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Zhang B, Ma Y, Duan W, Fan Q, Sun J. Pinewood nematode induced changes in the assembly process of gallery microbiomes benefit its vector beetle's development. Microbiol Spectr 2024:e0141224. [PMID: 39258937 DOI: 10.1128/spectrum.01412-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/03/2024] [Indexed: 09/12/2024] Open
Abstract
Microbiomes play crucial roles in insect adaptation, especially under stress such as pathogen invasion. Yet, how beneficial microbiomes assemble remains unclear. The wood-boring beetle Monochamus alternatus, a major pest and vector of the pine wilt disease (PWD) nematode, offers a unique model. We conducted controlled experiments using amplicon sequencing (16S rRNA and ITS) within galleries where beetles and microbes interact. PWD significantly altered bacterial and fungal communities, suggesting distinct assembly processes. Deterministic factors like priority effects, host selection, and microbial interactions shaped microbiome composition, distinguishing healthy from PWN-infected galleries. Actinobacteria, Firmicutes, and Ophiostomataceae emerged as potentially beneficial, aiding beetle's development and pathogen resistance. This study unveils how nematode-induced changes in gallery microbiomes influence beetle's development, shedding light on microbiome assembly amid insect-pathogen interactions. Insights gleaned enhance understanding of PWD spread and suggest novel management strategies via microbiome manipulation.IMPORTANCEThis study explores the assembly process of gallery microbiomes associated with a wood-boring beetles, Monochamus alternatus, a vector of the pine wilt disease (PWD). By conducting controlled comparison experiments and employing amplicon approaches, the study reveals significant changes in taxonomic composition and functional adaptation of bacterial and fungal communities induced by PWD. It identifies deterministic processes, including priority effects, host selection, and microbial interactions, as major drivers in microbiome assembly. Additionally, the study highlights the presence of potentially beneficial microbes such as Actinobacteria, Firmicutes, and Ophiostomataceae, which could enhance beetle development and resistance to pathogens. These findings shed light on the intricate interplay among insects, microbiomes, and pathogens, contributing to a deeper understanding of PWD prevalence and suggesting innovative management strategies through microbiome manipulation.
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Affiliation(s)
- Bin Zhang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yafei Ma
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Wenzhao Duan
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Qi Fan
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jianghua Sun
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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2
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Liu W, Wang S, He S, Shi Y, Hou C, Jiang X, Song Y, Zhang T, Zhang Y, Shen Z. Enzyme modified biodegradable plastic preparation and performance in anaerobic co-digestion with food waste. BIORESOURCE TECHNOLOGY 2024; 401:130739. [PMID: 38670291 DOI: 10.1016/j.biortech.2024.130739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
A modified biodegradable plastic (PLA/PBAT) was developed by through covalent bonding with proteinase K, porcine pancreatic lipase, or amylase, and was then investigated in anaerobic co-digestion mixed with food waste. Fluorescence microscope validated that enzymes could remain stable in modified the plastic, even after co-digestion. The results of thermophilic anaerobic co-digestion showed that, degradation of the plastic modified with Proteinase K increased from 5.21 ± 0.63 % to 29.70 ± 1.86 % within 30 days compare to blank. Additionally, it was observed that the cumulative methane production increased from 240.9 ± 0.5 to 265.4 ± 1.8 mL/gVS, and the methane production cycle was shortened from 24 to 20 days. Interestingly, the kinetic model suggested that the modified the plastic promoted the overall hydrolysis progression of anaerobic co-digestion, possibly as a result of the enhanced activities of Bacteroidota and Thermotogota. In conclusion, under anaerobic co-digestion, the modified the plastic not only achieved effective degradation but also facilitated the co-digestion process.
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Affiliation(s)
- Wenjie Liu
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Shizhuo Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China; Shanghai Research Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai 200092, P. R. China
| | - Songting He
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Yang Shi
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Cheng Hou
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China; Shanghai Research Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai 200092, P. R. China
| | - Xintong Jiang
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Yuanbo Song
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Tao Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China; Shanghai Research Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai 200092, P. R. China
| | - Yalei Zhang
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China; Key Laboratory of Rural Toilet and SewageTreatment Technology, Ministry of Agricultureand Rural Affairs, Tongji University, Shanghai 201804, P. R. China; Shanghai Research Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai 200092, P. R. China
| | - Zheng Shen
- Institute of New Rural Development, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, P. R. China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, P. R. China; Key Laboratory of Rural Toilet and SewageTreatment Technology, Ministry of Agricultureand Rural Affairs, Tongji University, Shanghai 201804, P. R. China; Shanghai Research Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai 200092, P. R. China.
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3
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Chettri D, Verma AK, Ghosh S, Verma AK. Biogas from lignocellulosic feedstock: current status and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1-26. [PMID: 37697197 DOI: 10.1007/s11356-023-29805-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/06/2023] [Indexed: 09/13/2023]
Abstract
The organic wastes and residues generated from agricultural, industrial, and domestic activities have the potential to be converted to bioenergy. One such energy is biogas, which has already been included in rural areas as an alternative cooking energy source and agricultural activities. It is produced via anaerobic digestion of a wide range of organic nutrient sources and is an essential renewable energy source. The factors influencing biogas yield, i.e., the various substrate, their characteristics, pretreatment methods involved, different microbial types, sources, and inoculum properties, are analyzed. Furthermore, the optimization of these parameters, along with fermentation media optimization, such as optimum pH, temperature, and anaerobic digestion strategies, is discussed. Novel approaches of bioaugmentation, co-digestion, phase separation, co-supplementation, nanotechnology, and biorefinery approach have also been explored for biogas production. Finally, the current challenges and prospects of the process are discussed in the review.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, India, 737102
| | - Ashwani Kumar Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shilpi Ghosh
- Department of Biotechnology, University of North Bengal, Siliguri, West Bengal, India, 734104
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, India, 737102.
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4
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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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5
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Smith SK, Weaver JE, Ducoste JJ, de Los Reyes FL. Microbial community assembly in engineered bioreactors. WATER RESEARCH 2024; 255:121495. [PMID: 38554629 DOI: 10.1016/j.watres.2024.121495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/10/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.
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Affiliation(s)
- Savanna K Smith
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA
| | - Joseph E Weaver
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Joel J Ducoste
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA
| | - Francis L de Los Reyes
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA.
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6
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Krohn C, Jansriphibul K, Dias DA, Rees CA, Akker BVD, Boer JC, Plebanski M, Surapaneni A, O'Carroll D, Richard S, Batstone DJ, Ball AS. Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring. WATER RESEARCH 2024; 253:121354. [PMID: 38428359 DOI: 10.1016/j.watres.2024.121354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.
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Affiliation(s)
- Christian Krohn
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia.
| | - Kraiwut Jansriphibul
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia
| | - Daniel A Dias
- Centre for Advanced Sensory Science (CASS) Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, Victoria 3125, Australia
| | - Catherine A Rees
- Melbourne Water Corporation, 990 La Trobe Street, Docklands, Victoria 3008, Australia
| | - Ben van den Akker
- South Australian Water Corporation, Adelaide, South Australia 5000, Australia
| | - Jennifer C Boer
- Cancer Aging and Vaccine Laboratory, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Magdalena Plebanski
- Cancer Aging and Vaccine Laboratory, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia; South East Water, 101 Wells Street, Frankston, Victoria 3199, Australia
| | - Denis O'Carroll
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Stuetz Richard
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Damien J Batstone
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia; Australian Centre for Water and Environmental Biotechnology (ACWEB), Gehrmann Building, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew S Ball
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia
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7
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Pei L, Song Y, Chen G, Mu L, Yan B, Zhou T. Enhancement of methane production from anaerobic digestion of Erigeron canadensis via O 2-nanobubble water supplementation. CHEMOSPHERE 2024; 354:141732. [PMID: 38499072 DOI: 10.1016/j.chemosphere.2024.141732] [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: 08/01/2023] [Revised: 11/30/2023] [Accepted: 03/14/2024] [Indexed: 03/20/2024]
Abstract
Malignant invasive Erigeron canadensis, as a typical lignocellulosic biomass, is a formidable challenge for sustainable and efficient resource utilization, however nanobubble water (NBW) coupled with anaerobic digestion furnishes a prospective strategy with superior environmental and economic effectiveness. In this study, influence mechanism of various O2-NBW addition times on methanogenic performance of E. canadensis during anaerobic digestion were performed to achieve the optimal pollution-free energy conversion. Results showed that supplementation of O2-NBW in digestion system could significantly enhance the methane production by 10.70-16.17%, while the maximum cumulative methane production reached 343.18 mL g-1 VS in the case of one-time O2-NBW addition on day 0. Furthermore, addition of O2-NBW was conducive to an increase of 2-90% in the activities of dehydrogenase, α-glucosidase and coenzyme F420. Simultaneously, both facultative bacteria and methanogenic archaea were enriched as well, further indicating that O2-NBW might be responsible for facilitating hydrolytic acidification and methanogenesis. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) cluster analysis, provision of O2-NBW enhanced the metabolism of carbohydrate and amino acid, translation as well as membrane transport of bacteria and archaea. This study might offer the theoretical guidance and novel insights for efficient recovery of energy from lignocellulosic biomass on account of O2-NBW adhibition in anaerobic digestion system, progressing tenor of carbon-neutral vision.
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Affiliation(s)
- Legeng Pei
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Yingjin Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Double Carbon Research Institute, Tianjin, 300350, China.
| | - Guanyi Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; School of Mechanical Engineering, Tianjin University of Commerce, Tianjin, 300134, China; Double Carbon Research Institute, Tianjin, 300350, China
| | - Lan Mu
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin, 300134, China
| | - Beibei Yan
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Teng Zhou
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
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8
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Niya B, Yaakoubi K, Beraich FZ, Arouch M, Meftah Kadmiri I. Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches. Heliyon 2024; 10:e28221. [PMID: 38560681 PMCID: PMC10979216 DOI: 10.1016/j.heliyon.2024.e28221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.
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Affiliation(s)
- Btissam Niya
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Kaoutar Yaakoubi
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Fatima Zahra Beraich
- Biodome.sarl, Research and Development Design Office of Biogas Technology, Casablanca, Morocco
| | - Moha Arouch
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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9
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Nie E, He P, Peng W, Zhang H, Lü F. Microbial volatile organic compounds as novel indicators of anaerobic digestion instability: Potential and challenges. Biotechnol Adv 2023; 67:108204. [PMID: 37356597 DOI: 10.1016/j.biotechadv.2023.108204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
The wide application of anaerobic digestion (AD) technology is limited by process fluctuations. Thus, process monitoring based on screening state parameters as early warning indicators (EWI) is a top priority for AD facilities. However, predicting anaerobic digester stability based on such indicators is difficult, and their threshold values are uncertain, case-specific, and sometimes produce conflicting results. Thus, new EWI should be proposed to integrate microbial and metabolic information. These microbial volatile organic compounds (mVOCs) including alkanes, alkenes, alkynes, aromatic compounds are produced by microorganisms (bacteria, archaea and fungi), which might serve as a promising diagnostic tool for environmental monitoring. Moreover, mVOCs diffuse in both gas and liquid phases and are considered the language of intra kingdom microbial interactions. Herein, we highlight the potential of mVOCs as EWI for AD process instability, including discussions regarding characteristics and sources of mVOCs as well as sampling and determination methods. Furthermore, existing challenges must be addressed, before mVOCs profiling can be used as an early warning system for diagnosing AD process instability, such as mVOCs sampling, analysis and identification. Finally, we discuss the potential biotechnology applications of mVOCs and approaches to overcome the challenges regarding their application.
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Affiliation(s)
- Erqi Nie
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Wei Peng
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China
| | - Hua Zhang
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China
| | - Fan Lü
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China.
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10
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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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11
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Sierocinski P, Stilwell P, Padfield D, Bayer F, Buckling A. The ecology of scale: impact of volume on coalescence and function in methanogenic communities. Interface Focus 2023; 13:20220089. [PMID: 37303743 PMCID: PMC10251116 DOI: 10.1098/rsfs.2022.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/05/2023] [Indexed: 06/13/2023] Open
Abstract
Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.
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Affiliation(s)
- Pawel Sierocinski
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Peter Stilwell
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Daniel Padfield
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Florian Bayer
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Angus Buckling
- ESI, Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
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12
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Kirubaharan CJ, Wang JW, Abbas SZ, Shah SB, Zhang Y, Wang JX, Yong YC. Self-assembly of cell-embedding reduced graphene oxide/ polypyrrole hydrogel as efficient anode for high-performance microbial fuel cell. CHEMOSPHERE 2023; 318:137937. [PMID: 36925003 DOI: 10.1016/j.chemosphere.2023.137937] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 05/23/2023]
Abstract
A three-dimensional (3D) macroporous reduced graphene oxide/polypyrrole (rGO/Ppy) hydrogel assembled by bacterial cells was fabricated and applied for microbial fuel cells. By taking the advantage of electroactive cell-induced bioreduction of graphene oxide and in-situ polymerization of Ppy, a facile self-assembly by Shewanella oneidensis MR-1and in-situ polymerization approach for 3D rGO/Ppy hydrogel preparation was developed. This facile one-step self-assembly process enabled the embedding of living electroactive cells inside the hydrogel electrode, which showed an interconnected 3D macroporous structures with high conductivity and biocompatibility. Electrochemical analysis indicated that the self-assembly of cell-embedding rGO/Ppy hydrogel enhanced the electrochemical activity of the bioelectrode and reduced the electron charge transfer resistance between the cells and the electrode. Impressively, extremely high power output of 3366 ± 42 mW m-2 was achieved from the MFC with cell-embedding rGO/Ppy hydrogel rGO/Ppy, which was 8.6 times of that delivered from the MFC with bare electrode. Further analysis indicated that the increased cell loading by the hydrogel and improved electrochemical activity by the rGO/Ppy composite would be the underlying mechanism for this performance improvement. This study provided a facile approach to fabricate the biocompatible and electrochemical active 3D nanocomposites for MFC, which would also be promising for performance optimization of various bioelectrochemical systems.
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Affiliation(s)
- C Joseph Kirubaharan
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Jian-Wei Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Syed Zaghum Abbas
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Syed Bilal Shah
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Yafei Zhang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Jing-Xian Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China; School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China.
| | - Yang-Chun Yong
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China.
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13
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Sethi S, Gupta R, Bharshankh A, Sahu R, Biswas R. Celebrating 50 years of microbial granulation technologies: From canonical wastewater management to bio-product recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162213. [PMID: 36796691 DOI: 10.1016/j.scitotenv.2023.162213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Microbial granulation technologies (MGT) in wastewater management are widely practised for more than fifty years. MGT can be considered a fine example of human innovativeness-driven nature wherein the manmade forces applied during operational controls in the biological process of wastewater treatment drive the microbial communities to modify their biofilms into granules. Mankind, over the past half a century, has been refining the knowledge of triggering biofilm into granules with some definite success. This review captures the journey of MGT from inception to maturation providing meaningful insights into the process development of MGT-based wastewater management. The full-scale application of MGT-based wastewater management is discussed with an understanding of functional microbial interactions within the granule. The molecular mechanism of granulation through the secretion of extracellular polymeric substances (EPS) and signal molecules is also highlighted in detail. The recent research interest in the recovery of useful bioproducts from the granular EPS is also emphasized.
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Affiliation(s)
- Shradhanjali Sethi
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, Uttar Pradesh 201002, India; Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, Maharashtra 440020, India
| | - Rohan Gupta
- Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, Maharashtra 440020, India
| | - Ankita Bharshankh
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, Uttar Pradesh 201002, India; Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, Maharashtra 440020, India
| | - Rojalin Sahu
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, Uttar Pradesh 201002, India; Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, Maharashtra 440020, India
| | - Rima Biswas
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, Uttar Pradesh 201002, India; Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, Maharashtra 440020, India.
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14
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Liu YC, Ramiro-Garcia J, Paulo LM, Maria Braguglia C, Cristina Gagliano M, O'Flaherty V. Psychrophilic and mesophilic anaerobic treatment of synthetic dairy wastewater with long chain fatty acids: Process performances and microbial community dynamics. BIORESOURCE TECHNOLOGY 2023; 380:129124. [PMID: 37127168 DOI: 10.1016/j.biortech.2023.129124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
Facilitating the anaerobic degradation of long chain fatty acids (LCFA) is the key to unlock the energy potential of lipids-rich wastewater. In this study, the feasibility of psychrophilic anaerobic treatment of LCFA-containing dairy wastewater was assessed and compared to mesophilic anaerobic treatment. The results showed that psychrophilic treatment at 15 ℃ was feasible for LCFA-containing dairy wastewater, with high removal rates of soluble COD (>90%) and LCFA (∼100%). However, efficient long-term treatment required prior acclimation of the biomass to psychrophilic temperatures. The microbial community analysis revealed that putative syntrophic fatty acid bacteria and Methanocorpusculum played a crucial role in LCFA degradation during both mesophilic and psychrophilic treatments. Additionally, a fungal-bacterial biofilm was found to be important during the psychrophilic treatment. Overall, these findings demonstrate the potential of psychrophilic anaerobic treatment for industrial wastewaters and highlight the importance of understanding the microbial communities involved in the process.
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Affiliation(s)
- Yu-Chen Liu
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, University Road, Galway, H91 TK33, Ireland.
| | - Javier Ramiro-Garcia
- Instituto de la Grasa. Consejo Superior de Investigaciones Científicas. Campus Universitario Pablo de Olavide- Ed. 46, Ctra. de Utrera, km. 1, Seville 41013, Spain
| | - Lara M Paulo
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Camilla Maria Braguglia
- Water Research institute, CNR, Area di Ricerca RM1-Montelibretti, Via Salaria km 29.300, 00015 Monterotondo (Roma), Italy
| | - Maria Cristina Gagliano
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, MA 8911 Leeuwarden, the Netherlands
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, University Road, Galway, H91 TK33, Ireland
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15
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Ahmad A, Senaidi AS. Sustainability for wastewater treatment: bioelectricity generation and emission reduction. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:48703-48720. [PMID: 36862299 DOI: 10.1007/s11356-023-26063-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/16/2023] [Indexed: 04/16/2023]
Abstract
This review covers the technological measures of a self-sustainable anaerobic up-flow sludge blanket (UASB) system compared with an aerobic activated sludge process (ASP) for wastewater treatment plants (WWTPs). The ASP requires a huge amount of electricity and chemicals and also results in the emission of carbon. The UASB system, instead, is based on greenhouse gas (GHG) emission reduction and is associated with biogas production for cleaner electricity. WWTPs including the ASP system are not sustainable due to the massive financial power required for clean wastewater. When the ASP system was used, the amount of production was estimated to be 10658.98 tonnes CO2eq-d- of carbon dioxide. Whereas it was 239.19 tonnes CO2eq-d-1 with the UASB. The UASB system is advantageous over the ASP system as it has a high production of biogas, needs low maintenance, yields a low amount of sludge, and is also a source of electricity that can be used as a power source for the WWTPs. Also, the UASB system produces less biomass, and this helps in reducing costs and maintaining work. Moreover, the aeration tank of the ASP needs 60% of energy distribution; on the other hand, the UASB consumes less energy, approximately 3-11%.
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Affiliation(s)
- Anwar Ahmad
- Civil and Environmental Engineering Department, College of Engineering and Architecture, University of Nizwa, PO 33 Postal Code 616, Nizwa, Sultanate of Oman.
| | - Alaya Said Senaidi
- Civil and Environmental Engineering Department, College of Engineering and Architecture, University of Nizwa, PO 33 Postal Code 616, Nizwa, Sultanate of Oman
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16
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Krohn C, Khudur L, Dias DA, van den Akker B, Rees CA, Crosbie ND, Surapaneni A, O'Carroll DM, Stuetz RM, Batstone DJ, Ball AS. The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge. Front Microbiol 2022; 13:1079136. [PMID: 36590430 PMCID: PMC9801413 DOI: 10.3389/fmicb.2022.1079136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.
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Affiliation(s)
- Christian Krohn
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia,*Correspondence: Christian Krohn,
| | - Leadin Khudur
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia
| | - Daniel Anthony Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, STEM College, RMIT University, Bundoora, VIC, Australia
| | | | | | | | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia
| | - Denis M. O'Carroll
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Richard M. Stuetz
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Damien J. Batstone
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia,Australian Centre for Water and Environmental Biotechnology, Gehrmann Building, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew S. Ball
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia
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17
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Sharma P, Nadda AK, Kumar S. Microbial community profiling in bio-stimulated municipal solid waste for effective removal of organic pollutants containing endocrine disrupting chemicals. Microbiol Res 2022; 267:127273. [PMID: 36481500 DOI: 10.1016/j.micres.2022.127273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/01/2022] [Accepted: 11/24/2022] [Indexed: 11/26/2022]
Abstract
The study was aimed to improve the degradation of organic pollutants in municipal solid waste (MSW) through the bio-stimulation process. The results showed that the physico-chemical properties of MSW (control) had a high value of pH (9.2 ± 0.02); total suspended solids (TSS: 1547 ± 23 mg/kg-1), and total dissolved solids (TDS:76 ± 0.67 mg/kg-1). After the biostimulation process (biostimulated MSW), the physico-chemical parameters of MSW were reduced as pH (7.1 ± 0.01); TSS (41 ± 0.01 mg/kg-1), and TDS (789 ± 03 mg/kg-1). Furthermore, the major organic pollutants detected from MSW by gas chromatography-mass spectroscopy (GC-MS) analysis at different retention time (RT) were hexadecane (RT-8.79); pentadecane (RT-9.36); and hexasiloxane (RT-9.43) while these organic pollutants were degraded after the biostimulation process. The whole-genome metagenome sequencing size (%) analyses showed major groups of bacteria (40.82%) followed by fungi (0.05%), virus (0.0032%), and archaea (0.0442%) in MSW. The species richness and evenness of the microbial community were decreased substantially due to the biostimulation treatment. The total number of genes in the biostimulated MSW (PS-3_11267) sample were 465302 whereas the number of genes in the control MSW (PS-4_11268) sample were 256807. Furthermore, the biostimulated MSW (PS-3_11267) aligned the reads to bacteria (19502525), fungi (40030), virus (3339), and archaea (12759) genomes whereas the control sample (PS-4_11268) aligned the reads to bacteria (17057259), fungi (19148), virus (1335), and archaea (18447) genomes. Moreover, the relative abundance at genus level in biostimulated MSW (PS-3_11267) (Ochrobactrum and Phenylobacterium), phylum; (Proteobacteria and Actinobacteria), and species (Chthoniobacter flavus and Vulgatibacter incomptus) level was the most abundant. The results provided valuable information regarding the degradation of organic pollutants in MSW by microbial communities through biostimulation for the prevention of soil pollution and health protection.
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Affiliation(s)
- Pooja Sharma
- Waste Re-processing Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, Maharashtra, India
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173 234, India
| | - Sunil Kumar
- Waste Re-processing Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, Maharashtra, India.
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18
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Zheng M, Shao S, Chen Y, Chen B, Wang M. Metagenomics analysis of microbial community distribution in large-scale and step-by-step purification system of swine wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120137. [PMID: 36089141 DOI: 10.1016/j.envpol.2022.120137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/22/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Biological treatment is one of the most widely used methods to treat swine wastewater in wastewater treatment plants. The microbial community plays an important role in the swine slurry treatment system. However, limited information is available regarding the correlation between pollutant concentration and dominant microbial community in swine wastewater. This work aimed to study the profiling of microbial communities and their abundance in the 40 M3/day large-scale and step-by-step treatment pools of swine wastewater. Metagenome sequencing was applied to study the changes of microbial community structure in biochemical reaction pools. The results showed that in the heavily polluted pools, it was mainly Proteobacteria, Cyanobacteria, Chlorella and other strains that could tolerate high concentration of ammonia nitrogen to remove nitrogen and absorb chemical oxygen demand (COD). In the moderately polluted pools, Nitrospirae, Actinobacteria and other strains further cooperated to purify swine wastewater. In the later stage, the emergence of Brachionus indicated the reduction of water pollution. The dominant microbes and their abundance changed with the purification of swine wastewater in different stages. Moreover, the dominant microflora of swine wastewater treatment pools at all levels reflected little difference in phylum classification level, while in genus classification level, the dominant microflora manifested great difference. Findings demonstrated that the microorganisms maintained ecological balance and absorbed the nutrients in the swine wastewater treatment pools, so as to play the role of purifying sewage. Therefore, the stepwise purification of swine wastewater can be realized by adding bacteria and microalgae of different genera.
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Affiliation(s)
- Mingmin Zheng
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, 350117,China
| | - Shanshan Shao
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Yanzhen Chen
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Bilian Chen
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, 350117,China
| | - Mingzi Wang
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, 350117,China.
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19
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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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20
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Lü F, Chen W, Duan H, Zhang H, Shao L, He P. Monitor process state of batch anaerobic digestion in reliance on volatile and semi-volatile metabolome. BIORESOURCE TECHNOLOGY 2022; 351:126953. [PMID: 35278621 DOI: 10.1016/j.biortech.2022.126953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
It has been a challenge to recognize appropriate compounds as indicators for monitoring and early-warning of the anaerobic digestion process. A strategy was initiated to explore the evolution of the panorama profile of volatile and semi-volatile metabolites. Non-target analysis using high-resolution gas chromatography coupled with Orbitrap mass spectrometry was applied to construct a time-series molecular fingerprint of 218 metabolites classified in 14 categories. Alkanes accounted for the main part in early and late stages of methanization and aromatic compounds were the major in middle stage. Spearman correlation analysis and partial least squares analysis unwind that Trichococcus (1.49%-83.96%) was positively related to most of metabolites at early and middle stages, while Brevundimonas (0%-24.04%) was positively related to acylamide at late stage. This indicated that microbial volatile organic compounds were possible to serve as biochemical indicators for anaerobic digestion performance and to build nexus of "what" (metabolites), "who" (microorganism), and "how" (kinetics).
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Affiliation(s)
- Fan Lü
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Wenwen Chen
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Haowen Duan
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Hua Zhang
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Liming Shao
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Shanghai Engineering Research Center of Multi-source Solid Wastes Co-processing and Energy Utilization, Shanghai 200092, PR China.
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21
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Li X, Wu M, Xue Y. Nickel-loaded shrimp shell biochar enhances batch anaerobic digestion of food waste. BIORESOURCE TECHNOLOGY 2022; 352:127092. [PMID: 35367323 DOI: 10.1016/j.biortech.2022.127092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
This study evaluated the effectiveness of shrimp shell biochar (SBC) and nickel (Ni) loaded SBC in increasing methane yield during anaerobic digestion of food waste. The results indicated that the methane yields of control (without SBC), SBC, SBC loaded with the low concentration of Ni, and SBC loaded with the high concentration of Ni were 81.8, 116.1, 134.7, and 99.2 mL/(g·VS), respectively. SBC promoted the efficiency and stability of the whole anaerobic digestion process including hydrolysis, volatile fatty acid conversion and methanogenesis. While the invigorating effect of loaded Ni at the low concentration of 0.88 mg/g was mainly concentrated in methanogenesis, the inhibition effect of the high Ni concentration was comprehensive. SBC helped Methanosarcina proliferation, and low concentration Ni promoted the number and activity of Methanosarcina and Methanosaeta. The results show that biochar loaded with a low level of trace elements such as Ni can promote the anaerobic digestion process.
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Affiliation(s)
- Xiao Li
- School of Civil Engineering, Wuhan University, Wuhan, China
| | - Mingxuan Wu
- School of Civil Engineering, Wuhan University, Wuhan, China
| | - Yingwen Xue
- School of Civil Engineering, Wuhan University, Wuhan, China.
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22
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Sharma P, Singh SP. Identification and profiling of microbial community from industrial sludge. Arch Microbiol 2022; 204:234. [PMID: 35362813 DOI: 10.1007/s00203-022-02831-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/05/2022] [Accepted: 03/06/2022] [Indexed: 02/03/2023]
Abstract
The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, 226 025, Uttar Pradesh, India.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208 001, India.
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23
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Varghese VK, Poddar BJ, Shah MP, Purohit HJ, Khardenavis AA. A comprehensive review on current status and future perspectives of microbial volatile fatty acids production as platform chemicals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152500. [PMID: 34968606 DOI: 10.1016/j.scitotenv.2021.152500] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/26/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.
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Affiliation(s)
- Vijay K Varghese
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India
| | - Bhagyashri J Poddar
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Maulin P Shah
- Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab, Enviro Technology Ltd., Ankleshwar 393002, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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24
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Zhao X, Liu M, Yang S, Gong H, Ma J, Li C, Wang K. Performance and microbial community evaluation of full-scale two-phase anaerobic digestion of waste activated sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152525. [PMID: 34954158 DOI: 10.1016/j.scitotenv.2021.152525] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
"Temperature Staging and Biological Phasing" (TSBP) is an improved two-phase anaerobic digestion (AD) technology. This technology hydrolyzes waste activated sludge (WAS) at 45 °C and converts methane at mesophilic temperature (35-38 °C), with hydraulic retention times of 3-5 d and 14-17 d, respectively. In this study, the performance and microbial community dynamics of full-scale TSBP-based sludge anaerobic digestion system were studied, and the technology was evaluated by energy balance and ecological benefit analysis. The stable operation for 390 d showed that the cumulative biogas yield was about 349,041 m3, the maximum biogas yield rate was 563.68 L/kg VS, and the VS degradation rate of organic matters in the sludge was 47.19%. Proteobacteria and Firmicutes were found to be the dominant bacteria in both thermophilic and mesophilic reactors. Methanobacterium and Methanosarcina were the two most abundant methanogenic genera in the AD samples. The aceticlastic methanogenesis was likely the predominant production pathway of methane in AD processes based on metagenomics. The TSBP system operated stably, and the recovered energy could achieve energy self-sufficiency, which provided technical reference for the anaerobic treatment of sludge.
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Affiliation(s)
- Xiaoling Zhao
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Henan Center for Outstanding Overseas Scientists, Zhengzhou 450001, China.
| | - Min Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shipeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jinyuan Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Caibin Li
- Beijing Sustainable Green ET. Co., Ltd., Beijing 100084, China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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25
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Villalobos Solis MI, Chirania P, Hettich RL. In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:32. [PMID: 35303956 PMCID: PMC8933973 DOI: 10.1186/s13068-022-02125-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Microbial-driven solubilization of lignocellulosic material is a natural mechanism that is exploited in anaerobic digesters (ADs) to produce biogas and other valuable bioproducts. Glycoside hydrolases (GHs) are the main enzymes that bacterial and archaeal populations use to break down complex polysaccharides in these reactors. Methodologies for rapidly screening the physical presence and types of GHs can provide information about their functional activities as well as the taxonomical diversity within AD systems but are largely unavailable. Targeted proteomic methods could potentially be used to provide snapshots of the GHs expressed by microbial consortia in ADs, giving valuable insights into the functional lignocellulolytic degradation diversity of a community. Such observations would be essential to evaluate the hydrolytic performance of a reactor or potential issues with it. RESULTS As a proof of concept, we performed an in silico selection and evaluation of groups of tryptic peptides from five important GH families derived from a dataset of 1401 metagenome-assembled genomes (MAGs) in anaerobic digesters. Following empirical rules of peptide-based targeted proteomics, we selected groups of shared peptides among proteins within a GH family while at the same time being unique compared to all other background proteins. In particular, we were able to identify a tractable unique set of peptides that were sufficient to monitor the range of GH families. While a few thousand peptides would be needed for comprehensive characterization of the main GH families, we found that at least 50% of the proteins in these families (such as the key families) could be tracked with only 200 peptides. The unique peptides selected for groups of GHs were found to be sufficient for distinguishing enzyme specificity or microbial taxonomy. These in silico results demonstrate the presence of specific unique GH peptides even in a highly diverse and complex microbiome and reveal the potential for development of targeted metaproteomic approaches in ADs or lignocellulolytic microbiomes. Such an approach could be valuable for estimating molecular-level enzymatic capabilities and responses of microbial communities to different substrates or conditions, which is a critical need in either building or utilizing constructed communities or defined cultures for bio-production. CONCLUSIONS This in silico study demonstrates the peptide selection strategy for quantifying relevant groups of GH proteins in a complex anaerobic microbiome and encourages the development of targeted metaproteomic approaches in fermenters. The results revealed that targeted metaproteomics could be a feasible approach for the screening of cellulolytic enzyme capacities for a range of anaerobic microbiome fermenters and thus could assist in bioreactor evaluation and optimization.
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Affiliation(s)
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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26
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Dzulkarnain ELN, Audu JO, Wan Dagang WRZ, Abdul-Wahab MF. Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook. BIORESOUR BIOPROCESS 2022; 9:16. [PMID: 38647867 PMCID: PMC10991117 DOI: 10.1186/s40643-022-00504-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/14/2022] [Indexed: 01/02/2023] Open
Abstract
Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.
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Affiliation(s)
| | - Jemilatu Omuwa Audu
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
- Department of Science Laboratory Technology, Modibbo Adama University, PMB 2076, Yola, Adamawa, Nigeria
| | - Wan Rosmiza Zana Wan Dagang
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Firdaus Abdul-Wahab
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
- Taiwan-Malaysia Innovation Centre for Clean Water and Sustainable Energy (WISE Centre), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
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27
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de Jonge N, Poulsen JS, Vechi NT, Kofoed MVW, Nielsen JL. Wood-Ljungdahl pathway utilisation during in situ H 2 biomethanation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151254. [PMID: 34710425 DOI: 10.1016/j.scitotenv.2021.151254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Biogas production from organic waste is a waste-to-energy technology with the potential to contribute significantly to sustainable energy production. Upgrading of biogas using in situ biomethanation with hydrogen has the potential for surplus electricity storage, and delivery of biogas with a methane content of >90%, allowing for easier integration into the natural gas grid, as well as conversion to other products. Microbial communities in biomethanation reactors undergo changes, however, these changes are largely unexplored. In the present study, metagenome-resolved protein stable isotope probing (Protein-SIP) was applied to laboratory scale batch incubations operating under anaerobic digestion, and (pre-adapted) biomethanation conditions, fed with 13C-labelled bicarbonate, in order to gain insight into the microbial activities during CO2-reduction. The strongest and most microbially diverse isotopic incorporation was observed in the pre-adapted biomethanation incubation. Furthermore, divergent incorporation of 13C-labelled bicarbonate was also observed in the Wood-Ljungdahl pathway, with the anaerobic digester incubations primarily showing labelled proteins in the peripheral pathways leading toward production of energy and biomass. The pre-adapted biomethanation incubations consumed H2 and CO2, but did not convert it to CH4, suggesting the production of acetate in these incubations, which was supported by heavy labelling of key enzymes in the Wood-Ljungdahl pathway. Twelve (ten high quality) metagenome-assembled genomes (MAGs) coding for 13C-incorporated proteins were extracted from the metagenome, eight of which contained one or more of the key genes in the Wood-Ljungdahl pathway, one of which was affiliated to Methanosarcina. Together, the findings in the present study deepen our knowledge surrounding microbial communities in biomethanation systems, and contribute to the development of better strategies for implementation of biogas upgrading and microbial management.
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Affiliation(s)
- Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg E, Denmark.
| | - Jan Struckmann Poulsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg E, Denmark.
| | - Nathalia Thygesen Vechi
- Department of Biological and Chemical Engineering, Aarhus University, Hangøvej 2, DK-8200 Aarhus N, Denmark.
| | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg E, Denmark.
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28
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Puig-Castellví F, Midoux C, Guenne A, Conteau D, Franchi O, Bureau C, Madigou C, Jouan-Rimbaud Bouveresse D, Kroff P, Mazéas L, Rutledge DN, Gaval G, Chapleur O. Metataxonomics, metagenomics and metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters. BIORESOURCE TECHNOLOGY 2022; 346:126612. [PMID: 34954354 DOI: 10.1016/j.biortech.2021.126612] [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: 10/18/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Full-scale anaerobic digesters' performance is regulated by modifying their operational conditions, but little is known about how these modifications affect their microbiome. In this work, we monitored two originally mesophilic (35 °C) full-scale anaerobic digesters during 476 days. One digester was submitted to sub-mesophilic (25 °C) conditions between days 123 and 373. We characterized the effect of temperature modification using a multi-omics (metataxonomics, metagenomics, and metabolomics) approach. The metataxonomics and metagenomics results revealed that the lower temperature allowed a substantial increase of the sub-dominant bacterial population, destabilizing the microbial community equilibrium and reducing the biogas production. After restoring the initial mesophilic temperature, the bacterial community manifested resilience in terms of microbial structure and functional activity. The metabolomic signature of the sub-mesophilic acclimation was characterized by a rise of amino acids and short peptides, suggesting a protein degradation activity not directed towards biogas production.
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Affiliation(s)
- Francesc Puig-Castellví
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 75005 Paris, France; Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France; Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France; Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, 78350, Jouy-en-Josas, France
| | - Angéline Guenne
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | | | - Oscar Franchi
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France; Universidad Adolfo Ibanez, Facultad de ingeniería y ciencias, 2520000 Viña del mar, Chile
| | - Chrystelle Bureau
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | - Céline Madigou
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | | | | | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France
| | - Douglas N Rutledge
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 75005 Paris, France; National Wine and Grape Industry Centre, Charles Sturt University, 2650 Wagga Wagga, Australia
| | | | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92160 Antony, France.
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29
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Verstraete W, Yanuka‐Golub K, Driesen N, De Vrieze J. Engineering microbial technologies for environmental sustainability: choices to make. Microb Biotechnol 2022; 15:215-227. [PMID: 34875143 PMCID: PMC8719809 DOI: 10.1111/1751-7915.13986] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 11/27/2022] Open
Abstract
Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.
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Affiliation(s)
- Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
- Avecom NVIndustrieweg 122PWondelgem9032Belgium
| | - Keren Yanuka‐Golub
- The Institute of Applied ResearchThe Galilee SocietyP.O. Box 437Shefa‐AmrIsrael
| | | | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
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30
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Kim NK, Lee SH, Kim Y, Park HD. Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches. BIORESOURCE TECHNOLOGY 2022; 344:126350. [PMID: 34813924 DOI: 10.1016/j.biortech.2021.126350] [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] [Received: 09/30/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) is a technique that can be used to treat high concentrations of various organic wastes using a consortium of functionally diverse microorganisms under anaerobic conditions. Methane gas, a beneficial by-product of the AD process, is a renewable energy source that can replace fossil fuels following purification. However, detailed functional roles and metabolic interactions between microbial populations involved in organic waste removal and methanogenesis are yet to be known. Recent metagenomic approaches based on advanced high-throughput sequencing techniques have enabled the exploration of holistic microbial taxonomy and functionality of complex microbial populations involved in the AD process. Gene-centric and genome-centric analyses based on metagenome-assembled genomes are a platform that can be used to study the composition of microbial communities and their roles during AD. This review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the AD process.
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Affiliation(s)
- Na-Kyung Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Yonghoon Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea.
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31
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Innard N, Chong JPJ. The challenges of monitoring and manipulating anaerobic microbial communities. BIORESOURCE TECHNOLOGY 2022; 344:126326. [PMID: 34780902 DOI: 10.1016/j.biortech.2021.126326] [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: 09/05/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.
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Affiliation(s)
- Nathan Innard
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
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32
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Chapleur O, Poirier S, Guenne A, Lê Cao KA. Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia. CHEMOSPHERE 2021; 283:131309. [PMID: 34467946 DOI: 10.1016/j.chemosphere.2021.131309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/01/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Omics longitudinal studies are effective experimental designs to inform on the stability and dynamics of microbial communities in response to perturbations, but time-course analytical frameworks are required to fully exploit the temporal information acquired in this context. In this study we investigate the influence of ammonia on the stability of anaerobic digestion (AD) microbiome with a new statistical framework. Ammonia can severely reduce AD performance. Understanding how it affects microbial communities development and the degradation progress is a key operational issue to propose more stable processes. Thirty batch digesters were set-up with different levels of ammonia. Microbial community structure and metabolomic profiles were monitored with 16 S-metabarcoding and GCMS (gas-chromatography-mass-spectrometry). Digesters were first grouped according to similar degradation performances. Within each group, time profiles of OTUs and metabolites were modelled, then clustered into similar time trajectories, evidencing for example a syntrophic interaction between Syntrophomonas and Methanoculleus that was maintained up to 387 mg FAN/L. Metabolites resulting from organic matter fermentation, such as dehydroabietic or phytanic acid, decreased with increasing ammonia levels. Our analytical framework enabled to fully account for time variability and integrate this parameter in data analysis.
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Affiliation(s)
- Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France.
| | - Simon Poirier
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France.
| | - Angéline Guenne
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France.
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and the School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia.
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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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Gralka M, Szabo R, Stocker R, Cordero OX. Trophic Interactions and the Drivers of Microbial Community Assembly. Curr Biol 2021; 30:R1176-R1188. [PMID: 33022263 DOI: 10.1016/j.cub.2020.08.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found in animal guts, oceans, or soils, it is still unclear whether there are generalizable biological or ecological processes that control their dynamics and function. Here, we review experimental and theoretical advances to argue that networks of trophic interactions, in which the metabolic excretions of one species are the primary resource for another, constitute the central drivers of microbial community assembly. Trophic interactions emerge from the deconstruction of complex forms of organic matter into a wealth of smaller metabolic intermediates, some of which are released to the environment and serve as a nutritional buffet for the community. The structure of the emergent trophic network and the rate at which primary resources are supplied control many features of microbial community assembly, including the relative contributions of competition and cooperation and the emergence of alternative community states. Viewing microbial community assembly through the lens of trophic interactions also has important implications for the spatial dynamics of communities as well as the functional redundancy of taxonomic groups. Given the ubiquity of trophic interactions across environments, they impart a common logic that can enable the development of a more quantitative and predictive microbial community ecology.
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Affiliation(s)
- Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel Szabo
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich 8093, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Costa RB, Lens PNL, Foresti E. Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies. Crit Rev Biotechnol 2021; 42:145-161. [PMID: 34157918 DOI: 10.1080/07388551.2021.1931014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NOx consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.
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Affiliation(s)
- R B Costa
- Department of Hydraulics and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil.,National University of Ireland, Galway, Ireland
| | - P N L Lens
- National University of Ireland, Galway, Ireland
| | - E Foresti
- Department of Hydraulics and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil
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Awasthi MK, Ferreira JA, Sirohi R, Sarsaiya S, Khoshnevisan B, Baladi S, Sindhu R, Binod P, Pandey A, Juneja A, Kumar D, Zhang Z, Taherzadeh MJ. A critical review on the development stage of biorefinery systems towards the management of apple processing-derived waste. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2021; 143:110972. [DOI: 10.1016/j.rser.2021.110972] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
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Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [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: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
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Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
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Khan MA, Khan ST, Sequeira MC, Faheem SM, Rais N. Illumina sequencing of 16S rRNA genes reveals a unique microbial community in three anaerobic sludge digesters of Dubai. PLoS One 2021; 16:e0249023. [PMID: 33793629 PMCID: PMC8016227 DOI: 10.1371/journal.pone.0249023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/09/2021] [Indexed: 01/12/2023] Open
Abstract
Understanding the microbial communities in anaerobic digesters, especially bacteria and archaea, is key to its better operation and regulation. Microbial communities in the anaerobic digesters of the Gulf region where climatic conditions and other factors may impact the incoming feed are not documented. Therefore, Archaeal and Bacterial communities of three full-scale anaerobic digesters, namely AD1, AD3, and AD5 of the Jebel Ali Sewage water Treatment Plant (JASTP) were analyzed by Illumina sequencing of 16S rRNA genes. Among bacteria, the most abundant genus was fermentative bacteria Acetobacteroides (Blvii28). Other predominant bacterial genera in the digesters included thermophilic bacteria (Fervidobacterium and Coprothermobacter) and halophilic bacteria like Haloterrigena and Sediminibacter. This can be correlated with the climatic condition in Dubai, where the bacteria in the incoming feed may be thermophilic or halophilic as much of the water used in the country is desalinated seawater. The predominant Archaea include mainly the members of the phyla Euryarchaeota and Crenarchaeota belonging to the genus Methanocorpusculum, Metallosphaera, Methanocella, and Methanococcus. The highest population of Methanocorpusculum (more than 50% of total Archaea), and other hydrogenotrophic archaea, is in agreement with the high population of bacterial genera Acetobacteroides (Blvii28) and Fervidobacterium, capable of fermenting organic substrates into acetate and H2. Coprothermobacter, which is known to improve protein degradation by establishing syntrophy with hydrogenotrophic archaea, is also one of the digesters’ dominant genera. The results suggest that the microbial community in three full-scale anaerobic digesters is different. To best of our knowledge this is the first detailed report from the UAE.
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Affiliation(s)
- Munawwar Ali Khan
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Shams Tabrez Khan
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- * E-mail:
| | - Milred Cedric Sequeira
- School of Life Sciences, Manipal Academy of Higher Education, Academic City, Dubai, United Arab Emirates
| | - Sultan Mohammad Faheem
- School of Life Sciences, Manipal Academy of Higher Education, Academic City, Dubai, United Arab Emirates
| | - Naushad Rais
- School of Life Sciences, Manipal Academy of Higher Education, Academic City, Dubai, United Arab Emirates
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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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Wang S, Lu H, Zhao C, Juneau P. A Systematic Approach To Promote Environmental Engineering Students' Learning in Environmental Molecular Microbiology. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:jmbe-22-11. [PMID: 33884048 PMCID: PMC7976779 DOI: 10.1128/jmbe.v22i1.1917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Environmental Molecular Microbiology (EMM) is a core course cluster for students majoring in environmental engineering. To help students learn the EMM courses, we developed a three-stage teaching approach to deliver EMM courses in a systematic manner: prerequisite course and survey studies; course cluster teaching; and feedback and improvement.
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Affiliation(s)
- Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China 510275
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China 510275
| | - Chunmei Zhao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China 510275
| | - Philippe Juneau
- Department of Biological Sciences, GRIL-TOXEN, University of Quebec in Montreal, Montreal, Canada H3C 3P8
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41
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Sharma P, Tripathi S, Chandra R. Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater. BIORESOURCE TECHNOLOGY 2021; 324:124681. [PMID: 33454444 DOI: 10.1016/j.biortech.2021.124681] [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: 12/03/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India
| | - Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India.
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Coelho JJ, Prieto ML, Hennessy A, Casey I, Woodcock T, Kennedy N. Determination of microbial numbers in anaerobically digested biofertilisers. ENVIRONMENTAL TECHNOLOGY 2021; 42:753-763. [PMID: 31314692 DOI: 10.1080/09593330.2019.1645214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
This study aimed to quantity total numbers of bacteria, fungi and archaea in different types of commercial liquid anaerobic digestates, and to identify common patterns in their microbial numbers post-digestion and possible implications of their use as biofertiliser. Relationships between microbial numbers and physical-chemical traits of the digestates were also investigated. Quantification was performed using culturable and molecular (quantitative PCR) approaches. Bacterial and fungal CFUs ranged up to five orders of magnitude (105-1010; 0-105 g-1 DW, respectively) between different types of anaerobic digestates. Bacterial, archaeal and fungal gene copy numbers (GCN) varied by two orders of magnitude (108-1010; 107-109; 104-106 g-1 DW, respectively) between digestates. All microbial variables analysed showed significant differences between the different types of anaerobic digestate investigated (p < 0.05). Culturable microbial numbers for fungi (6.43 × 104 CFU g-1 DW) were much lower than for bacteria (2.23 × 109 CFU g-1 DW). Gene copy numbers were highest for bacteria (16S) (1.09 × 1010 g-1 DW), followed by archaea (16S) (5.87 × 108 g-1 DW), and fungi (18S) (1.77 × 106 g-1 DW). Liquid anaerobic digestates were predominantly dominated by bacteria, followed by archaeal and fungal populations. At 50% similarity level, the microbial profiles of the eleven anaerobic digestates tested separated into just two groups, indicating a broad relative degree of similarity in terms of microbial numbers. Higher bacterial (16S) GCN was associated with low OM and C/N ratio in digestates.
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Affiliation(s)
- Janerson Jose Coelho
- Eco-Innovation Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Maria Luz Prieto
- Eco-Innovation Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Aoife Hennessy
- Eco-Innovation Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Imelda Casey
- Eco-Innovation Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Tony Woodcock
- Eco-Innovation Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Nabla Kennedy
- Eco-Innovation Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
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Liang Z, Xu G, Shi J, Yu S, Lu Q, Liang D, Sun L, Wang S. Sludge digestibility and functionally active microorganisms in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking. ENVIRONMENTAL RESEARCH 2021; 193:110539. [PMID: 33253703 DOI: 10.1016/j.envres.2020.110539] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/19/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Methanogenic sludge digestion plays a pivotal role in attenuating and hygienizing the massively-produced waste activated sludge (WAS), which is predominantly composed of microbial cells and extracellular polymeric substances (EPS). The efficient sludge digestion requires a variety of functionally active microorganisms working together closely to convert sludge organic matter into biogas. Nonetheless, the digestion efficiency (or digestibility quantified as carbon removal efficiency) of major sludge constituents (i.e., microbial cells and EPS) and associated functionally active microorganisms in sludge digesters remain elusive. In this study, we identified the digestibility of sludge microbial cells and the associated functionally active microorganisms by using Escherichia coli (E. coli)-fed digestion and microbial source tracking. The average carbon removals in four digesters fed with fresh WAS (WAS-AD), thermal pretreated WAS (Thermal-WAS-AD), E. coli cells (E.coli-AD) and thermal pretreated E. coli cells (Thermal-E.coli-AD) were 30.6 ± 3.4%, 45.8 ± 2.9%, 69.0 ± 3.4% and 68.9 ± 4.6%, respectively. Compared to WAS-AD and Thermal-WAS-AD, the significantly higher carbon removals in E. coli-AD and Thermal-E. coli-AD suggested the remarkably higher digestibility of microbial cells than EPS, and releasing organic matter from EPS might be a rate-limiting step in sludge digestion. Functionally active microorganisms for microbial cell digestion predominantly included fermenters (e.g., Petrimonas and Lentimicrobium), syntrophic acetogens (e.g., Synergistaceae) and methanogens (e.g., Methanosaeta and Methanosarcina). Microbial source tracking estimation showed that the microbial cell-digesting populations accounted for 35.6 ± 9.1% and 70.3 ± 10.1% of total microbial communities in the WAS-AD and Thermal-WAS-AD, respectively. Accordingly, the functionally active microorganisms for digestion of both microbial cells and EPS accounted for 64.5 ± 12.1% and 97.3 ± 2.0% of total digestion sludge microbiome in WAS-AD and Thermal-WAS-AD, respectively. By contrast, feeding WAS-derived microorganisms accounted for 23.2 ± 4.4% and 2.3 ± 1.2% of total microbial communities in the WAS-AD and Thermal-WAS-AD, respectively.
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Affiliation(s)
- 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
| | - Guofang Xu
- 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
| | - Jiangjian Shi
- 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
| | - Sining Yu
- 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
| | - 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
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Space & Environment, Beihang University, Beijing, 100191, 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
| | - 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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Tingley JP, Low KE, Xing X, Abbott DW. Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:16. [PMID: 33422151 PMCID: PMC7797155 DOI: 10.1186/s13068-020-01869-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/24/2020] [Indexed: 05/08/2023]
Abstract
The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common "-omics"-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.
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Affiliation(s)
- Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
- Department of Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 6T5, Canada
| | - Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
- Department of Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 6T5, Canada.
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Peng X, Wilken SE, Lankiewicz TS, Gilmore SP, Brown JL, Henske JK, Swift CL, Salamov A, Barry K, Grigoriev IV, Theodorou MK, Valentine DL, O’Malley MA. Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. Nat Microbiol 2021; 6:499-511. [PMID: 33526884 PMCID: PMC8007473 DOI: 10.1038/s41564-020-00861-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.
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Affiliation(s)
- Xuefeng Peng
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.133342.40000 0004 1936 9676Marine Science Institute, University of California, Santa Barbara, CA USA
| | - St. Elmo Wilken
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Thomas S. Lankiewicz
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.184769.50000 0001 2231 4551Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Sean P. Gilmore
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Jennifer L. Brown
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - John K. Henske
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Candice L. Swift
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Asaf Salamov
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Kerrie Barry
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Igor V. Grigoriev
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael K. Theodorou
- grid.417899.a0000 0001 2167 3798Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, UK
| | - David L. Valentine
- grid.133342.40000 0004 1936 9676Department of Earth Science, University of California, Santa Barbara, CA USA
| | - Michelle A. O’Malley
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.184769.50000 0001 2231 4551Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
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Monaco P, Divino F, Naclerio G, Bucci A. Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01604-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Purpose
Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).
Methods
Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.
Result
The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.
Conclusion
The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.
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Lim EY, Tian H, Chen Y, Ni K, Zhang J, Tong YW. Methanogenic pathway and microbial succession during start-up and stabilization of thermophilic food waste anaerobic digestion with biochar. BIORESOURCE TECHNOLOGY 2020; 314:123751. [PMID: 32619808 DOI: 10.1016/j.biortech.2020.123751] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 05/22/2023]
Abstract
One of the major obstacles for thermophilic anaerobic digestion is the process instability during start-up. This study proposed the use of a cost-effective additive, biochar, to accelerate and stabilize the start-up of thermophilic semi-continuous food waste anaerobic digestion. The results showed that the reactors with biochar addition resulted in up to 18% higher methane yield as compared to the control reactors (without biochar). The key microbial networks were elucidated through thermochemical and microbial analysis. Particularly, the addition of biochar promoted the growth of electroactive Clostridia and other electroactive bacteria, while the absence of biochar promoted the growth of homoacetogenic Clostridia and syntrophic acetate oxidizing bacteria. It was revealed that biochar promoted direct interspecies electron transfer between the microbes and was responsible for the faster degradation of volatile fatty acids. Furthermore, reactors with biochar also enhanced the thermodynamically favourable acetoclastic methanogenic pathway due to the higher abundance of Methanosarcina.
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Affiliation(s)
- Ee Yang Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, S117576 Singapore, Singapore
| | - Hailin Tian
- NUS Environment Research Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Yangyang Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Kewei Ni
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Jingxin Zhang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China
| | - Yen Wah Tong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, S117576 Singapore, Singapore; NUS Environment Research Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore.
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Assessment of Multiple Anaerobic Co-Digestions and Related Microbial Community of Molasses with Rice-Alcohol Wastewater. ENERGIES 2020. [DOI: 10.3390/en13184866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molasses is a highly dense and refined byproduct produced in the sugarcane industry, and it contains high amounts of degradable compounds. Through bioconversion, these compounds can be transformed into renewable products. However, the involved biological process is negatively influenced by the high chemical oxygen demand (COD) of molasses and ion concentration. The co-digestion of molasses with rice-alcohol wastewater (RAW) was compared with its mono-digestion at an increasing organic loading rate (OLR). Both processes were assessed by detecting the COD removal rate, the methane contents of biogas, and the structure and composition of microbial communities at different stages. Results showed that the co-digestion is stable up to a maximum OLR of 16 g COD L−1 d−1, whereas after the acclimatization phase, the mono-digestion process was disturbed two times, which occurred at a maximum OLR of 9 and 10 g COD L−1 d−1. The volatile fatty acids (VFAs) observed were 2059.66 mg/L and 1896.9 mg/L, which in mono-digestion causes the inhibition at maximum OLRs. In the co-digestion process, the concomitant COD removal rates and methane content recorded was 90.72 ± 0.63% 64.47% ± 0.59% correspondingly. While in the mono-digestion process, high COD removal rate and methane contents observed were 89.29 ± 0.094% and 61.37 ± 1.06% respectively. From the analysis of microbial communities, it has been observed that both the bacterial and archaeal communities respond differently at unlike stages. However, in both processes, Propionibacteriaceae was the most abundant family in the bacterial communities, whereas Methanosaetaceae was abundant in the archaeal communities. From the current study, it has been concluded that that rice-alcohol wastewater could be a good co-substrate for the anaerobic digestion of molasses in terms of COD removal rate and methane contents production, that could integrate molasses into progressive biogas production with high OLR.
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Suleiman M, Krüger A, Antranikian G. Biomass-degrading glycoside hydrolases of archaeal origin. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:153. [PMID: 32905355 PMCID: PMC7469102 DOI: 10.1186/s13068-020-01792-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.
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Affiliation(s)
- Marcel Suleiman
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anna Krüger
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
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