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Shi K, Liang B, Cheng HY, Wang HC, Liu WZ, Li ZL, Han JL, Gao SH, Wang AJ. Regulating microbial redox reactions towards enhanced removal of refractory organic nitrogen from wastewater. WATER RESEARCH 2024; 258:121778. [PMID: 38795549 DOI: 10.1016/j.watres.2024.121778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024]
Abstract
Biotechnology for wastewater treatment is mainstream and effective depending upon microbial redox reactions to eliminate diverse contaminants and ensure aquatic ecological health. However, refractory organic nitrogen compounds (RONCs, e.g., nitro-, azo-, amide-, and N-heterocyclic compounds) with complex structures and high toxicity inhibit microbial metabolic activity and limit the transformation of organic nitrogen to inorganic nitrogen. This will eventually result in non-compliance with nitrogen discharge standards. Numerous efforts suggested that applying exogenous electron donors or acceptors, such as solid electrodes (electrostimulation) and limited oxygen (micro-aeration), could potentially regulate microbial redox reactions and catabolic pathways, and facilitate the biotransformation of RONCs. This review provides comprehensive insights into the microbial regulation mechanisms and applications of electrostimulation and micro-aeration strategies to accelerate the biotransformation of RONCs to organic amine (amination) and inorganic ammonia (ammonification), respectively. Furthermore, a promising approach involving in-situ hybrid anaerobic biological units, coupled with electrostimulation and micro-aeration, is proposed towards engineering applications. Finally, employing cutting-edge methods including multi-omics analysis, data science driven machine learning, technology-economic analysis, and life-cycle assessment would contribute to optimizing the process design and engineering implementation. This review offers a fundamental understanding and inspiration for novel research in the enhanced biotechnology towards RONCs elimination.
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Affiliation(s)
- Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
| | - Hao-Yi Cheng
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Hong-Cheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Wen-Zong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jing-Long Han
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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2
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Zhang X, Wang Y, Jiao P, Zhang M, Deng Y, Jiang C, Liu XW, Lou L, Li Y, Zhang XX, Ma L. Microbiome-functionality in anaerobic digesters: A critical review. WATER RESEARCH 2024; 249:120891. [PMID: 38016221 DOI: 10.1016/j.watres.2023.120891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023]
Abstract
Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.
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Affiliation(s)
- Xingxing Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yiwei Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Pengbo Jiao
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ming Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xian-Wei Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Liping Ma
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai 200062, PR China.
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3
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Wang M, Chen X, Fang Y, Zheng X, Huang T, Nie Y, Wu XL. The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities. Cell Syst 2024; 15:63-74.e5. [PMID: 38237552 DOI: 10.1016/j.cels.2023.12.004] [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: 05/25/2023] [Revised: 09/17/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
In microbial systems, a metabolic pathway can be either completed by one autonomous population or distributed among a consortium performing metabolic division of labor (MDOL). MDOL facilitates the system's function by reducing the metabolic burden; however, it may hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the function of a community is influenced by the trade-offs between the metabolic specialization and versatility of individuals. To experimentally test this hypothesis, we deconstructed the naphthalene degradation pathway into four steps and introduced them individually or combinatorically into different strains with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia and found that 74 consortia exhibited higher degradation function than both the autonomous population and rigorous MDOL consortium. Quantitative modeling provides general strategies for identifying the most effective MDOL configuration. Our study provides critical insights into the engineering of high-performance microbial systems.
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Affiliation(s)
- Miaoxiao Wang
- College of Engineering, Peking University, Beijing 100871, China; Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Dübendorf 8600, Switzerland
| | - Xiaoli Chen
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China
| | - Yuan Fang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Xin Zheng
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Ting Huang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China; Institute of Ecology, Peking University, Beijing 100871, China.
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4
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Ulčar B, Regueira A, Podojsteršek M, Boon N, Ganigué R. Why do lactic acid bacteria thrive in chain elongation microbiomes? Front Bioeng Biotechnol 2024; 11:1291007. [PMID: 38274012 PMCID: PMC10809155 DOI: 10.3389/fbioe.2023.1291007] [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: 09/08/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024] Open
Abstract
Efficient waste management is necessary to transition towards a more sustainable society. An emerging trend is to use mixed culture biotechnology to produce chemicals from organic waste. Insights into the metabolic interactions between community members and their growth characterization are needed to mediate knowledge-driven bioprocess development and optimization. Here, a granular sludge bioprocess for the production of caproic acid through sugar-based chain elongation metabolism was established. Lactic acid and chain-elongating bacteria were identified as the two main functional guilds in the granular community. The growth features of the main community representatives (isolate Limosilactobacillus musocae G03 for lactic acid bacteria and type strain Caproiciproducens lactatifermentans for chain-elongating bacteria) were characterized. The measured growth rates of lactic acid bacteria (0.051 ± 0.005 h-1) were two times higher than those of chain-elongating bacteria (0.026 ± 0.004 h-1), while the biomass yields of lactic acid bacteria (0.120 ± 0.005 g biomass/g glucose) were two times lower than that of chain-elongating bacteria (0.239 ± 0.007 g biomass/g glucose). This points towards differential growth strategies, with lactic acid bacteria resembling that of a r-strategist and chain-elongating bacteria resembling that of a K-strategist. Furthermore, the half-saturation constant of glucose for L. mucosae was determined to be 0.35 ± 0.05 g/L of glucose. A linear trend of caproic acid inhibition on the growth of L. mucosae was observed, and the growth inhibitory caproic acid concentration was predicted to be 13.6 ± 0.5 g/L, which is the highest reported so far. The pre-adjustment of L. mucosae to 4 g/L of caproic acid did not improve the overall resistance to it, but did restore the growth rates at low caproic acid concentrations (1-4 g/L) to the baseline values (i.e., growth rate at 0 g/L of caproic acid). High resistance to caproic acid enables lactic acid bacteria to persist and thrive in the systems intended for caproic acid production. Here, insights into the growth of two main functional guilds of sugar-based chain elongation systems are provided which allows for a better understanding of their interactions and promotes future bioprocess design and optimization.
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Affiliation(s)
- Barbara Ulčar
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Gent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Gent, Belgium
| | - Alberte Regueira
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Gent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Gent, Belgium
- Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maja Podojsteršek
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Gent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Gent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Gent, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Gent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Gent, Belgium
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5
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Seto M, Kondoh M. Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity. Ecol Lett 2023; 26:1714-1725. [PMID: 37458207 DOI: 10.1111/ele.14287] [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: 01/30/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 10/19/2023]
Abstract
Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.
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Affiliation(s)
- Mayumi Seto
- Department of Chemistry, Biology, and Environmental Sciences, Nara Women's University, Nara, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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6
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George AB, Wang T, Maslov S. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. THE ISME JOURNAL 2023; 17:1482-1494. [PMID: 37380829 PMCID: PMC10432562 DOI: 10.1038/s41396-023-01455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
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Affiliation(s)
- Ashish B George
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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7
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Martinez-Rabert E, Sloan WT, Gonzalez-Cabaleiro R. Multiscale models driving hypothesis and theory-based research in microbial ecology. Interface Focus 2023; 13:20230008. [PMID: 37303746 PMCID: PMC10251115 DOI: 10.1098/rsfs.2023.0008] [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: 02/13/2023] [Accepted: 03/17/2023] [Indexed: 06/13/2023] Open
Abstract
Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach (piecing together sub-systems to give rise to more complex systems) can be used as a framework to generate mechanistic hypotheses and theories (in-silico bottom-up methodology). To accomplish this, formal comprehension of the mathematical model design is required together with a systematic procedure for the application of the in-silico bottom-up methodology. Ruling out the belief that experimentation before modelling is indispensable, we propose that mathematical modelling can be used as a tool to direct experimentation by validating theoretical principles of microbial ecology. Our goal is to develop methodologies that effectively integrate experimentation and modelling efforts to achieve superior levels of predictive capacity.
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Affiliation(s)
- Eloi Martinez-Rabert
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Advanced Research Centre, Glasgow, UK
| | - William T. Sloan
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Advanced Research Centre, Glasgow, UK
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8
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Turner CB, Blount ZD, Mitchell DH, Lenski RE. Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001390. [PMID: 37650867 PMCID: PMC10482366 DOI: 10.1099/mic.0.001390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
The evolution of a novel trait can profoundly change an organism's effects on its environment, which can in turn affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following the evolution of a novel function in the Long-Term Evolution Experiment (LTEE) with Escherichia coli. A characteristic feature of E. coli is its inability to grow aerobically on citrate (Cit-). Nonetheless, a Cit+ variant with this capacity evolved in one LTEE population after 31 000 generations. The Cit+ clade then coexisted stably with another clade that retained the ancestral Cit- phenotype. This coexistence was shaped by the evolution of a cross-feeding relationship based on C4-dicarboxylic acids, particularly succinate, fumarate, and malate, that the Cit+ variants release into the medium. Both the Cit- and Cit+ cells evolved to grow on these excreted resources. The evolution of aerobic growth on citrate thus led to a transition from an ecosystem based on a single limiting resource, glucose, to one with at least five resources that were either shared or partitioned between the two coexisting clades. Our findings show that evolutionary novelties can change environmental conditions in ways that facilitate diversity by altering ecosystem structure and the evolutionary trajectories of coexisting lineages.
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Affiliation(s)
- Caroline B. Turner
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
- Present address: Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Zachary D. Blount
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Daniel H. Mitchell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Present address: Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Richard E. Lenski
- Department of Microbiology and Molecular Genetics; and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
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9
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Sakarika M, Regueira A, Rabaey K, Ganigué R. Thermophilic caproic acid production from grass juice by sugar-based chain elongation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160501. [PMID: 36436634 DOI: 10.1016/j.scitotenv.2022.160501] [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: 09/27/2022] [Revised: 11/04/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Medium chain carboxylic acids (MCCA) such as caproic acid have a plethora of applications, ranging from food additives to bioplastics. MCCA can be produced via microbial chain elongation using waste and side-streams as substrates, a process that can be more sustainable than conventional production routes. Most chain elongation studies have focused on mesophilic conditions, with only two recent studies hinting at the possibility of thermophilic chain elongation, but a systematic study of its mechanisms is lacking. Here, we investigated thermophilic chain elongation from grass juice, to understand the effect of key operational parameters (pH, temperature, substrate) on the process performance and to establish the key microbial genera and their role in the system. The genus Caproiciproducens was identified as responsible for thermophilic chain elongation, and caproic acid production was most favorable at pH 6.0 and 50 °C among the conditions tested, reaching an average concentration of 3.4 g/L. Batch experiments showed that the substrate for caproic acid production were glucose and xylose, while lactic acid led to the production of only butyric acid. Fed-batch experiments showed that substrate availability and the presence of caproic acid in the system play a major role in shaping the profile of thermophilic chain elongation. The increase of the total sugar concentration by glucose addition (without changing the organic load) during continuous operation led to a microbial community dominated (75 %) by Caproiciproducens and increased by 76 % the final average caproic acid concentration to 6.0 g/L (13 gCOD/L) which represented 32 % (g/g) of the total carboxylic acids. The highest concentration achieved was 7.2 g/L (day 197) which is the highest concentration reported under thermophilic conditions thus far. The results of this work pave the way to the potential development of thermophilic systems for upgrading various underexplored abundant and cheap sugar-rich side-streams to caproic acid.
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Affiliation(s)
- Myrsini Sakarika
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat, 9052 Ghent, Belgium
| | - Alberte Regueira
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat, 9052 Ghent, Belgium; Cross-disciplinary Research in Environmental Technologies (CRETUS), Department of Chemical Engineering, Universidade de Santiago de Compostela, Spain
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat, 9052 Ghent, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat, 9052 Ghent, Belgium.
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10
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Hu H, Wang M, Huang Y, Xu Z, Xu P, Nie Y, Tang H. Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. MLIFE 2022; 1:382-398. [PMID: 38818482 PMCID: PMC10989833 DOI: 10.1002/mlf2.12043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/01/2024]
Abstract
Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.
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Affiliation(s)
- Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Miaoxiao Wang
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyETH ZürichEawagSwitzerland
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoyong Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yong Nie
- College of EngineeringPeking UniversityBeijingChina
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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11
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Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor. Cell Rep 2022; 40:111410. [PMID: 36170826 DOI: 10.1016/j.celrep.2022.111410] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/10/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.
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12
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Yin Q, Sun Y, Li B, Feng Z, Wu G. The r/K selection theory and its application in biological wastewater treatment processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153836. [PMID: 35176382 DOI: 10.1016/j.scitotenv.2022.153836] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/23/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Understanding the characteristics of functional organisms is the key to managing and updating biological processes for wastewater treatment. This review, for the first time, systematically characterized two typical types of strategists in wastewater treatment ecosystems via the r/K selection theory and provided novel strategies for selectively enriching microbial community. Functional organisms involved in nitrification (e.g., Nitrosomonas and Nitrosococcus), anammox (Candidatus Brocadia), and methanogenesis (Methanosarcinaceae) are identified as r-strategists with fast growth capacities and low substrate affinities. These r-strategists can achieve high pollutant removal loading rates. On the other hand, other organisms such as Nitrosospira spp., Candidatus Kuenenia, and Methanosaetaceae, are characterized as K-strategists with slow growth rates but high substrate affinities, which can decrease the pollutant concentration to low levels. More importantly, K-strategists may play crucial roles in the biodegradation of recalcitrant organic pollutants. The food-to-microorganism ratio, mass transfer, cell size, and biomass morphology are the key factors determining the selection of r-/K-strategists. These factors can be related with operating parameters (e.g., solids and hydraulic retention time), biomass morphology (biofilm or granules), and operating modes (continuous-flow or sequencing batch), etc., to achieve the efficient acclimation of targeted r-/K-strategists. For practical applications, the concept of substrate flux was put forward to further benefit the selective enrichment of r-/K-strategists, fulfilling effective management and improvement of engineered pollution control bioprocesses. Finally, the future perspectives regarding the development of the r/K selection theory in wastewater treatment processes were discussed.
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Affiliation(s)
- Qidong Yin
- College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland; Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Yuepeng Sun
- Department of Civil and Environmental Engineering, Virginia Tech, Ashburn, VA 20147, United States
| | - Bo Li
- Department of Civil & Environmental Engineering, University of Washington, Seattle, WA 98105, United States
| | - Zhaolu Feng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Guangxue Wu
- College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland.
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13
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Wang M, Chen X, Tang Y, Nie Y, Wu X. Substrate availability and toxicity shape the structure of microbial communities engaged in metabolic division of labor. MLIFE 2022; 1:131-145. [PMID: 38817679 PMCID: PMC10989799 DOI: 10.1002/mlf2.12025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 06/01/2024]
Abstract
Metabolic division of labor (MDOL) represents a widespread natural phenomenon, whereby a complex metabolic pathway is shared between different strains within a community in a mutually beneficial manner. However, little is known about how the composition of such a microbial community is regulated. We hypothesized that when degradation of an organic compound is carried out via MDOL, the concentration and toxicity of the substrate modulate the benefit allocation between the two microbial populations, thus affecting the structure of this community. We tested this hypothesis by combining modeling with experiments using a synthetic consortium. Our modeling analysis suggests that the proportion of the population executing the first metabolic step can be simply estimated by Monod-like formulas governed by substrate concentration and toxicity. Our model and the proposed formula were able to quantitatively predict the structure of our synthetic consortium. Further analysis demonstrates that our rule is also applicable in estimating community structures in spatially structured environments. Together, our work clearly demonstrates that the structure of MDOL communities can be quantitatively predicted using available information on environmental factors, thus providing novel insights into how to manage artificial microbial systems for the wide application of the bioindustry.
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Affiliation(s)
- Miaoxiao Wang
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyEawagDübendorfSwitzerland
- Department of Environmental Science and Engineering, College of Architecture and EnvironmentSichuan UniversityChengduChina
| | - Xiaoli Chen
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
- Institute of Ocean ResearchPeking UniversityBeijingChina
| | - Yue‐Qin Tang
- Department of Environmental Science and Engineering, College of Architecture and EnvironmentSichuan UniversityChengduChina
| | - Yong Nie
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
| | - Xiao‐Lei Wu
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
- Institute of Ocean ResearchPeking UniversityBeijingChina
- Institute of EcologyPeking UniversityBeijingChina
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14
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Lopez JG, Wingreen NS. Noisy metabolism can promote microbial cross-feeding. eLife 2022; 11:70694. [PMID: 35380535 PMCID: PMC8983042 DOI: 10.7554/elife.70694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Cross-feeding, the exchange of nutrients between organisms, is ubiquitous in microbial communities. Despite its importance in natural and engineered microbial systems, our understanding of how inter-species cross-feeding arises is incomplete, with existing theories limited to specific scenarios. Here, we introduce a novel theory for the emergence of such cross-feeding, which we term noise-averaging cooperation (NAC). NAC is based on the idea that, due to their small size, bacteria are prone to noisy regulation of metabolism which limits their growth rate. To compensate, related bacteria can share metabolites with each other to ‘average out’ noise and improve their collective growth. According to the Black Queen Hypothesis, this metabolite sharing among kin, a form of ‘leakage’, then allows for the evolution of metabolic interdependencies among species including de novo speciation via gene deletions. We first characterize NAC in a simple ecological model of cell metabolism, showing that metabolite leakage can in principle substantially increase growth rate in a community context. Next, we develop a generalized framework for estimating the potential benefits of NAC among real bacteria. Using single-cell protein abundance data, we predict that bacteria suffer from substantial noise-driven growth inefficiencies, and may therefore benefit from NAC. We then discuss potential evolutionary pathways for the emergence of NAC. Finally, we review existing evidence for NAC and outline potential experimental approaches to detect NAC in microbial communities.
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Affiliation(s)
- Jaime G Lopez
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States
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15
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Bekiaris PS, Klamt S. Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PLoS Comput Biol 2021; 17:e1009093. [PMID: 34129600 PMCID: PMC8232427 DOI: 10.1371/journal.pcbi.1009093] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/25/2021] [Accepted: 05/18/2021] [Indexed: 01/01/2023] Open
Abstract
Microbial communities have become a major research focus due to their importance for biogeochemical cycles, biomedicine and biotechnological applications. While some biotechnological applications, such as anaerobic digestion, make use of naturally arising microbial communities, the rational design of microbial consortia for bio-based production processes has recently gained much interest. One class of synthetic microbial consortia is based on specifically designed strains of one species. A common design principle for these consortia is based on division of labor, where the entire production pathway is divided between the different strains to reduce the metabolic burden caused by product synthesis. We first show that classical division of labor does not automatically reduce the metabolic burden when metabolic flux per biomass is analyzed. We then present ASTHERISC (Algorithmic Search of THERmodynamic advantages in Single-species Communities), a new computational approach for designing multi-strain communities of a single-species with the aim to divide a production pathway between different strains such that the thermodynamic driving force for product synthesis is maximized. ASTHERISC exploits the fact that compartmentalization of segments of a product pathway in different strains can circumvent thermodynamic bottlenecks arising when operation of one reaction requires a metabolite with high and operation of another reaction the same metabolite with low concentration. We implemented the ASTHERISC algorithm in a dedicated program package and applied it on E. coli core and genome-scale models with different settings, for example, regarding number of strains or demanded product yield. These calculations showed that, for each scenario, many target metabolites (products) exist where a multi-strain community can provide a thermodynamic advantage compared to a single strain solution. In some cases, a production with sufficiently high yield is thermodynamically only feasible with a community. In summary, the developed ASTHERISC approach provides a promising new principle for designing microbial communities for the bio-based production of chemicals. Communities of microbes are ubiquitous in nature and also of high relevance for industrial applications, e.g. for the production of biogas. The development and use of non-natural communities for biotechnological applications has become an important subject of research. In this work, we present a new computational method to design synthetic communities with improved capabilities for the synthesis of desired target metabolites. Our method takes a constraint-based metabolic model of an organism as input and searches for a suitable partitioning of the product pathway via different strains of the organism such that the thermodynamic driving force for product synthesis is maximized. Essentially, this approach exploits the fact that having multiple strains allows adjustment of different metabolite concentrations in the different strains by which the thermodynamic driving force for product synthesis can often be increased. We tested this approach with a core and with a genome-scale metabolic network model of Escherichia coli. We found that, for dozens of metabolites, there exist communities with specifically designed strains of E. coli where the maximal thermodynamic driving force can be increased compared to a single E. coli strain. In summary, our presented method provides a new approach, together with a new design principle, for the computational design of microbial communities.
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Affiliation(s)
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- * E-mail:
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16
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Kleerebezem R, Lücker S. Cyclic Conversions in the Nitrogen Cycle. Front Microbiol 2021; 12:622504. [PMID: 33859625 PMCID: PMC8043111 DOI: 10.3389/fmicb.2021.622504] [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: 10/28/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
The cyclic nature of specific conversions in the nitrogen cycle imposes strict limitations to the conversions observed in nature and explains for example why anaerobic ammonium oxidation (anammox) bacteria can only use nitrite – and not nitrate – as electron acceptor in catabolism, and why nitrite is required as additional electron donor for inorganic carbon fixation in anabolism. Furthermore, the biochemistry involved in nitrite-dependent anaerobic methane oxidation excludes the feasibility of using nitrate as electron acceptor. Based on the cyclic nature of these nitrogen conversions, we propose two scenarios that may explain the ecological role of recently discovered complete ammonia-oxidizing (comammox) Nitrospira spp., some of which were initially found in a strongly oxygen limited environment: (i) comammox Nitrospira spp. may actually catalyze an anammox-like metabolism using a biochemistry similar to intra-oxic nitrite-dependent methane oxidation, or (ii) scavenge all available oxygen for ammonia activation and use nitrate as terminal electron acceptor. Both scenarios require the presence of the biochemical machinery for ammonia oxidation to nitrate, potentially explaining a specific ecological niche for the occurrence of comammox bacteria in nature.
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Affiliation(s)
- Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
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17
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Regueira A, Lema JM, Mauricio-Iglesias M. Microbial inefficient substrate use through the perspective of resource allocation models. Curr Opin Biotechnol 2021; 67:130-140. [PMID: 33540363 DOI: 10.1016/j.copbio.2021.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/15/2023]
Abstract
Microorganisms extract energy from substrates following strategies that may seem suboptimal at first glance. Beyond the so-called yield-rate trade-off, resource allocation models, which focus on assigning different functional roles to the limited number of enzymes that a cell can support, offer a framework to interpret the inefficient substrate use by microorganisms. We review here relevant examples of substrate conversions where a significant part of the available energy is not utilised and how resource allocation models offer a mechanistic interpretation thereof, notably for open mixed cultures. Future developments are identified, in particular, the challenge of considering metabolic flexibility towards uncertain environmental changes instead of strict fixed optimality objectives, with the final goal of increasing the prediction capabilities of resource allocation models. Finally, we highlight the relevance of resource allocation to understand and enable a promising biorefinery platform revolving around lactate, which would increase the flexibility of waste-to-chemical biorefinery schemes.
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Affiliation(s)
- Alberte Regueira
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Juan M Lema
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel Mauricio-Iglesias
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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18
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González-Cabaleiro R, Martinez-Rabert E, Argiz L, van Kessel MA, Smith CJ. A framework based on fundamental biochemical principles to engineer microbial community dynamics. Curr Opin Biotechnol 2021; 67:111-118. [PMID: 33540361 DOI: 10.1016/j.copbio.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
Microbial communities are complex but there are basic principles we can apply to constrain the assumed stochasticity of their activity. By understanding the trade-offs behind the kinetic parameters that define microbial growth, we can explain how local interspecies dependencies arise and shape the emerging properties of a community. If we integrate these theoretical descriptions with experimental 'omics' data and bioenergetics analysis of specific environmental conditions, predictions on activity, assembly and spatial structure can be obtained reducing the a priori unpredictable complexity of microbial communities. This information can be used to define the appropriate selective pressures to engineer bioprocesses and propose new hypotheses which can drive experimental research to accelerate innovation in biotechnology.
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Affiliation(s)
- Rebeca González-Cabaleiro
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK.
| | - Eloi Martinez-Rabert
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
| | - Lucia Argiz
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - Maartje Ahj van Kessel
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Cindy J Smith
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
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19
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Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
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Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
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20
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Regueira A, Rombouts JL, Wahl SA, Mauricio-Iglesias M, Lema JM, Kleerebezem R. Resource allocation explains lactic acid production in mixed-culture anaerobic fermentations. Biotechnol Bioeng 2020; 118:745-758. [PMID: 33073364 DOI: 10.1002/bit.27605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/28/2020] [Accepted: 10/11/2020] [Indexed: 02/04/2023]
Abstract
Lactate production in anaerobic carbohydrate fermentations with mixed cultures of microorganisms is generally observed only in very specific conditions: the reactor should be run discontinuously and peptides and B vitamins must be present in the culture medium as lactic acid bacteria (LAB) are typically auxotrophic for amino acids. State-of-the-art anaerobic fermentation models assume that microorganisms optimise the adenosine triphosphate (ATP) yield on substrate and therefore they do not predict the less ATP efficient lactate production, which limits their application for designing lactate production in mixed-culture fermentations. In this study, a metabolic model taking into account cellular resource allocation and limitation is proposed to predict and analyse under which conditions lactate production from glucose can be beneficial for microorganisms. The model uses a flux balances analysis approach incorporating additional constraints from the resource allocation theory and simulates glucose fermentation in a continuous reactor. This approach predicts lactate production is predicted at high dilution rates, provided that amino acids are in the culture medium. In minimal medium and lower dilution rates, mostly butyrate and no lactate is predicted. Auxotrophy for amino acids of LAB is identified to provide a competitive advantage in rich media because less resources need to be allocated for anabolic machinery and higher specific growth rates can be achieved. The Matlab™ codes required for performing the simulations presented in this study are available at https://doi.org/10.5281/zenodo.4031144.
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Affiliation(s)
- Alberte Regueira
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Julius L Rombouts
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Miguel Mauricio-Iglesias
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan M Lema
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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21
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Gorochowski TE, Hauert S, Kreft JU, Marucci L, Stillman NR, Tang TYD, Bandiera L, Bartoli V, Dixon DOR, Fedorec AJH, Fellermann H, Fletcher AG, Foster T, Giuggioli L, Matyjaszkiewicz A, McCormick S, Montes Olivas S, Naylor J, Rubio Denniss A, Ward D. Toward Engineering Biosystems With Emergent Collective Functions. Front Bioeng Biotechnol 2020; 8:705. [PMID: 32671054 PMCID: PMC7332988 DOI: 10.3389/fbioe.2020.00705] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
Many complex behaviors in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans many length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modeling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modeling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underpinning these behaviors offers a means to take synthetic biology beyond single molecules or cells and toward the creation of systems with functions that can only emerge from collectives at multiple scales.
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Affiliation(s)
| | - Sabine Hauert
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Jan-Ulrich Kreft
- School of Biosciences and Institute of Microbiology and Infection and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Namid R. Stillman
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - T.-Y. Dora Tang
- Max Plank Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Physics of Life, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
| | - Lucia Bandiera
- School of Engineering, University of Edinburgh, Edinburgh, United Kingdom
| | - Vittorio Bartoli
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | | | - Alex J. H. Fedorec
- Division of Biosciences, University College London, London, United Kingdom
| | - Harold Fellermann
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alexander G. Fletcher
- Bateson Centre and School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
| | - Tim Foster
- School of Biosciences and Institute of Microbiology and Infection and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Luca Giuggioli
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | | | - Scott McCormick
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Sandra Montes Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Jonathan Naylor
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ana Rubio Denniss
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Daniel Ward
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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22
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Johnson DR, Noack S. Editorial overview: Causes and biotechnological application of microbial metabolic specialization. Curr Opin Biotechnol 2020; 62:iii-vi. [DOI: 10.1016/j.copbio.2020.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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