17
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Yan X, Deng P, Ding T, Zhang Z, Li X, Wu Z. Effect of Temperature on Anaerobic Fermentation of Poplar Ethanol Wastewater: Performance and Microbial Communities. ACS OMEGA 2023; 8:5486-5496. [PMID: 36816634 PMCID: PMC9933484 DOI: 10.1021/acsomega.2c06721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Temperature plays an important role in anaerobic digestion (AD), and different substrates have different optimum temperatures in AD. However, the effect of temperature on the performance of AD when cellulosic ethanol wastewater was used as a substrate was rarely reported. Therefore, the digestion characteristics of cellulosic ethanol wastewater at 25, 35, 45, and 55 °C were investigated, and the microbial communities of the sludge sample were analyzed after fermentation. The results showed that the cumulative methane production was the highest at 55 °C, 906.40 ± 50.67 mL/g VS, which was 81.06, 72.42, and 13.33% higher than that at 25, 35, and 45 °C, respectively. The content of methane was 68.13, 49.26, 70.46, and 85.84% at the terminal period of fermentation at temperatures of 25, 35, 45, and 55 °C, respectively. The testing of volatile fatty acids (VFAs) indicated that the accumulation of VFAs did not occur when the fermentation was carried out at 25, 35, and 45 °C; however, the VFA content at 55 °C was much larger than that in the three groups (25, 35, and 45 °C), and the ratio of propionic acid to acetic acid was larger than 1.4 at the late stage of fermentation, so it inhibited the fermentation. The diversity of the microbial community indicated that the floral structure and metabolic pathway of fermentation were alike at 25 and 35 °C. Firmicutes and Proteobacteria were the main flora covering the 25-55 °C-based phylum or below it. The relative abundance of Methanosaeta was the highest when fermentation temperatures were 25 and 35 °C; however, its relative abundance decreased sharply and the relative abundance of Methanosarcina increased substantially when the temperature increased from 35 to 45 °C, which indicated that Methanosarcina can exist in higher temperatures. At the same time, hydrogenotrophic methanogens such as Methanoculleus and Methanothermobacter were dominant when fermentation temperatures were 45 and 55 °C, which indicated that the metabolic pathway changed from acetoclastic methanogenesis to hydrogenotrophic methanogenesis.
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18
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Chai L, Wang H, Li X, Wang H. Comparison of the characteristics of gut microbiota response to lead in Bufo gargarizans tadpole at different developmental stages. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20907-20922. [PMID: 36261638 DOI: 10.1007/s11356-022-23671-9] [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: 06/08/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
In amphibians, lead (Pb) exposure could alter the composition and structure of gut microbiota, but changes involving microbiota of several successive phases following Pb exposure have been less studied. In the present study, we compared the effects of Pb exposure on morphological parameters and gut microbiota of Bufo gargarizans at Gosner stage (Gs) 33, Gs36, and Gs42. Our results showed that total length (TL), snout-vent length (SVL), and body wet weight (TW) of B. gargarizans at Gs33, as well as TL and SVL at Gs42, were significantly increased after Pb exposure. In addition, high-throughput sequencing analysis indicated that gut microbiota has distinct responses to Pb exposure at different developmental stages. The diversity of gut microbiota was significantly reduced under Pb exposure at Gs33, while it was significantly increased at Gs42. In terms of community composition, Spirochaetota, Armatimonadota, and Patescibacteria appeared in the control groups at Gs42, but not after Pb treatment. Furthermore, functional prediction indicated that the relative abundance of metabolism pathway was significantly decreased at Gs33 and Gs36, and significantly increased at Gs42. Our results fill an important knowledge gap and provide comparative information on the gut microbiota of tadpoles at different developmental stages following Pb exposure.
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Affiliation(s)
- Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710062, China
| | - Hemei Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xinyi Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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Zhang K, Deng Y, Liu Z, Feng Y, Hu C, Wang Z. Biochar Facilitated Direct Interspecies Electron Transfer in Anaerobic Digestion to Alleviate Antibiotics Inhibition and Enhance Methanogenesis: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20032296. [PMID: 36767663 PMCID: PMC9915179 DOI: 10.3390/ijerph20032296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/04/2023]
Abstract
Efficient conversion of organic waste into low-carbon biofuels such as methane through anaerobic digestion (AD) is a promising technology to alleviate energy shortages. However, issues such as inefficient methane production and poor system stability remain for AD technology. Biochar-facilitated direct interspecies electron transfer (DIET) has recently been recognized as an important strategy to improve AD performance. Nonetheless, the underlying mechanisms of biochar-facilitated DIET are still largely unknown. For this reason, this review evaluated the role of biochar-facilitated DIET mechanism in enhancing AD performance. First, the evolution of DIET was introduced. Then, applications of biochar-facilitated DIET for alleviating antibiotic inhibition and enhancing methanogenesis were summarized. Next, the electrochemical mechanism of biochar-facilitated DIET including electrical conductivity, redox-active characteristics, and electron transfer system activity was discussed. It can be concluded that biochar increased the abundance of potential DIET microorganisms, facilitated microbial aggregation, and regulated DIET-associated gene expression as a microbial mechanism. Finally, we also discussed the challenges of biochar in practical application. This review elucidated the role of DIET facilitated by biochar in the AD system, which would advance our understanding of the DIET mechanism underpinning the interaction of biochar and anaerobic microorganisms. However, direct evidence for the occurrence of biochar-facilitated DIET still requires further investigation.
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Affiliation(s)
- Kaoming Zhang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou 510006, China
| | - Yuepeng Deng
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou 510006, China
| | - Zhiquan Liu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou 510006, China
| | - Yiping Feng
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Chun Hu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou 510006, China
| | - Zhu Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou 510006, China
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20
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Bai S, Chen J, Guo M, Ren N, Zhao X. Vertical-scale spatial influence of radial oxygen loss on rhizosphere microbial community in constructed wetland. ENVIRONMENT INTERNATIONAL 2023; 171:107690. [PMID: 36516673 DOI: 10.1016/j.envint.2022.107690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Complex interactions between plants and microorganisms form the basis of constructed wetlands (CWs) for pollutant removal. In the rhizosphere, radial oxygen loss (ROL) plays a key role in the activity and abundance of functional microorganisms. However, little has been done to explore how ROL would influence the niche differentiation of microbial communities at different vertical spatial scales. We demonstrate that ROL decreases with depth, promoting an oxidation-reduction rhizosphere microecosystem in CWs. The high level of ROL in the upper layer could support the oxygen supply for aerobic bacteria (Haliangium), facilitating the COD (60%) and NH4+-N (50%) removal, whereas the enrichment of denitrifiers (e.g., Hydrogenophaga and Ralstonia) and methanotrophs (Methanobaterium) in the lower layer could stimulate denitrification. The function prediction results further certified that the abundance of genes catalyzing nitrifying and denitrification processes were significantly enhanced in the upper and bottom layers, respectively, which was attributed to the oxygen concentration gradient in the rhizosphere. This study contributes to further unraveling the rhizosphere effect and enables an improved understanding of the decontamination mechanisms of CWs.
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Affiliation(s)
- Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Juntong Chen
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Nanqi Ren
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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21
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Mercado JV, Koyama M, Nakasaki K. Complexity of acclimatization substrate affects anaerobic digester microbial community response to organic load shocks. ENVIRONMENTAL RESEARCH 2023; 216:114722. [PMID: 36343710 DOI: 10.1016/j.envres.2022.114722] [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: 12/21/2021] [Revised: 10/15/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
This study elucidated the changes in the short-term response to organic load shocks of the anaerobic digestion (AD) microbiome acclimatized to a simple substrate and a complex substrate. Batch vial reactors were inoculated with AD sludge acclimatized to either a simple (starch and hipolypeptone) or a complex (dog food and starch) substrate, both with carbon-to-nitrogen ratio of 25. Organic loads in the form of an easily degradable substrate mix (starch and hipolypeptone) with concentrations varying from 0 to 5 g VS/L were applied to the reactors. Runs utilizing the inoculum acclimatized to a complex substrate sustained its methane productivity despite the high organic load shocks which the inoculum acclimatized to a simple substrate was unable to handle efficiently. The alpha-diversity of the microbiome decreased with increase in organic load for inoculum acclimatized with a simple substrate but was unaffected for the case of the inoculum acclimatized with a complex substrate. LactobacillalesandCloacimonadales were inferred to be major players in starch degradation pathways for the inoculum acclimatized using a simple substrate as predicted by the bioinformatics package PICRUSt2. However, acclimatizing using a complex substrate did not support their growth and were replaced by Coriobacteriales which provided higher flexibility in terms of the predicted regulated metabolic functions. The predicted functional regulation of Synergistales and Syntrophales increased with acclimatization using a complex substrate which also showed increase in the flexibility of the microbiome towards handling organic load shocks. Acetoclastic pathway was upregulated with increase in organic load regardless of the acclimatization substrate while the hydrogenotrophic pathway was downregulated. Overall, acclimatization using a complex substrate increased the robustness and flexibility of the microbiome towards organic load shocks.
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Affiliation(s)
- Jericho Victor Mercado
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Mitsuhiko Koyama
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Kiyohiko Nakasaki
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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22
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Characterization of Biofilm Microbiome Formation Developed on Novel 3D-Printed Zeolite Biocarriers during Aerobic and Anaerobic Digestion Processes. FERMENTATION 2022. [DOI: 10.3390/fermentation8120746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Aerobic or anaerobic digestion is involved in treating agricultural and municipal waste, and the addition of biocarriers has been proven to improve them further. We synthesized novel biocarriers utilizing zeolites and different inorganic binders and compared their efficiency with commercially available biocarriers in aerobic and anaerobic digestion systems. Methods: We examined BMP and several physicochemical parameters to characterize the efficiency of novel biocarriers on both systems. We also determined the SMP and EPS content of synthesized biofilm and measured the adherence and size of the forming biofilm. Finally, we characterized the samples by 16S rRNA sequencing to determine the crucial microbial communities involved. Results: Evaluating BMP results, ZSM-5 zeolite with bentonite binder emerged, whereas ZSM-5 zeolite with halloysite nanotubes binder stood out in the wastewater treatment experiment. Twice the relative frequencies of archaea were found on novel biocarriers after being placed in AD batch reactors, and >50% frequencies of Proteobacteria after being placed in WWT reactors, compared to commercial ones. Conclusions: The newly synthesized biocarriers were not only equally efficient with the commercially available ones, but some were even superior as they greatly enhanced aerobic or anaerobic digestion and showed strong biofilm formation and unique microbiome signatures.
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23
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Cazaudehore G, Guyoneaud R, Lallement A, Gassie C, Monlau F. Biochemical methane potential and active microbial communities during anaerobic digestion of biodegradable plastics at different inoculum-substrate ratios. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 324:116369. [PMID: 36202034 DOI: 10.1016/j.jenvman.2022.116369] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The influence of the inoculum-substrate ratio (ISR) on the mesophilic and thermophilic biochemical methane potential test of two biodegradable plastics was evaluated. Poly(lactic acid) (PLA) and polyhydroxybutyrate (PHB) were selected for this study, the first for being recalcitrant to mesophilic anaerobic digestion (AD) and the second, by contrast, for being readily biodegradable. Several ISRs, calculated on the basis of volatile solids (VS), were tested: 1, 2, 2.85, 4, and 10 g(VS of inoculum).g(VS of substrate)-1. A high ISR was associated with an enhanced methane production rate (i.e., biodegradation kinetics). However, the ultimate methane production did not change, except when inhibition was observed. Indeed, applying the lowest ISR to readily biodegradable plastics such as PHB resulted in inhibition of methane production. Based on these experiments, in order to have reproducible degradation kinetics and optimal methane production, an ISR between 2.85 and 4 is recommended for biodegradable plastics. The active microbial communities were analyzed, and the active bacteria differed depending on the plastic digested (PLA versus PHB) and the temperature of the process (mesophilic versus thermophilic). Previously identified PHB degraders (Ilyobacter delafieldii and Enterobacter) were detected in PHB-fed reactors. Thermogutta and Tepidanaerobacter were detected during the thermophilic AD of PLA, and they are probably involved in PLA hydrolysis and lactate conversion, respectively.
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Affiliation(s)
- G Cazaudehore
- APESA, Pôle Valorisation, 64121 Montardon, France; Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France.
| | - R Guyoneaud
- Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France
| | - A Lallement
- APESA, Pôle Valorisation, 64121 Montardon, France
| | - C Gassie
- Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France
| | - F Monlau
- APESA, Pôle Valorisation, 64121 Montardon, France
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24
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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: 0] [Impact Index Per Article: 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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25
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Yue Y, Wang F, Pan J, Chen XP, Tang Y, Yang Z, Ma J, Li M, Yang M. Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load. FEMS Microbiol Ecol 2022; 98:6701916. [PMID: 36111740 DOI: 10.1093/femsec/fiac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023] Open
Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
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Affiliation(s)
- Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xue-Ping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Yi Tang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Zhihong Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
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26
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Wang B, Liu W, Liang B, Jiang J, Wang A. Microbial fingerprints of methanation in a hybrid electric-biological anaerobic digestion. WATER RESEARCH 2022; 226:119270. [PMID: 36323204 DOI: 10.1016/j.watres.2022.119270] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/26/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biomethane as a sustainable, alternative, and carbon-neutral renewable energy source to fossil fuels is highly needed to alleviate the global energy crisis and climate change. The conventional anaerobic digestion (AD) process for biomethane production from waste(water) streams has been widely employed while struggling with a low production rate, low biogas qualities, and frequent instability. The electric-biologically hybrid microbial electrochemical anaerobic digestion system (MEC-AD) prospects more stable and robust biomethane generation, which facilitates complex organic substrates degradation and mediates functional microbial populations by giving a small input power (commonly voltages < 1.0 V), mainly enhancing the communication between electroactive microorganisms and (electro)methanogens. Despite numerous bioreactor tests and studies that have been conducted, based on the MEC-AD systems, the integrated microbial fingerprints, and cooperation, accelerating substrate degradation, and biomethane production, have not been fully summarized. Herein, we present a comprehensive review of this novel developing biotechnology, beginning with the principles of MEC-AD. First, we examine the fundamentals, configurations, classifications, and influential factors of the whole system's performances (reactor types, applied voltages, temperatures, conductive materials, etc.,). Second, extracellular electron transfer either between diverse microbes or between microbes and electrodes for enhanced biomethane production are analyzed. Third, we further conclude (electro)methanogenesis, and microbial interactions, and construct ecological networks of microbial consortia in MEC-AD. Finally, future development and perspectives on MEC-AD for biomethane production are proposed.
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Affiliation(s)
- Bo Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China; Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark; Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Wenzong Liu
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China.
| | - Bin Liang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China
| | - Jiandong Jiang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Aijie Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
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27
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Zhang J, Li X, Klümper U, Lei H, Berendonk TU, Guo F, Yu K, Yang C, Li B. Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches. MICROBIOME 2022; 10:180. [PMID: 36280854 PMCID: PMC9590159 DOI: 10.1186/s40168-022-01361-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND As a widely used broad-spectrum antibiotic, chloramphenicol is prone to be released into environments, thus resulting in the disturbance of ecosystem stability as well as the emergence of antibiotic resistance genes. Microbes play a vital role in the decomposition of chloramphenicol in the environment, and the biotransformation processes are especially dependent on synergistic interactions and metabolite exchanges among microbes. Herein, the comprehensive chloramphenicol biotransformation pathway, key metabolic enzymes, and interspecies interactions in an activated sludge-enriched consortium were elucidated using integrated multi-omics and cultivation-based approaches. RESULTS The initial biotransformation steps were the oxidization at the C1-OH and C3-OH groups, the isomerization at C2, and the acetylation at C3-OH of chloramphenicol. Among them, the isomerization is an entirely new biotransformation pathway of chloramphenicol discovered for the first time. Furthermore, we identified a novel glucose-methanol-choline oxidoreductase responsible for the oxidization of the C3-OH group in Sphingomonas sp. and Caballeronia sp. Moreover, the subsequent biotransformation steps, corresponding catalyzing enzymes, and the microbial players responsible for each step were deciphered. Synergistic interactions between Sphingomonas sp. and Caballeronia sp. or Cupriavidus sp. significantly promoted chloramphenicol mineralization, and the substrate exchange interaction network occurred actively among key microbes. CONCLUSION This study provides desirable strain and enzyme resources for enhanced bioremediation of chloramphenicol-contaminated hotspot sites such as pharmaceutical wastewater and livestock and poultry wastewater. The in-depth understanding of the chloramphenicol biotransformation mechanisms and microbial interactions will not only guide the bioremediation of organic pollutants but also provide valuable knowledge for environmental microbiology and biotechnological exploitation. Video Abstract.
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Affiliation(s)
- Jiayu Zhang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- School of Environment, Tsinghua University, Beijing, China
| | - Xiaoyan Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Huaxin Lei
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- School of Environment, Tsinghua University, Beijing, China
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Fangliang Guo
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- School of Environment, Tsinghua University, Beijing, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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28
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Zhuravleva EA, Shekhurdina SV, Kotova IB, Loiko NG, Popova NM, Kryukov E, Kovalev AA, Kovalev DA, Litti YV. Effects of various materials used to promote the direct interspecies electron transfer on anaerobic digestion of low-concentration swine manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156073. [PMID: 35618137 DOI: 10.1016/j.scitotenv.2022.156073] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 05/23/2023]
Abstract
The activation of direct interspecies electron transfer (DIET) by the supplementation of conductive materials is one of the effective and available methods to enhance anaerobic digestion (AD). Microorganisms that colonize the surface of these materials form biofilms, the study of which could provide new insights into the character of the DIET process and its effect on AD. The present study focused on AD performance, microbial community, as well as morphological and topological features of biofilms on various materials used to promote DIET during AD of low-concentration swine manure. The best AD characteristics were observed in stainless steel mesh (SM)/digested cow manure (CM) and polyester felt (PF)/digested sewage sludge (SS) combinations used as material/inoculum, respectively. Thus, potential methane yields in CM-SM and SS-PF were up to 26.4% and 26.2% higher compared to the corresponding controls. Microbial analysis of biofilms revealed the dominance of putatively syntrophic bacteria of the MBA03 group of the Limnochordia class in CM inoculated reactors, and syntrophic proteolytic bacteria of the genus Coprothermobacter and acetogenic Clostridium sensu stricto 1, known for their ability to carry out DIET, in SS inoculated reactors. Biofilms on non-conductive materials contained pili-like structures, which were observed only in SS inoculated reactors. Polyester felt tended to biofoul better than carbon felt, resulting in up to 2.8, 3.2 and 1.8 higher nucleic acid, extracellular polymeric substances, and total biomass content, respectively, depending on the inoculum. These results provide new insights into the different types of DIET that can occur in low-loaded AD systems with attached growth.
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Affiliation(s)
- Elena A Zhuravleva
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia
| | - Svetlana V Shekhurdina
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia
| | - Irina B Kotova
- Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia
| | - Natalia G Loiko
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia
| | - Nadezhda M Popova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky prospect, 119071 Moscow, Russia
| | - Emil Kryukov
- Department of Physiology and Pharmacology, Karolinska Institute, 17165 Stockholm, Sweden; International School 'Future Medicine', IM Sechenov First Moscow State Medical University, 8-2 Trubetskaya str., 119435 Moscow, Russia
| | - Andrey A Kovalev
- Federal Scientific Agroengineering Center VIM, 1st Institutsky proezd, 5, 109428 Moscow, Russia
| | - Dmitriy A Kovalev
- Federal Scientific Agroengineering Center VIM, 1st Institutsky proezd, 5, 109428 Moscow, Russia
| | - Yuriy V Litti
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia.
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Abstract
Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized by their ultrasmall cell size and symbiotic lifestyles (potentially commensal, mutualistic, and parasitic relationships), namely, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) and DPANN archaea, respectively. Cultivation-based approaches have revealed that Ca. Patescibacteria and DPANN symbiotically interact with bacterial and archaeal partners and hosts, respectively, but that cross-domain symbiosis and parasitism have never been observed. By amending wastewater treatment sludge samples with methanogenic archaea, we observed increased abundances of Ca. Patescibacteria (Ca. Yanofskybacteria/UBA5738) and, using fluorescence in situ hybridization (FISH), discovered that nearly all of the Ca. Yanofskybacteria/UBA5738 cells were attached to Methanothrix (95.7 ± 2.1%) and that none of the cells were attached to other lineages, implying high host dependency and specificity. Methanothrix filaments (multicellular) with Ca. Yanofskybacteria/UBA5738 attached had significantly more cells with no or low detectable ribosomal activity (based on FISH fluorescence) and often showed deformations at the sites of attachment (based on transmission electron microscopy), suggesting that the interaction is parasitic. Metagenome-assisted metabolic reconstruction showed that Ca. Yanofskybacteria/UBA5738 lacks most of the biosynthetic pathways necessary for cell growth and universally conserves three unique gene arrays that contain multiple genes with signal peptides in the metagenome-assembled genomes of the Ca. Yanofskybacteria/UBA5738 lineage. The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR and DPANN.
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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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Dyksma S, Gallert C. Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:664-678. [PMID: 35615789 DOI: 10.1111/1758-2229.13080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 05/23/2023]
Abstract
Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H2 ), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H2 and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.
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Affiliation(s)
- Stefan Dyksma
- 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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32
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Mei R, Liu WT. Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6689-6698. [PMID: 35510767 DOI: 10.1021/acs.est.2c01029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Immigration has been recently recognized as an important ecological process that affects the microbial community structure in diverse ecosystems. However, the fate of microbial immigrants in the new environment and their involvement in the local biochemical network remain unclear. In this study, we performed meta-omics-supervised characterization of immigrants' activities in anaerobic sludge digesters. Metagenomic analyses revealed that immigrants from the feed sludge accounted for the majority of populations capable of anaerobic respiration in a digester. Electron acceptors that were predicted to be respired, including nitrate, nitrite, sulfate, and elemental sulfur, were added to digester sludge in batch tests. Consumption of up to 91% of the added electron acceptors was observed within the experiment period. 16S rRNA sequencing detected populations that were stimulated by the electron acceptors, largely overlapping with respiration-capable immigrants identified by metagenomic analysis. Metatranscriptomic analysis of the batch tests provided additional evidence for upregulated expression of respiration genes and concomitant suppressed expression of methanogenesis. Anaerobic respiration activity was further evaluated in full-scale digesters in nine wastewater treatment plants. Although nitrate and sulfate respiration were ubiquitous, the expression level of respiration genes was generally 2-3 orders of magnitude lower than the expression of methanogenesis in most digesters, suggesting marginal ecological roles by immigrants in full-scale digester ecosystems.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Watanabe T, Kubo K, Kamei Y, Kojima H, Fukui M. Dissimilatory microbial sulfur and methane metabolism in the water column of a shallow meromictic lake. Syst Appl Microbiol 2022; 45:126320. [DOI: 10.1016/j.syapm.2022.126320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 01/04/2023]
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Dai C, Yang L, Wang J, Li D, Zhang Y, Zhou X. Enhancing anaerobic digestion of pharmaceutical industries wastewater with the composite addition of zero valent iron (ZVI) and granular activated carbon (GAC). BIORESOURCE TECHNOLOGY 2022; 346:126566. [PMID: 34921919 DOI: 10.1016/j.biortech.2021.126566] [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: 10/18/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Anaerobic digestion of pharmaceutical wastewater is challenged by its contained toxic compounds which limits the stability and efficiency of methane production and organic degradation. In this study, zero valent iron (ZVI) and granular activated carbon (GAC) were added with different strategies to improve anaerobic digestion of pharmaceutical wastewater. The results confirmed synergy effects of ZVI + GAC for both COD removal (increased by 13.4%) and methane production (increased by 11.0%). Furthermore, ZVI + GAC improved the removal of pharmaceutical intermediates, in particular, the residues (%) of dehydroepiandrosterone (DHEA) and 2,2'-methylenebis(6-tert-butyl-4-methylphenol) were only 30.48 ± 6.53 and 39.92 ± 4.50, and effectively reduced biotoxicity. The promoted results were attributed to the establishment of direct interspecies electron transfer (DIET). Microbial community analysis revealed that ZVI + GAC decreased species evenness and richness in bacterial whereas increased in archaeal. The relative abundance of acetotrophic methanogens decreased but hydrogenotrophic and methylotrophic methanogens increased, which broadening the pathway of methane production.
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Affiliation(s)
- Chenbo Dai
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Libin Yang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, PR China
| | - Jun Wang
- SPH XingLing Sci&Tech.Pharmaceutical Co.,Ltd., Shanghai 201703, PR China
| | - Dezhen Li
- SPH XingLing Sci&Tech.Pharmaceutical Co.,Ltd., Shanghai 201703, PR China
| | - Yalei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, PR China
| | - Xuefei Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, PR China.
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Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation. Appl Environ Microbiol 2021; 87:e0170621. [PMID: 34524899 DOI: 10.1128/aem.01706-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, nonsoil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone Spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of 13 distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g., FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine learning approaches based on a set of 634 genes informative of social lifestyle predicted a nonsocial behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities but carried genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 million years ago (Mya) in response to the rise of soil as a distinct habitat on Earth. IMPORTANCE The phylum Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of nonsoil, predominantly anaerobic habitats, and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA, that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of 13 pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on Earth.
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Yao J, Zeng Y, Wang M, Tang YQ. Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid-Fed Anaerobic Methanogenic Chemostats. Front Microbiol 2021; 12:744834. [PMID: 34671332 PMCID: PMC8521154 DOI: 10.3389/fmicb.2021.744834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.
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Affiliation(s)
| | | | - Miaoxiao Wang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, China
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Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M. Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater. Microbes Environ 2021; 36. [PMID: 34588388 PMCID: PMC8674449 DOI: 10.1264/jsme2.me21045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Atsushi Tobo
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
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Owusu-Agyeman I, Plaza E, Cetecioglu Z. A pilot-scale study of granule-based anaerobic reactors for biogas recovery from municipal wastewater under sub-mesophilic conditions. BIORESOURCE TECHNOLOGY 2021; 337:125431. [PMID: 34198242 DOI: 10.1016/j.biortech.2021.125431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The influence of hydraulic retention time (HRT of 3-5 h) and temperature (20-25 °C) on performance and microbial dynamics of two pilot-scale upflow anaerobic sludge blanket (UASB) reactors with different granule size distribution (UASB1 = 3-4 mm and UASB2 = 1-2 mm) were investigated for 217 days. Increasing the HRT to 5 h even at a lower temperature of 20 °C enhanced COD removal and biogas production with average of 59 ± 16% (up to 85%) and 73 ± 9 L/(m3·d) (up to 102 L/(m3·d)) for UASB1; 63 ± 16% (up to 85%) and 75 ± 9 L/(m3·d) (up to 90 L/(m3·d)) for UASB2, respectively. This is explained by sufficient contact time between microorganisms and substrate. Acetoclastic methanogenic activity was higher in UASB1 because Methanosaetaceae (produces methane from acetate) dominated (64 ± 4%). However, Methanoregulaceae (29 ± 3%) and Methanomicrobiales_unassigned (20 ± 6%) which produce methane from H2/CO2 and formate were significant in UASB2. The extent of change in the microbial dynamics with HRT and temperature was more obvious in the smaller granule reactor.
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Affiliation(s)
- Isaac Owusu-Agyeman
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
| | - Elzbieta Plaza
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
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Kakuk B, Wirth R, Maróti G, Szuhaj M, Rakhely G, Laczi K, Kovács KL, Bagi Z. Early response of methanogenic archaea to H 2 as evaluated by metagenomics and metatranscriptomics. Microb Cell Fact 2021; 20:127. [PMID: 34217274 PMCID: PMC8254922 DOI: 10.1186/s12934-021-01618-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies. RESULTS The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria. CONCLUSIONS External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.
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Affiliation(s)
- Balázs Kakuk
- Institute of Medical Biology, University of Szeged, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
- Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary.
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
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Mei R, Nobu MK, Narihiro T, Liu WT. Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Front Microbiol 2020; 11:593006. [PMID: 33193263 PMCID: PMC7661554 DOI: 10.3389/fmicb.2020.593006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023] Open
Abstract
Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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