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Dueholm MKD, Andersen KS, Korntved AKC, Rudkjøbing V, Alves M, Bajón-Fernández Y, Batstone D, Butler C, Cruz MC, Davidsson Å, Erijman L, Holliger C, Koch K, Kreuzinger N, Lee C, Lyberatos G, Mutnuri S, O'Flaherty V, Oleskowicz-Popiel P, Pokorna D, Rajal V, Recktenwald M, Rodríguez J, Saikaly PE, Tooker N, Vierheilig J, De Vrieze J, Wurzbacher C, Nielsen PH. MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters. Nat Commun 2024; 15:5361. [PMID: 38918384 PMCID: PMC11199495 DOI: 10.1038/s41467-024-49641-y] [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: 10/02/2023] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anne-Kirstine C Korntved
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vibeke Rudkjøbing
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Madalena Alves
- Centre of Biological Engineering, University of Minho, Minho, Portugal
| | | | - Damien Batstone
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, Brisbane, Australia
| | - Caitlyn Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mercedes Cecilia Cruz
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Åsa Davidsson
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Leonardo Erijman
- INGEBI-CONICET, University of Buenos Aires, Buenos Aires, Argentina
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Changsoo Lee
- Department of Civil, Urban, Earth, and Environmental Engineering & Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Gerasimos Lyberatos
- School of Chemical Engineering, National Technical University of Athens, Zografou, Greece
| | - Srikanth Mutnuri
- Applied Environmental Biotechnology Laboratory, Birla Institute of Technology and Science (BITS-Pilani), Pilani, Goa campus, Goa, India
| | - Vincent O'Flaherty
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, Ireland
| | - Piotr Oleskowicz-Popiel
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Poznan, Poland
| | - Dana Pokorna
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Veronica Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | | | - Jorge Rodríguez
- Chemical Engineering Department, Khalifa University, Khalifa, UAE
| | - Pascal E Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Nick Tooker
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Julia Vierheilig
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Bahadur A, Zhang L, Guo W, Sajjad W, Ilahi N, Banerjee A, Faisal S, Usman M, Chen T, Zhang W. Temperature-dependent transformation of microbial community: A systematic approach to analyzing functional microbes and biogas production. ENVIRONMENTAL RESEARCH 2024; 249:118351. [PMID: 38331158 DOI: 10.1016/j.envres.2024.118351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 12/24/2023] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
The stability and effectiveness of the anaerobic digestion (AD) system are significantly influenced by temperature. While majority research has focused on the composition of the microbial community in the AD process, the relationships between functional gene profile deduced from gene expression at different temperatures have received less attention. The current study investigates the AD process of potato peel waste and explores the association between biogas production and microbial gene expression at 15, 25, and 35 °C through metatranscriptomic analysis. The production of total biogas decreased with temperature at 15 °C (19.94 mL/g VS), however, it increased at 35 °C (269.50 mL/g VS). The relative abundance of Petrimonas, Clostridium, Aminobacterium, Methanobacterium, Methanothrix, and Methanosarcina were most dominant in the AD system at different temperatures. At the functional pathways level 3, α-diversity indices, including Evenness (Y = 5.85x + 8.85; R2 = 0.56), Simpson (Y = 2.20x + 2.09; R2 = 0.33), and Shannon index (Y = 1.11x + 4.64; R2 = 0.59), revealed a linear and negative correlation with biogas production. Based on KEGG level 3, several dominant functional pathways associated with Oxidative phosphorylation (ko00190) (25.09, 24.25, 24.04%), methane metabolism (ko00680) (30.58, 32.13, and 32.89%), and Carbon fixation pathways in prokaryotes (ko00720) (27.07, 26.47, and 26.29%), were identified at 15 °C, 25 °C and 35 °C. The regulation of biogas production by temperature possibly occurs through enhancement of central function pathways while decreasing the diversity of functional pathways. Therefore, the methanogenesis and associated processes received the majority of cellular resources and activities, thereby improving the effectiveness of substrate conversion to biogas. The findings of this study illustrated the crucial role of central function pathways in the effective functioning of these systems.
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Affiliation(s)
- Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Cryosphere and Eco-Environment Research Station of Shule River Headwaters, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Lu Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Guo
- Lanzhou Xinrong Environmental Energy Engineering Technology Co. Ltd. Lanzhou 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Shah Faisal
- Department of Environmental Engineering, School of Architecture and Civil Engineering, Chengdu University, Chengdu 610106, China
| | - Muhammad Usman
- State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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Niu S, Xie J, Wang G, Li Z, Zhang K, Li H, Xia Y, Tian J, Yu E, Xie W, Gong W. Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167913. [PMID: 37858824 DOI: 10.1016/j.scitotenv.2023.167913] [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: 08/22/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.
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Affiliation(s)
- Shuhui Niu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Guangjun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Zhifei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Kai Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Hongyan Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Yun Xia
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Jingjing Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Ermeng Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Wenping Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China.
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Yu J, Lee JYY, Tang SN, Lee PKH. Niche differentiation in microbial communities with stable genomic traits over time in engineered systems. THE ISME JOURNAL 2024; 18:wrae042. [PMID: 38470313 PMCID: PMC10987969 DOI: 10.1093/ismejo/wrae042] [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: 12/02/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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5
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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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6
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Kieft B, Finke N, McLaughlin RJ, Nallan AN, Krzywinski M, Crowe SA, Hallam SJ. Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nat Commun 2023; 14:5380. [PMID: 37666802 PMCID: PMC10477309 DOI: 10.1038/s41467-023-40907-5] [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: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Niko Finke
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ryan J McLaughlin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Aditi N Nallan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.
- Bradshaw Research Institute for Minerals and Mining (BRIMM), University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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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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8
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Yu J, Tang SN, Lee PKH. Universal Dynamics of Microbial Communities in Full-Scale Textile Wastewater Treatment Plants and System Prediction by Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3345-3356. [PMID: 36795777 DOI: 10.1021/acs.est.2c08116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The performance of full-scale biological wastewater treatment plants (WWTPs) depends on the operational and environmental conditions of treatment systems. However, we do not know how much these conditions affect microbial community structures and dynamics across systems over time and predictability of the treatment performance. For over a year, the microbial communities of four full-scale WWTPs processing textile wastewater were monitored. During temporal succession, the environmental conditions and system treatment performance were the main drivers, which explained up to 51% of community variations within and between all plants based on the multiple regression models. We identified the universality of community dynamics in all systems using the dissimilarity-overlap curve method, with the significant negative slopes suggesting that the communities containing the same taxa from different plants over time exhibited a similar composition dynamic. The Hubbell neutral theory and the covariance neutrality test indicated that all systems had a dominant niche-based assembly mechanism, supporting that the communities had a similar composition dynamic. Phylogenetically diverse biomarkers for the system conditions and treatment performance were identified by machine learning. Most of the biomarkers (83%) were classified as generalist taxa, and the phylogenetically related biomarkers responded similarly to the system conditions. Many biomarkers for treatment performance perform functions that are crucial for wastewater treatment processes (e.g., carbon and nutrient removal). This study clarifies the relationships between community composition and environmental conditions in full-scale WWTPs over time.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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9
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Wang C, Yang Y, Wang Y, Wang D, Xu X, Wang Y, Li L, Yang C, Zhang T. Absolute quantification and genome-centric analyses elucidate the dynamics of microbial populations in anaerobic digesters. WATER RESEARCH 2022; 224:119049. [PMID: 36108398 DOI: 10.1016/j.watres.2022.119049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/25/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion (AD) relies on myriads of functions performed by complex microbial communities in customized settings, thus, a comprehensive investigation on the AD microbiome is central to the fine-tuned control. Most current AD microbiome studies are based on relative abundance, which hinders the interpretation of microbes' dynamics and inter-sample comparisons. Here, we developed an absolute quantification (AQ) approach that integrated cellular spike-ins with metagenomic sequencing to elucidate microbial community variations and population dynamics in four anaerobic digesters. Using this method, 253 microbes were defined as decaying populations with decay rates ranging from -0.05 to -5.85 d-1, wherein, a population from Flavobacteriaceae family decayed at the highest rates of -3.87 to -5.85 d-1 in four digesters. Meanwhile, 25 microbes demonstrated the growing trend in the AD processes with growth rates ranging from 0.11 to 1.77 d-1, and genome-centric analysis assigned some of the populations to the functional niches of hydrolysis, short-chain fatty acids metabolism, and methane generation. Additionally, we observed that the specific activity of methanogens was lower in the prolonged digestion stage, and redundancy analysis revealed that the feedstock composition and the digestion duration were the two key parameters in governing the AD microbial compositions.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
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10
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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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11
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Wang C, Wang Y, Wang Y, Liu L, Wang D, Ju F, Xia Y, Zhang T. Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters. WATER RESEARCH 2022; 219:118590. [PMID: 35597218 DOI: 10.1016/j.watres.2022.118590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/18/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
| | - Yubo Wang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Yu Xia
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
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12
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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: 3] [Impact Index Per Article: 1.5] [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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13
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Effects of Stepwise Temperature Shifts in Anaerobic Digestion for Treating Municipal Wastewater Sludge: A Genomic Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095728. [PMID: 35565123 PMCID: PMC9099789 DOI: 10.3390/ijerph19095728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Abstract
In wastewater treatment plants (WWTP), anaerobic digester (AD) units are commonly operated under mesophilic and thermophilic conditions. In some cases, during the dry season, maintaining a stable temperature in the digester requires additional power to operate a conditioning system. Without proper conditioning systems, methanogens are vulnerable to temperature shifts. This study investigated the effects of temperature shifts on CH4 gas production and microbial diversity during anaerobic digestion of anaerobic sewage sludge using a metagenomic approach. The research was conducted in lab-scale AD under stepwise upshifted temperature from 42 to 48 °C. The results showed that significant methanogen population reduction during the temperature shift affected the CH4 production. With 70 days of incubation each, CH4 production decreased from 4.55 L·g−1-chemical oxygen demand (COD) at 42 °C with methanogen/total population (M·TP−1) ratio of 0.041 to 1.52 L·g−1 COD (M·TP−1 ratio 0.027) and then to 0.94 L·g−1 COD ( M·TP−1 ratio 0.026) after the temperature was shifted to 45 °C and 48 °C, respectively. Methanosaeta was the most prevalent methanogen during the thermal change. This finding suggests that the Methanosaeta genus was a thermotolerant archaea. Anaerobaculum, Fervidobacterium, and Tepidanaerobacter were bacterial genera and grew well in shifted-up temperatures, implying heat-resistant characteristics.
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14
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Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica. ENERGIES 2022. [DOI: 10.3390/en15093252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.
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15
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Brison A, Rossi P, Gelb A, Derlon N. The capture technology matters: Composition of municipal wastewater solids drives complexity of microbial community structure and volatile fatty acid profile during anaerobic fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152762. [PMID: 34990680 DOI: 10.1016/j.scitotenv.2021.152762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/14/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
The production of volatile fatty acids (VFAs) represents a relevant option to valorize municipal wastewater (MWW). In this context, different capture technologies can be used to recover organic carbon from wastewater in form of solids, while pre-treatment of those solids has the potential to increase VFA production during subsequent fermentation. Our study investigates how VFA composition produced by fermentation is influenced (i) by the choice of the capture technology, as well as (ii) by the use of thermal alkaline pre-treatment (TAP). Therefore, the fermentation of solids originating from a primary settler, a micro-sieve, and a high-rate activated sludge (HRAS) system was investigated in continuous lab-scale fermenters, with and without TAP. Our study demonstrates that the capture technology strongly influences the composition of the produced solids, which in turn drives the complexity of the fermenter's microbial community and ultimately, of the VFA composition. Solids captured with the primary settler or micro-sieve consisted primarily of polysaccharides, and led to the establishment of a microbial community specialized in the degradation of complex carbohydrates. The produced VFA composition was relatively simple, with acetate and propionate accounting for >90% of the VFAs. In contrast, the HRAS system produced biomass-rich solids associated with higher protein contents. The microbial community which then developed in the fermenter was therefore more diversified and capable of converting a wider range of substrates (polysaccharides, proteins, amino acids). Ultimately, the produced VFA composition was more complex, with equal fractions of isoacids and propionate (both ~20%), while acetate remained the dominant acid (~50%). Finally, TAP did not significantly modify the VFA composition while increasing VFA yields on HRAS and sieved material by 35% and 20%, respectively. Overall, we demonstrated that the selection of the technology used to capture organic substrates from MWW governs the composition of the VFA cocktail, ultimately with implications for their further utilization.
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Affiliation(s)
- Antoine Brison
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Institute of Environmental Engineering, 8093 Zürich, Switzerland.
| | - Pierre Rossi
- Central Environmental Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
| | - Arnaud Gelb
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Nicolas Derlon
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
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16
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Abstract
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.
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17
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Insights into the Anaerobic Hydrolysis Process for Extracting Embedded EPS and Metals from Activated Sludge. Microorganisms 2021; 9:microorganisms9122523. [PMID: 34946124 PMCID: PMC8703515 DOI: 10.3390/microorganisms9122523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023] Open
Abstract
The amount of sewage sludge generated from wastewater treatment plants globally is unavoidably increasing. In recent years, significant attention has been paid to the biorefinery concept based on the conversion of waste streams to high-value products, material, and energy by microorganisms. However, one of the most significant challenges in the field is the possibility of controlling the microorganisms’ pathways in the anaerobic environment. This study investigated two different anaerobic fermentation tests carried out with real waste activated sludge at high organic loading rate (10 g COD L−1d−1) and short hydraulic retention time (HRT) to comprehensively understand whether this configuration enhances extracellular polymeric substance (EPS) and metal solubilisation. The quantity of EPS recovered increased over time, while the chemical oxygen demand to EPS ratio remained in the range 1.31–1.45. Slightly acidic conditions and sludge floc disintegration promoted EPS matrix disruption and release, combined with the solubilisation of organically bound toxic metals, such as As, Be, Cu, Ni, V, and Zn, thereby increasing the overall metal removal efficiency due to the action of hydrolytic microorganisms. Bacteroidetes, Firmicutes, and Chloroflexi were the most abundant phyla observed, indicating that the short HRT imposed on the systems favoured the hydrolytic and acidogenic activity of these taxa.
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18
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Guimarães de Oliveira M, Marques Mourão JM, Souza Silva FS, Bezerra Dos Santos A, Lopes Pereira E. Effect of microaerophilic treatment on swine wastewater (SWW) treatment: Engineering and microbiological aspects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113598. [PMID: 34481377 DOI: 10.1016/j.jenvman.2021.113598] [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: 04/27/2021] [Revised: 07/22/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
The microaerobic process on swine wastewater (SWW) treatment was investigated, evaluating its effect on organic matter hydrolysis and removal, biogas production, operational stability, and microbial community structure. UASB reactors operating under higher organic loading rates (OLRs) and lower hydraulic retention times (HRTs) than those found in the SWW treatment literature were also assessed. The microaerophilic reactor R2 presented a higher total and particulate organic matter removals and operational stability than the anaerobic reactor R1, reaching CODP removals of 79.4 ± 4.6%. In the specific methanogenic activity (SMA) tests, the microaerobic sludge (R2) showed hydrolytic and acetogenic/methanogenic activity superior to inoculum and anaerobic sludge (R1). The microbiological evaluation of R2 revealed the high presence of hydrolytic microorganisms, therefore justifying the higher hydrolytic activity found in the SMA tests and higher particulate organic matter removal found in the microaerobic reactor.
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Affiliation(s)
| | - José Marcos Marques Mourão
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Erlon Lopes Pereira
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
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19
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De Vrieze J, Heyer R, Props R, Van Meulebroek L, Gille K, Vanhaecke L, Benndorf D, Boon N. Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles. WATER RESEARCH 2021; 202:117422. [PMID: 34280807 DOI: 10.1016/j.watres.2021.117422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium; Division of Soil and Water Management, Department of Earth and Environmental sciences, KU Leuven, Kasteelpark Arenberg 20, PO box 2411, B-3001, Leuven, Belgium; Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, PO box 2424, B-3001, Leuven, Belgium.
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Karen Gille
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany; Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354, Köthen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
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20
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Cheng Z, Yao S, Yuan H. Linking population dynamics to microbial kinetics for hybrid modeling of bioelectrochemical systems. WATER RESEARCH 2021; 202:117418. [PMID: 34273778 DOI: 10.1016/j.watres.2021.117418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/25/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Mechanistic and data-driven models have been developed to provide predictive insights into the design and optimization of engineered bioprocesses. These two modeling strategies can be combined to form hybrid models to address the issues of parameter identifiability and prediction interpretability. Herein, we developed a novel and robust hybrid modeling strategy by incorporating microbial population dynamics into model construction. The hybrid model was constructed using bioelectrochemical systems (BES) as a platform system. We collected 77 samples from 13 publications, in which the BES were operated under diverse conditions, and performed holistic processing of the 16S rRNA amplicon sequencing data. Community analysis revealed core populations composed of putative electroactive taxa Geobacter, Desulfovibrio, Pseudomonas, and Acinetobacter. Primary Bayesian networks were trained with the core populations and environmental parameters, and directed Bayesian networks were trained by defining the operating parameters to improve the prediction interpretability. Both networks were validated with Bray-Curtis similarly, relative root-mean-square error (RMSE), and a null model. A hybrid model was developed by first building a three-population mechanistic component and subsequently feeding the estimated microbial kinetic parameters into network training. The hybrid model generated a simulated community that shared a Bray-Curtis similarity of 72% with the actual microbial community at the genus level and an average relative RMSE of 7% for individual taxa. When examined with additional samples that were not included in network training, the hybrid model achieved accurate prediction of current production with a relative error-based RMSE of 0.8 and outperformed the data-driven models. The genomics-enabled hybrid modeling strategy represents a significant step toward robust simulation of a variety of engineered bioprocesses.
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Affiliation(s)
- Zhang Cheng
- Department of Civil & Environmental Engineering, Temple University, 1947N. 12th Street, Philadelphia, PA 19122, USA
| | - Shiyun Yao
- Department of Civil & Environmental Engineering, Temple University, 1947N. 12th Street, Philadelphia, PA 19122, USA
| | - Heyang Yuan
- Department of Civil & Environmental Engineering, Temple University, 1947N. 12th Street, Philadelphia, PA 19122, USA.
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21
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Du W, Huang X, Zhang J, Wang D, Yang Q, Li X. Enhancing methane production from anaerobic digestion of waste activated sludge with addition of sodium lauroyl sarcosinate. BIORESOURCE TECHNOLOGY 2021; 336:125321. [PMID: 34091271 DOI: 10.1016/j.biortech.2021.125321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
In this study, sodium lauroyl sarcosinate (SLS) was used to promote anaerobic digestion of waste activated sludge for producing methane. It was found maximum cumulative methane production increased from 98.1 ± 3.1 to 166.0 ± 4.3 mL/g Volatile Suspended Solids (VSS) with dosage increasing from 0 (control) to 40 mg SLS/g TSS. But the addition of SLS (>10 mg SLS/g Total Suspended Solids (TSS)) resulted in prolonged lag phase time. Microbiological analysis showed that Syntrophobacter and Syntrophomonas both got enriched in reactors fed with SLS. Furthermore, hydrogenotrophic methanogens genus got more enrichment in contrast to acetoclastic methanogens. Mechanism analysis indicated that addition SLS could decrease surface tension, and promote release of organic matters as well as improve activities of hydrolytic enzymes. Besides, SLS could be nearly degraded completely within 3 days, and its degradation intermediates could be further transformed into methane gradually, thus enhancing methane production eventually.
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Affiliation(s)
- Wenjie Du
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaoding Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jiamin Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Qi Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaoming Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
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22
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Hassa J, Klang J, Benndorf D, Pohl M, Hülsemann B, Mächtig T, Effenberger M, Pühler A, Schlüter A, Theuerl S. Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants. Microorganisms 2021; 9:1457. [PMID: 34361893 PMCID: PMC8307424 DOI: 10.3390/microorganisms9071457] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/24/2022] Open
Abstract
There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.); (A.P.); (A.S.)
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany;
| | - Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany;
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06366 Köthen, Germany
| | - Marcel Pohl
- Biochemical Conversion Department, DBFZ Deutsches Biomasseforschungszentrum Gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany;
| | - Benedikt Hülsemann
- The State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Garbenstraße 9, 70599 Stuttgart, Germany;
| | - Torsten Mächtig
- Institute of Agricultural Engineering, Kiel University, Max-Eyth-Str. 6, 24118 Kiel, Germany;
| | - Mathias Effenberger
- Institute for Agricultural Engineering and Animal Husbandry, Bavarian State Research Center for Agriculture, Vöttinger Str. 36, 85354 Freising, Germany;
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.); (A.P.); (A.S.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.); (A.P.); (A.S.)
| | - Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany;
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Jiang F, Wang S, Zhang Y, Ma S, Huang Y, Fan H, Li Q, Wang H, Wang A, Liu H, Cheng L, Deng Y, Fan W. Variation of Metagenome From Feedstock to Digestate in Full-Scale Biogas Plants. Front Microbiol 2021; 12:660225. [PMID: 34122376 PMCID: PMC8193575 DOI: 10.3389/fmicb.2021.660225] [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] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion (AD) has been widely used to resolve the problem of organic wastes worldwide. Previous studies showed that the types of feedstock have a great influence on the AD microbiome, and a huge number of AD populations are migrated from upstream feedstocks. However, the changes of microbial compositions from feedstock to AD digestate are still less understood. We collected feedstock samples from 56 full-scale biogas plants, generated 1,716 Gb feedstock metagenomic data in total, and constructed the first comprehensive microbial gene catalog of feedstock containing 25.2 million genes. Our result indicated that the predominant phyla in feedstock are Firmicutes, Bacteroidetes, and Proteobacteria, which is similar to that in AD digestate, and the microbial diversity of feedstock samples is higher than that of AD digestate samples. In addition, the relative abundance of most genes involved in methanogenesis increase from feedstock to AD digestate. Besides, the amount of antibiotic resistance genes (ARGs) and pathogenic bacteria in AD are effectively reduced compared to feedstocks. This study provides a comprehensive microbial gene catalog of feedstock, and deepens the understanding of variation of microbial communities from feedstock to AD digestate of full-scale AD. The results also suggest the potential of AD to reduce the level of ARGs and pathogens in animal manure.
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Affiliation(s)
- Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shichun Ma
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Chengdu, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Chengdu, China
| | - Yan Huang
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Chengdu, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Chengdu, China
| | - Hui Fan
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Chengdu, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Chengdu, China
| | - Qiang Li
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Chengdu, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Chengdu, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lei Cheng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Chengdu, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Chengdu, China
| | - Yu Deng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Chengdu, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Chengdu, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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24
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Yu J, Tang SN, Lee PKH. Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5312-5323. [PMID: 33784458 DOI: 10.1021/acs.est.0c06732] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's r = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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25
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Jiang C, Peces M, Andersen MH, Kucheryavskiy S, Nierychlo M, Yashiro E, Andersen KS, Kirkegaard RH, Hao L, Høgh J, Hansen AA, Dueholm MS, Nielsen PH. Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers. WATER RESEARCH 2021; 193:116871. [PMID: 33578056 DOI: 10.1016/j.watres.2021.116871] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/11/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.
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Affiliation(s)
- Chenjing Jiang
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; Key Laboratory of Engineering Oceanography, Second Institute of Oceanography, SOA, Hangzhou, China
| | - Miriam Peces
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Martin Hjorth Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sergey Kucheryavskiy
- Section of Chemical Engineering, Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Erika Yashiro
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Rasmus Hansen Kirkegaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Liping Hao
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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26
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Ma S, Jiang F, Huang Y, Zhang Y, Wang S, Fan H, Liu B, Li Q, Yin L, Wang H, Liu H, Ren Y, Li S, Cheng L, Fan W, Deng Y. A microbial gene catalog of anaerobic digestion from full-scale biogas plants. Gigascience 2021; 10:giaa164. [PMID: 33506264 PMCID: PMC7842101 DOI: 10.1093/gigascience/giaa164] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/10/2020] [Accepted: 12/18/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood. FINDINGS In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination. CONCLUSIONS This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.
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Affiliation(s)
- Shichun Ma
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120,China
| | - Yan Huang
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hui Fan
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Bo Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Qiang Li
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Lijuan Yin
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Yuwei Ren
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Shuqu Li
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Lei Cheng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfai Road, Shenzhen 518120, China
| | - Yu Deng
- Biogas Institute of Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
- Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agricultural and Rural Affairs, Section 4-13, Renmin South Road, Chengdu 610041, China
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Zhu K, Zhang L, Wang X, Mu L, Li C, Li A. Inhibition of norfloxacin on anaerobic digestion: Focusing on the recoverability and shifted microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141733. [PMID: 32896787 DOI: 10.1016/j.scitotenv.2020.141733] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 05/23/2023]
Abstract
Antibacterial properties of norfloxacin (NOR) could cause adverse impact on engineered biological process. In this study, the objective was to investigate the inhibitory effects of NOR on anaerobic digestion focusing on the recoverability and microbial community changes. The effects of different concentrations of NOR on anaerobic digestion were studied with three continuous feed cycles. Results showed that NOR seriously inhibited the methane production with an 50% inhibitory concentration (IC50) of 0.41 mM. In addition, with extending of exposure time, inhibitory effect increasingly strengthened and the IC50 values decreased to 0.16 mM and 0.07 mM in the second and third feeding cycle, respectively. However, when the inhibitor in supernatant was removed, the performance recovered and the relative methane yield increased by 9 times from 25.38 mL/g VS to 257.05 mL/g VS. The transformation of NOR showed that the degradation of NOR in the anaerobic digestion was difficult and the recovery was due to the removal of NOR. The microbial analysis revealed that the inhibition of NOR on bacteria of Candidatus_Cloacimonas, Petrimonas, Ercella, Sphaerochaeta and hydrogenotrophic methanogens of Methanoculleus and Methanobacterium was recoverable when NOR was removed. However, it was irreversible for acetoclastic methanogen of Methanosaeta. These findings provided comprehensive understanding on the characteristics of NOR inhibition and also provided feasible strategy to recover the NOR inhibited anaerobic digestion.
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Affiliation(s)
- Kongyun Zhu
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Lei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China.
| | - Xuexue Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Lan Mu
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Changjing Li
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Aimin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
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28
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Kim J, Mei R, Wilson FP, Yuan H, Bocher BTW, Liu WT. Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity. Front Microbiol 2020; 11:595036. [PMID: 33343535 PMCID: PMC7738435 DOI: 10.3389/fmicb.2020.595036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
Fermentation of waste activated sludge (WAS) is an alternative approach to reduce solid wastes while providing valuable soluble products, such as volatile fatty acids and alcohols. This study systematically identified optimal fermentation conditions and key microbial populations by conducting two sets of experiments under different combinations of biochemical and physical parameters. Based on fermentation product concentrations, methane production, and solid removal, fermentation performance was enhanced under the combined treatments of inoculum heat shock (>60°C), pH 5, 55°C, and short solid retention time (<10 days). An ecogenomics-based mass balance (EGMB) approach was used to determine the net growth rates of individual microbial populations, and classified them into four microbial groups: known syntrophs, known methanogens, fermenters, and WAS-associated populations. Their growth rates were observed to be affected by the treatment conditions. The growth rates of syntrophs and fermenters, such as Syntrophomonas and Parabacteroides increased with a decrease in SRT. In contrast, treatment conditions, such as inoculum heat shock and high incubation temperature inhibited the growth of WAS-associated populations, such as Terrimonas and Bryobacter. There were also populations insensitive to the treatment conditions, such as those related to Microbacter and Rikenellaceae. Overall, the EGMB approach clearly revealed the ecological roles of important microbial guilds in the WAS fermentation system, and guided the selection of optimal conditions for WAS fermentation in future pilot-scale operation.
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Affiliation(s)
- Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Fernanda P Wilson
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Benjamin T W Bocher
- British Petroleum America, Petrochemicals Technology, Naperville, IL, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
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Saha S, Basak B, Hwang JH, Salama ES, Chatterjee PK, Jeon BH. Microbial Symbiosis: A Network towards Biomethanation. Trends Microbiol 2020; 28:968-984. [DOI: 10.1016/j.tim.2020.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 11/28/2022]
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Fernandez-Gonzalez N, Braz GHR, Regueiro L, Lema JM, Carballa M. Microbial invasions in sludge anaerobic digesters. Appl Microbiol Biotechnol 2020; 105:21-33. [PMID: 33205286 DOI: 10.1007/s00253-020-11009-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/31/2020] [Accepted: 11/08/2020] [Indexed: 12/13/2022]
Abstract
Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.
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Affiliation(s)
- Nuria Fernandez-Gonzalez
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. .,Institute of Sustainable Processes, University of Valladolid, Valladolid, Spain.
| | - G H R Braz
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.,, Ribeirão Preto, Brazil
| | | | - J M Lema
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - M Carballa
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge. Appl Environ Microbiol 2020; 86:AEM.01920-20. [PMID: 32948522 DOI: 10.1128/aem.01920-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 01/12/2023] Open
Abstract
Pretreatment of waste-activated sludge (WAS) is an effective way to destabilize sludge floc structure and release organic matter for improving sludge digestion efficiency. Nonetheless, information on the impact of WAS pretreatment on digestion sludge microbiomes, as well as mechanistic insights into how sludge pretreatment improves digestion performance, remains elusive. In this study, a genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different types of feeding sludge: WAS pretreated with 0.25 mol/liter alkaline/acid (APAD), WAS pretreated with 0.8 mol/liter alkaline/acid (HS-APAD), thermally pretreated WAS (thermal-AD), and fresh WAS (control-AD). We retrieved 254 metagenome-assembled genomes (MAGs) to identify the key functional populations involved in the methanogenic digestion process. These MAGs span 28 phyla, including 69 yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were enriched in APAD and HS-APAD, while lineages related to protein and lipid fermentation were enriched in thermal-AD, corroborating the idea that different substrates are released from alkaline/acid and thermal pretreatments. Among the major functional populations (i.e., fermenters, syntrophic acetogens, and methanogens), significant correlations between genome sizes and abundance of the fermenters were observed, particularly in APAD and HS-APAD, which had improved digestion performance.IMPORTANCE Wastewater treatment generates large amounts of waste-activated sludge (WAS), which consists mainly of recalcitrant microbial cells and particulate organic matter. Though WAS pretreatment is an effective way to release sludge organic matter for subsequent digestion, detailed information on the impact of the sludge pretreatment on the digestion sludge microbiome remains scarce. Our study provides unprecedented genome-centric metagenomic insights into how WAS pretreatments change the digestion sludge microbiomes, as well as their metabolic networks. Moreover, digestion sludge microbiomes could be a unique source for exploring microbial dark matter. These results may inform future optimization of methanogenic sludge digestion and resource recovery.
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Ribera-Pi J, Campitelli A, Badia-Fabregat M, Jubany I, Martínez-Lladó X, McAdam E, Jefferson B, Soares A. Hydrolysis and Methanogenesis in UASB-AnMBR Treating Municipal Wastewater Under Psychrophilic Conditions: Importance of Reactor Configuration and Inoculum. Front Bioeng Biotechnol 2020; 8:567695. [PMID: 33224930 PMCID: PMC7667289 DOI: 10.3389/fbioe.2020.567695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Three upflow anaerobic sludge blanket (UASB) pilot scale reactors with different configurations and inocula: flocculent biomass (F-UASB), flocculent biomass and membrane solids separation (F-AnMBR) and granular biomass and membrane solids separation (G-AnMBR) were operated to compare start-up, solids hydrolysis and effluent quality. The parallel operation of UASBs with these different configurations at low temperatures (9.7 ± 2.4°C) and the low COD content (sCOD 54.1 ± 10.3 mg/L and pCOD 84.1 ± 48.5 mg/L), was novel and not previously reported. A quick start-up was observed for the three reactors and could be attributed to the previous acclimation of the seed sludge to the settled wastewater and to low temperatures. The results obtained for the first 45 days of operation showed that solids management was critical to reach a high effluent quality. Overall, the F-AnMBR showed higher rates of hydrolysis per solid removed (38%) among the three different UASB configurations tested. Flocculent biomass promoted slightly higher hydrolysis than granular biomass. The effluent quality obtained in the F-AnMBR was 38.0 ± 5.9 mg pCOD/L, 0.4 ± 0.9 mg sCOD/L, 9.9 ± 1.3 mg BOD5/L and <1 mg TSS/L. The microbial diversity of the biomass was also assessed. Bacteroidales and Clostridiales were the major bacterial fermenter orders detected and a relative high abundance of syntrophic bacteria was also detected. Additionally, an elevated abundance of sulfate reducing bacteria (SRB) was also identified and was attributed to the low COD/SO4 2- ratio of the wastewater (0.5). Also, the coexistence of acetoclastic and hydrogenotrophic methanogenesis was suggested. Overall this study demonstrates the suitability of UASB reactors coupled with membrane can achieve a high effluent quality when treating municipal wastewater under psychrophilic temperatures with F-AnMBR promoting slightly higher hydrolysis rates.
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Affiliation(s)
- Judit Ribera-Pi
- Eurecat, Centre Tecnològic de Catalunya, Water, Air and Soil Unit, Manresa, Spain
| | - Antonio Campitelli
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
| | | | - Irene Jubany
- Eurecat, Centre Tecnològic de Catalunya, Water, Air and Soil Unit, Manresa, Spain
| | | | - Ewan McAdam
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
| | - Bruce Jefferson
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
| | - Ana Soares
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
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Lu Q, Yu Z, Wang L, Liang Z, Li H, Sun L, Shim H, Qiu R, Wang S. Sludge pre-treatments change performance and microbiome in methanogenic sludge digesters by releasing different sludge organic matter. BIORESOURCE TECHNOLOGY 2020; 316:123909. [PMID: 32739582 DOI: 10.1016/j.biortech.2020.123909] [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: 06/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
In this study, temporal impacts of thermal, alkaline/acid and thermal-alkaline sludge pre-treatments on digestion performance and microbiome were investigated and compared in methanogenic sludge digesters. Results showed that thermal and alkaline/acid pre-treatments were efficient in releasing intracellular and EPS organic matter, respectively. The thermal-alkaline pre-treatment showed synergistic impacts of both thermal and alkaline/acid pre-treatments by releasing the major portion of sludge organic matter from solid- to liquid-phase, which result in 60-65% organic carbon removal in subsequent sludge digestion and further optimizing digestion temperature had negligible improvement. The 16S rRNA gene-based analyses suggested that organic matter released from sludge pre-treatments is a major deterministic parameter in shaping sludge microbiome. Pre-treatment specific lineages were identified in different sludge digesters, whereas several taxa were identified as common functionally active populations in sludge digestion. This study provided mechanistic insights into impacts of pre-treatments on digestion performance and microbiome in methanogenic sludge digesters.
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Affiliation(s)
- Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Zehui Yu
- Beijing Enterprises Water Group (China) Investment Limited, Beijing 100102, China
| | - Li Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Haocong Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Lianpeng Sun
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR 999078, China
| | - Rongliang Qiu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China.
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Quaiyum S, Igarashi K, Narihiro T, Kato S. Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes Environ 2020; 35. [PMID: 32921647 PMCID: PMC7511781 DOI: 10.1264/jsme2.me20002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment cultures fed peptidoglycan from E. coli or M. luteus were similar, but distinctly different. A number of phylogenetically novel and uncultured bacteria, particularly in the phyla Bacteroidetes, WWE1, Armatimonadetes, and Verrucomicrobia, dominated the enrichment cultures, suggesting their involvement in anaerobic peptidoglycan degradation.
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Affiliation(s)
- Samia Quaiyum
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
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35
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Theuerl S, Klang J, Hülsemann B, Mächtig T, Hassa J. Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants. Microorganisms 2020; 8:microorganisms8081169. [PMID: 32752188 PMCID: PMC7464807 DOI: 10.3390/microorganisms8081169] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022] Open
Abstract
Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L-1 and 193 mg L-1 or volatile fatty acid concentrations of 0.75 g L-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.
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Affiliation(s)
- Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
- Correspondence: ; Tel.: +49-331-5699-900
| | - Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
| | - Benedikt Hülsemann
- University of Hohenheim, The State Institute of Agricultural Engineering and Bioenergy, 70599 Stuttgart, Germany;
| | - Torsten Mächtig
- Kiel University, Institute of Agricultural Engineering, 24098 Kiel, Germany;
| | - Julia Hassa
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, 33615 Bielefeld, Germany
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Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. MICROBIOME 2020; 8:111. [PMID: 32709258 PMCID: PMC7382037 DOI: 10.1186/s40168-020-00885-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored. RESULTS To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate. CONCLUSION Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.
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Affiliation(s)
- Masaru K. Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, HK Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, UK
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
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Lam TYC, Mei R, Wu Z, Lee PKH, Liu WT, Lee PH. Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. WATER RESEARCH 2020; 178:115815. [PMID: 32380296 DOI: 10.1016/j.watres.2020.115815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 04/08/2020] [Indexed: 05/24/2023]
Abstract
In the past decade, the characterisation of the microbial community in anaerobic digestion was primarily done by using high-throughput short-read amplicon sequencing. However, the short-read approach has inherent primer bias and low phylogenetic resolution. Our previous study using Illumina MiSeq suggested that the heterogeneity of AD microbiome was operation-driven. To advance our knowledge towards the complexity of the AD microbiome, we performed full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for a more accurate phylogenetic identification. To this end, purified DNA samples from 19 global anaerobic digesters were sequenced. Sixteen methanogenic archaea were identified at the species level. Among them, Methanosarcina horonobensis and Methanosarcina flavescens had significant presence under specific operating conditions. Methanothrix concilii presented in all digesters sequenced. Unexpectedly, over 90% of the Smithella detected were closely related to alkane-degrading Smithella strains D17 and M82, not Smithella propionica. Using LEfSe and network analysis, the interspecies relationship between the fermentative and syntrophic bacteria was addressed. Comparison of the short- and long-read sequencing results were performed and discussed. From sample preparation to data analysis, this work characterised the digester microbiomes in a superior resolution.
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Affiliation(s)
- Theo Y C Lam
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK.
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Ni J, Hatori S, Wang Y, Li YY, Kubota K. Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR. MICROBIAL ECOLOGY 2020; 79:925-932. [PMID: 31701171 DOI: 10.1007/s00248-019-01449-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.
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Affiliation(s)
- Jialing Ni
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Shingo Hatori
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Yin Wang
- Institute of Urban Environment, Chinese Academy of Sciences, 1799 JiMei Road, Xiamen, 361021, China
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
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Mei R, Nobu MK, Liu WT. Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:173-184. [PMID: 31965729 DOI: 10.1111/1758-2229.12821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Degradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well-recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short-term enrichment (SE) and long-term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long-term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- 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, Illinois, USA
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Wang S, Yu S, Lu Q, Liao Y, Li H, Sun L, Wang H, Zhang Y. Development of an alkaline/acid pre-treatment and anaerobic digestion (APAD) process for methane generation from waste activated sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:134564. [PMID: 31784169 DOI: 10.1016/j.scitotenv.2019.134564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic sludge digesters are biorefineries for energy recovery from waste activated sludge (WAS) via methane production, in which disintegration of floc structure and microbial cells is a major challenge in releasing extracellular polymeric substances (EPS) and cytoplasmic macromolecules for subsequent hydrolysis and fermentation. Here, we developed a new process combining alkaline/acid pre-treatments and anaerobic digestion (APAD) to improve sludge digestion. Both alkaline and acid pre-treatments effectively disintegrated the floc structure and microbial cells to release sludge organic contents. Under the optimized alkaline/acid pre-treatment condition, carbon removal achieved 52.8 ± 1.7% in APAD digesters, in contrast to 30.9 ± 2.2% and 42.4 ± 1.6% in anaerobic digesters fed with fresh WAS (control-AD) and thermal pre-treated sludge (thermal-AD), respectively. Both alkaline/acid and thermal pre-treatments largely shifted sludge community composition and function, but in distinct ways, possibly due to their different sludge constitutes (i.e., dissolved organic matter and NaCl). Correspondingly, microbial network analysis identified three modules with varied keystone taxa and interaction patterns in the three digesters. Life cycle assessment showed the comparable environmental impacts of APAD, thermal-AD and control-AD. In all, this study provided a new solution for WAS treatment and insights into impact of sludge pre-treatments on sludge digestion microbiome.
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Affiliation(s)
- Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China; Environmental Microbiomics Research Center, Sun Yat-Sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, China.
| | - Sining Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yingying Liao
- College of Architecture and Environment, Sichuan University, Chengdu 610064, China
| | - Haocong Li
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, China
| | - Hongtao Wang
- College of Architecture and Environment, Sichuan University, Chengdu 610064, China
| | - Yang Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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41
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Wang L, Hossen EH, Aziz TN, Ducoste JJ, de Los Reyes FL. Increased loading stress leads to convergence of microbial communities and high methane yields in adapted anaerobic co-digesters. WATER RESEARCH 2020; 169:115155. [PMID: 31671296 DOI: 10.1016/j.watres.2019.115155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/29/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
Enhancing biogas production, while avoiding inhibition of methanogenesis during co-digestion of grease interceptor waste (GIW), can help water resource recovery facilities reduce their carbon footprint. Here we used pre-adapted and non-adapted digesters to link microbial community structure to digester function. Before disturbance, the pre-adapted and non-adapted digesters showed similar methane production and microbial community diversity but dissimilar community composition. When exposed to an identical disturbance, the pre-adapted digester achieved better performance, while the non-adapted digester was inhibited. When re-exposed to disturbance after recovery, communities and performance of both digesters converged, regardless of the temporal variations. Co-digestion of up to 75% GIW added on a volatile solids (VS) basis was achieved, increasing methane yield by 336% from 0.180 to 0.785 l-methane/g-VS-added, the highest methane yield reported to date for lipid-rich waste. Progressive perturbation substantially enriched fatty acid-degrading Syntrophomonas from less than 1% to 24.6% of total 16S rRNA gene sequences, acetoclastic Methanosaeta from 2.3% to 11.9%, and hydrogenotrophic Methanospirillum from less than 1% to 6.6% in the pre-adapted digester. Specific hydrolytic and fermentative populations also increased. These ecological insights demonstrated how progressive perturbation can be strategically used to influence methanogenic microbiomes and improve co-digestion of GIW.
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Affiliation(s)
- Ling Wang
- Department of Civil, Construction and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Elvin H Hossen
- Department of Civil, Construction and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tarek N Aziz
- Department of Civil, Construction and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Joel J Ducoste
- Department of Civil, Construction and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Francis L de Los Reyes
- Department of Civil, Construction and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA
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Zheng W, Wen X. How exogenous influent communities and environmental conditions affect activated sludge communities in the membrane bioreactor of a wastewater treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:622-630. [PMID: 31539970 DOI: 10.1016/j.scitotenv.2019.07.310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
In this study, the residual population of influent and activated sludge (AS) communities was defined based on their occurrence frequency and relative abundance through long-term and fine-scale sampling from the membrane bioreactor (MBR) of a wastewater treatment plant (WWTP). There were 481 OTUs defined as the residual OTUs, which taken up 67.90 ± 9.36% of relative abundance in the influent community. Besides, 6.76 ± 5.71% of the residual population migrated to and remained in the AS community. Additionally, the residual populations were more likely to be anaerobes and microaerobes. As the most predominant genus from residual community, the relative abundance of Arcobacter was reduced from 15.78 ± 3.58% in the influent to 1.15 ± 1.35% in the AS. The residues that migrated from the influent have increased the richness and evenness of AS community, as well as the dissimilarities among samples over long-term. The rank-abundance distribution showed identical pattern for the residual species between influent and AS. By adopting the analysis of neutral model, 2766 out of 7491 shared OTUs between influent and AS communities were identified as neutral OTUs, which respectively made up 53.9% and 41.8% of the total relative abundance of influent and AS communities. These indicated that the AS community was to some extent, but not entirely assembled by neutral process. For the residual community in the AS, dissolved oxygen (DO) was positively associated with several aerobic genera, meanwhile influent chemical oxygen demand (COD) had positive relationship with genus Pseudomonas. Last but most importantly, the influent community could not inoculate the nitrifiers in the AS, but instead, was able to inoculate the denitrifiers; as well as enhance the biodiversity and the ability of resisting external disturbance for the AS community in MBR.
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Affiliation(s)
- Wanlin Zheng
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xianghua Wen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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43
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Mei R, Liu WT. Quantifying the contribution of microbial immigration in engineered water systems. MICROBIOME 2019; 7:144. [PMID: 31694700 PMCID: PMC6836541 DOI: 10.1186/s40168-019-0760-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/17/2019] [Indexed: 05/03/2023]
Abstract
Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
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Saha S, Jeon BH, Kurade MB, Govindwar SP, Chatterjee PK, Oh SE, Roh HS, Lee SS. Interspecies microbial nexus facilitated methanation of polysaccharidic wastes. BIORESOURCE TECHNOLOGY 2019; 289:121638. [PMID: 31212174 DOI: 10.1016/j.biortech.2019.121638] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Compositional variations in organic wastes influence microbial abundancy and syntrophy during anaerobic digestion (AD), impacting the normal performance of digesters for methanation. Investigation of the microbial dynamics during AD following augmentation with polysaccharidic wastes (PW) revealed the association of effective digester performance and methane yields with the microbial nexus. Dominance of the acidogenic saccharolytic genera, Prevotella, Eubacterium, and Lachnoclostridium, enhanced the utilization of carbohydrates (54%) in PW-augmented digesters. Spearman's rs correlation showed dynamic interspecies interactions among acetogenic syntrophs, and that of iron oxidizers/reducers with acetoclastic and hydrogenotrophic methanogens. Propionate oxidizers in Chloroflexi (i.e., Bellilinea, Levilinea, and Longilinea) exhibited positive associations with acetoclastic methanogens. Increase in the population of acetoclastic methanogens (Methanosaeta, 77% and Methanosarcina, 9%) accelerated the methanogenic activity of PW-augmented digesters by 7 times during the exponential phase, increasing the methane yield (75%) compared to the control. Thus, microbial syntrophy facilitated the effective methanation of PW during AD process.
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Affiliation(s)
- Shouvik Saha
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanjay P Govindwar
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Pradip K Chatterjee
- Energy Research and Technology Group, CSIR Central Mechanical Engineering Research Institute, Durgapur 713-209, India
| | - Sang-Eun Oh
- Department of Biological Environment, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Hyun-Seog Roh
- Department of Environmental Engineering, Yonsei University, Wonju, Gangwon-do 26493, Republic of Korea
| | - Sean S Lee
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
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45
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Lu Q, Yu Z, Yu S, Liang Z, Li H, Sun L, Wang S. Organic matter rather than salinity as a predominant feature changes performance and microbiome in methanogenic sludge digesters. JOURNAL OF HAZARDOUS MATERIALS 2019; 377:349-356. [PMID: 31173985 DOI: 10.1016/j.jhazmat.2019.05.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/01/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
Due to low digestibility and long retention time of anaerobic sludge digestion, pre-treatment with alkaline/acid has been widely employed to enhance the rate and extent of sludge digestion. Nonetheless, effects of gradient concentrations of alkaline/acid pre-treatments and resulting salinity on digestion performance and sludge microbiome remain poorly understood. To elucidate these effects, both batch- and reactor-experiments were setup with varied feeding sludge. Significant digestion improvement and sludge microbiome changes were observed with alkaline/acid sludge pre-treatment, compared to non-pretreatment controls, e.g., ˜88% increase of carbon removal in sludge digesters. Surprisingly, with the same concentration of influent sludge, no notable change in digestion performance and sludge microbiome was observed in digesters when increasing alkaline/acid concentrations from 0.25 to 0.8 mol/L, and in batch serum bottles with or without NaCl amendment. Consequently, organic compounds dissolved in sludge pre-treatment could be a predominant selective pressure driving the performance and microbiome changes. By contrast, salinity as a consequence of the alkaline/acid pre-treatment could only enrich specific lineages, without altering the overall community profile and function. Together, this study provided insights into specific impacts of major factors on digester performance and sludge microbiome, and shed lights on optimization of sludge digestion.
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Affiliation(s)
- Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zehui Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Sining Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhiwei Liang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Haocong Li
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China.
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46
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Zealand AM, Mei R, Roskilly AP, Liu W, Graham DW. Molecular microbial ecology of stable versus failing rice straw anaerobic digesters. Microb Biotechnol 2019; 12:879-891. [PMID: 31233284 PMCID: PMC6681398 DOI: 10.1111/1751-7915.13438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/01/2022] Open
Abstract
Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1 day-1 ), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1 day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.
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Affiliation(s)
- Andrew M. Zealand
- School of EngineeringNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| | - Ran Mei
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐Champaign205 North Mathews AveUrbanaIL61801USA
| | - Anthony P. Roskilly
- Sir Joseph Swan Centre for Energy ResearchNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| | - WenTso Liu
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐Champaign205 North Mathews AveUrbanaIL61801USA
| | - David W. Graham
- School of EngineeringNewcastle UniversityNewcastle upon TyneNE1 7RUUK
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Yuan H, Mei R, Liao J, Liu WT. Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems. Front Microbiol 2019; 10:1536. [PMID: 31333629 PMCID: PMC6621641 DOI: 10.3389/fmicb.2019.01536] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/20/2019] [Indexed: 12/03/2022] Open
Abstract
Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan’s Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.
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Affiliation(s)
- Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Junhui Liao
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Tian Z, Chi Y, Yu B, Yang M, Zhang Y. Thermophilic anaerobic digestion reduces ARGs in excess sludge even under high oxytetracycline concentrations. CHEMOSPHERE 2019; 222:305-313. [PMID: 30708164 DOI: 10.1016/j.chemosphere.2019.01.139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
The feasibility of thermophilic anaerobic digestion (AD) for the attenuation of antibiotic resistance genes (ARGs) in biomass wastes under high antibiotic concentrations remains unclear. In this study, a thermophilic completely stirred digester (55 °C) was fed with municipal excess sludge spiked with increasing concentrations of oxytetracycline (OTC) (0-1000 mg/L) over a period of 280 days. Results showed that thermophilic AD could maintain stable methane production (338.40 ± 26.26 mL/d/gVS) even at an OTC dose of 1000 mg/L with the sludge phase OTC concentration reaching around 24,000 mg/kg. More important, the abundance of resistome detected by high-throughput quantitative PCR in the substrate was reduced (p < 0.01) by 55.54%-86.27% by thermophilic AD over the whole period. Partial canonical correspondence and network analyses showed that the reduction of ARGs was achieved mainly through two ways: eliminating the original hosts of ARGs in the substrate (from 41.74% ± 2.60% in the substrate to 12.08% ± 1.02% in digested sludge), and blocking the horizontal proliferation of ARGs in the digested sludge by reducing the abundance of mobile genetic elements and restricting their horizontal exchange within a small number of thermophilic genera. This study showed that thermophilic AD is feasible for the attenuation of ARGs in biomass even containing high level of OTC.
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Affiliation(s)
- Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongzhi Chi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin, 300384, China
| | - Bo Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin, 300384, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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49
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Braz GHR, Fernandez-Gonzalez N, Lema JM, Carballa M. Organic overloading affects the microbial interactions during anaerobic digestion in sewage sludge reactors. CHEMOSPHERE 2019; 222:323-332. [PMID: 30708166 DOI: 10.1016/j.chemosphere.2019.01.124] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/21/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
There is still a lack of information about microbial interactions of anaerobic digestion microbiome during process disturbance which limits our ability to predict the mechanisms that drive community dynamics on these events. This paper aims to determine how an organic overloading affects these interactions and to characterize in detail the microbiome structure and diversity in sewage sludge anaerobic reactors during an acidosis event. Two identical sewage sludge anaerobic reactors were subjected to an organic loading shock by adding glycerol waste. As consequence, volatile fatty acids accumulated after only 24 h (up to 2.5 g/L) while Bacteroidales and Methanomicrobiales became displaced by Firmicutes and Methanosaeta sp, showing that reactor acidosis can occur without an immediate decline of this methanogen. Network analysis revealed 9 clusters of co-occurring microorganisms with different behaviors during overloading. At first, Veillonellaceae family, the main glycerol degrading, associated with Candidatus Cloacimonetes, volatile fatty acids fermenters, increased their relative abundance in detriment of the syntrophic bacteria; although as conditions become more acidic, these groups were displaced by other fermenters like Porphyromonadaceae and Chitinophagaceae. Eventually, the methanogenesis failed 72 h after organic overloading, when pH reached values lower than 6. Overall, our results showed a succession of functionally redundant microorganisms, most likely because of niche specialization during organic overloading. The detailed temporal analysis elucidated the processes governing the dynamics anaerobic digestion microbiome, a knowledge required to develop anaerobic digestion management strategies based on its microbiome during process disturbances.
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Affiliation(s)
- Guilherme H R Braz
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
| | - Nuria Fernandez-Gonzalez
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings, Venue Dr. Mergelina, C/ Dr. Mergelina, s/n, Valladolid 47011, Spain; Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
| | - Juan M Lema
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
| | - Marta Carballa
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
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50
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Microbial immigration in wastewater treatment systems: analytical considerations and process implications. Curr Opin Biotechnol 2019; 57:151-159. [PMID: 31030172 DOI: 10.1016/j.copbio.2019.02.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/12/2019] [Accepted: 02/24/2019] [Indexed: 11/21/2022]
Abstract
Microbial immigration from sewers to wastewater treatment systems is attracting increasing attention for understanding community assembly mechanisms, and improving process modeling and operation. While there is no consensus on approaches to analyze immigration, we suggest to classify them as relevant to either rare (non-observable) diffusive immigration or to time-continuous high-rate mass flow immigration (i.e. mass effects). When analyzed by a mass flow approach, heterotrophs appear to be strongly influenced by deterministic selection, suggesting that the heterotrophs should be subdivided into several functional guilds when assessing their assembly mechanisms. Conversely, nitrifiers appear to transfer neutrally from sewer to activated sludge, and this immigration can restore full nitrification in otherwise non-nitrifying reactors. With further refinement, these findings could be included in predictive process models with various objectives.
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