1
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Ngo ACR, Celebi B, Hermann Hadewig SN, Mügge C, Tischler D. Selective pressure leads to an improved synthetic consortium fit for dye degradation. CHEMOSPHERE 2024; 361:142489. [PMID: 38825247 DOI: 10.1016/j.chemosphere.2024.142489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Microorganisms have great potential for bioremediation as they have powerful enzymes and machineries that can transform xenobiotics. The use of a microbial consortium provides more advantages in application point of view than pure cultures due to cross-feeding, adaptations, functional redundancies, and positive interactions among the organisms. In this study, we screened about 107 isolates for their ability to degrade dyes in aerobic conditions and without additional carbon source. From our screening results, we finally limited our synthetic consortium to Gordonia and Rhodococcus isolates. The synthetic consortium was trained and optimized for azo dye degradation using sequential treatment of small aromatic compounds such as phenols that act as selective pressure agents. After four rounds of optimization with different aims for each round, the consortium was able to decolorize and degrade various dyes after 48 h (80%-100% for brilliant black bn, methyl orange, and chromotrop 2b; 50-70% for orange II and reactive orange 16; 15-30% for chlorazol black e, reactive red 120, and allura red ac). Through rational approaches, we can show that treatment with phenolic compounds at micromolar dosages can significantly improve the degradation of bulky dyes and increase its substrate scope. Moreover, our selective pressure approach led to the production of various dye-degrading enzymes as azoreductase, laccase-like, and peroxidase-like activities were detected from the phenol-treated consortium. Evidence of degradation was also shown as metabolites arising from the degradation of methyl red and brilliant black bn were detected using HPLC and LC-MS analysis. Therefore, this study establishes the importance of rational and systematic screening and optimization of a consortium. Not only can this approach be applied to dye degradation, but this study also offers insights into how we can fully maximize microbial consortium activity for other applications, especially in biodegradation and biotransformation.
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Affiliation(s)
| | - Beyzanur Celebi
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
| | | | - Carolin Mügge
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
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2
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Guo L, Xi B, Lu L. Strategies to enhance production of metabolites in microbial co-culture systems. BIORESOURCE TECHNOLOGY 2024; 406:131049. [PMID: 38942211 DOI: 10.1016/j.biortech.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.
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Affiliation(s)
- Lichun Guo
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bingwen Xi
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China
| | - Liushen Lu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China.
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3
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Le Bec M, Pouzet S, Cordier C, Barral S, Scolari V, Sorre B, Banderas A, Hersen P. Optogenetic spatial patterning of cooperation in yeast populations. Nat Commun 2024; 15:75. [PMID: 38168087 PMCID: PMC10761962 DOI: 10.1038/s41467-023-44379-5] [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: 05/17/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial communities are shaped by complex metabolic interactions such as cooperation and competition for resources. Methods to control such interactions could lead to major advances in our ability to better engineer microbial consortia for synthetic biology applications. Here, we use optogenetics to control SUC2 invertase production in yeast, thereby shaping spatial assortment of cooperator and cheater cells. Yeast cells behave as cooperators (i.e., transform sucrose into hexose, a public good) upon blue light illumination or cheaters (i.e., consume hexose produced by cooperators to grow) in the dark. We show that cooperators benefit best from the hexoses they produce when their domain size is constrained between two cut-off length-scales. From an engineering point of view, the system behaves as a bandpass filter. The lower limit is the trace of cheaters' competition for hexoses, while the upper limit is defined by cooperators' competition for sucrose. Cooperation mostly occurs at the frontiers with cheater cells, which not only compete for hexoses but also cooperate passively by letting sucrose reach cooperators. We anticipate that this optogenetic method could be applied to shape metabolic interactions in a variety of microbial ecosystems.
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Affiliation(s)
- Matthias Le Bec
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Sylvain Pouzet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Céline Cordier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Simon Barral
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Vittore Scolari
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005, Paris, France
| | - Benoit Sorre
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Alvaro Banderas
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
| | - Pascal Hersen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
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4
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Wu L, Zhao L, Tao Y, Zhang D, He A, Ma X, Zhang H, Li G, Rong L, Li R. Improving the aroma profile of inoculated fermented sausages by constructing a synthetic core microbial community. J Food Sci 2023; 88:4388-4402. [PMID: 37750814 DOI: 10.1111/1750-3841.16764] [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: 05/13/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023]
Abstract
Commercial starter cultures play a critical role in the industrial production of fermented sausages. However, commercial starter cultures could not reproduce the metabolic actions of diverse microorganisms and the aroma profile of the traditional spontaneously fermented sausages. Identifying the core microbial community in spontaneously fermented sausages will facilitate the construction of a synthetic microbial community for reproducing metabolic actions and flavor compounds in spontaneously fermented sausages. This study aimed to reveal the core microbial community of spontaneously fermented sausages based on their relative abundance, flavor-producing ability, and co-occurrence performance. We identified five promising genera to construct the synthetic core microbial community, these were Lactobacillus, Staphylococcus, Macrococcus, Streptococcus, and Pediococcus. Sausages inoculated with a synthetic core microbial community presented higher quality of aroma profile than the fermented sausages inoculated with a commercial starter culture. Some important volatile flavor compounds of spontaneously fermented sausage, such as (-)-β-pinene, β-caryophyllene, 3-methyl-1-butanol, α-terpineol, ethyl 2-methylpropanoate, and ethyl 3-methylbutanoate which are associated with floral, fruity, sweet, and fresh aromas, were also detected in fermented sausage inoculated with synthetic microbial community. This indicated that the synthetic core microbial community efficiently reproduced flavor metabolism. Overall, this study provides a practical strategy to design a synthetic microbial community applicable to different scientific fields.
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Affiliation(s)
- Liu Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
| | - Linyu Zhao
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
| | - Yingmei Tao
- Gansu Polytechnic College of Animal Husbandry & Engineering, Wuwei, Gansu, China
- Sichuan University of Science & Engineering, Yibin, Sichuan, China
| | - Di Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
| | - An He
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
| | | | - Huan Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Liangyan Rong
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
| | - Ruren Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
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5
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Zhang D, Yang P, Liu K, Wu L, Li G, Zhang H, Ma X, Rong L, Li R. The effective of bacterial community dynamics driven by different starter cultures on the flavor development of Chinese fermented sausages. Food Chem X 2023; 19:100838. [PMID: 37780305 PMCID: PMC10534179 DOI: 10.1016/j.fochx.2023.100838] [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: 04/17/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023] Open
Abstract
This study aimed to understand the community successions driven by different starters and their effects on the flavor development of Chinese fermented sausages. The results showed that the bacterial genus (67.6%) and pH (32.4%) were the key factors influencing the volatile profile. Inoculated the starters composed of Pediococcus and staphylococci maintained the stable community succession patterns dominated by staphylococci (samples T and S). Although the highly acidic environment (pH < 5.2) caused the community to exhibit a fluctuation in succession pattern, the inoculation of Latilactobacillus paracasei (sample Y) maintained microbial diversity and was conducive to the accumulation of aldehydes and esters. In sample P, inoculated the starter with Latilactobacillus and Staphylococcus also maintained microbial diversity, the moderately acidic environment (pH > 5.4) resulted in a stable succession pattern of the microbial community, and it was not conducive to the accumulation of aldehydes, alcohols and esters.
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Affiliation(s)
- Di Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Peng Yang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Kaihao Liu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Liu Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
| | - Huan Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
| | - Xiaozhong Ma
- Jinzi Ham Co., Ltd., No. 1000, Jinfan Street, Industrial Park, Jinhua, Zhejiang 321016, China
| | - Liangyan Rong
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
| | - Ruren Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi 710021, China
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6
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Pauli B, Ajmera S, Kost C. Determinants of synergistic cell-cell interactions in bacteria. Biol Chem 2023; 404:521-534. [PMID: 36859766 DOI: 10.1515/hsz-2022-0303] [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: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
Bacteria are ubiquitous and colonize virtually every conceivable habitat on earth. To achieve this, bacteria require different metabolites and biochemical capabilities. Rather than trying to produce all of the needed materials by themselves, bacteria have evolved a range of synergistic interactions, in which they exchange different commodities with other members of their local community. While it is widely acknowledged that synergistic interactions are key to the ecology of both individual bacteria and entire microbial communities, the factors determining their establishment remain poorly understood. Here we provide a comprehensive overview over our current knowledge on the determinants of positive cell-cell interactions among bacteria. Taking a holistic approach, we review the literature on the molecular mechanisms bacteria use to transfer commodities between bacterial cells and discuss to which extent these mechanisms favour or constrain the successful establishment of synergistic cell-cell interactions. In addition, we analyse how these different processes affect the specificity among interaction partners. By drawing together evidence from different disciplines that study the focal question on different levels of organisation, this work not only summarizes the state of the art in this exciting field of research, but also identifies new avenues for future research.
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Affiliation(s)
- Benedikt Pauli
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany
| | - Shiksha Ajmera
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastrasse 11, D-49076 Osnabrück, Germany
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7
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Ulmer A, Veit S, Erdemann F, Freund A, Loesch M, Teleki A, Zeidan AA, Takors R. A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures. BIOENGINEERING (BASEL, SWITZERLAND) 2023; 10:bioengineering10010103. [PMID: 36671675 PMCID: PMC9854596 DOI: 10.3390/bioengineering10010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
To fulfil the growing interest in investigating microbial interactions in co-cultures, a novel two-compartment bioreactor system was developed, characterised, and implemented. The system allowed for the exchange of amino acids and peptides via a polyethersulfone membrane that retained biomass. Further system characterisation revealed a Bodenstein number of 18, which hints at backmixing. Together with other physical settings, the existence of unwanted inner-compartment substrate gradients could be ruled out. Furthermore, the study of Damkoehler numbers indicated that a proper metabolite supply between compartments was enabled. Implementing the two-compartment system (2cs) for growing Streptococcus thermophilus and Lactobacillus delbrueckii subs. bulgaricus, which are microorganisms commonly used in yogurt starter cultures, revealed only a small variance between the one-compartment and two-compartment approaches. The 2cs enabled the quantification of the strain-specific production and consumption rates of amino acids in an interacting S. thermophilus-L. bulgaricus co-culture. Therefore, comparisons between mono- and co-culture performance could be achieved. Both species produce and release amino acids. Only alanine was produced de novo from glucose through potential transaminase activity by L. bulgaricus and consumed by S. thermophilus. Arginine availability in peptides was limited to S. thermophilus' growth, indicating active biosynthesis and dependency on the proteolytic activity of L. bulgaricus. The application of the 2cs not only opens the door for the quantification of exchange fluxes between microbes but also enables continuous production modes, for example, for targeted evolution studies.
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Affiliation(s)
- Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefan Veit
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Florian Erdemann
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Andreas Freund
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maren Loesch
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ahmad A. Zeidan
- Systems Biology, R&D Discovery, Chr. Hansen A/S, 2970 Hørsholm, Denmark
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
- Correspondence:
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8
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Zhang C, Mu Y, Li T, Jin FJ, Jin CZ, Oh HM, Lee HG, Jin L. Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere". Front Microbiol 2023; 14:1181967. [PMID: 37138608 PMCID: PMC10150012 DOI: 10.3389/fmicb.2023.1181967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.
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Affiliation(s)
- Chengxiao Zhang
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yulin Mu
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Taihua Li
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
- Hyung-Gwan Lee,
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Long Jin,
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Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
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Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia,Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,*Correspondence: Matthew Lee,
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10
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Deter HS, Lu T. Engineering microbial consortia with rationally designed cellular interactions. Curr Opin Biotechnol 2022; 76:102730. [PMID: 35609504 PMCID: PMC10129393 DOI: 10.1016/j.copbio.2022.102730] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/22/2022] [Accepted: 04/03/2022] [Indexed: 12/14/2022]
Abstract
Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. We then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.
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Affiliation(s)
- Heather S Deter
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Intelligence Community Postdoctoral Research Fellowship Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; National Center for Supercomputing Applications, Urbana, IL, USA.
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11
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Biofilm cultivation facilitates coexistence and adaptive evolution in an industrial bacterial community. NPJ Biofilms Microbiomes 2022; 8:59. [PMID: 35858930 PMCID: PMC9300721 DOI: 10.1038/s41522-022-00323-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
The majority of ecological, industrial and medical impacts of bacteria result from diverse communities containing multiple species. This diversity presents a significant challenge as co-cultivation of multiple bacterial species frequently leads to species being outcompeted and, with this, the possibility to manipulate, evolve and improve bacterial communities is lost. Ecological theory predicts that a solution to this problem will be to grow species in structured environments, which reduces the likelihood of competitive exclusion. Here, we explored the ability of cultivation in a structured environment to facilitate coexistence, evolution, and adaptation in an industrially important community: Lactococcus lactis and Leuconostoc mesenteroides frequently used as dairy starter cultures. As commonly occurs, passaging of these two species together in a liquid culture model led to the loss of one species in 6 of 20 lineages (30%). By contrast, when we co-cultured the two species as biofilms on beads, a stable coexistence was observed in all lineages studied for over 100 generations. Moreover, we show that the co-culture drove evolution of new high-yield variants, which compared to the ancestor grew more slowly, yielded more cells and had enhanced capability of biofilm formation. Importantly, we also show that these high-yield biofilm strains did not evolve when each species was passaged in monoculture in the biofilm model. Therefore, both co-culture and the biofilm model were conditional for these high-yield strains to evolve. Our study underlines the power of ecological thinking—namely, the importance of structured environments for coexistence—to facilitate cultivation, evolution, and adaptation of industrially important bacterial communities.
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12
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Reprogramming microbial populations using a programmed lysis system to improve chemical production. Nat Commun 2021; 12:6886. [PMID: 34824227 PMCID: PMC8617184 DOI: 10.1038/s41467-021-27226-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
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13
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Yang P, Zhong G, Yang J, Zhao L, Sun D, Tian Y, Li R, Rong L. Metagenomic and metabolomic profiling reveals the correlation between the microbiota and flavor compounds and nutrients in fermented sausages. Food Chem 2021; 375:131645. [PMID: 34838398 DOI: 10.1016/j.foodchem.2021.131645] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 01/15/2023]
Abstract
Understanding the interrelationships between the differentially abundant microorganisms and metabolites of traditional "Fuet" fermented sausages (FSs) and inoculated fermented sausages (IFSs) can help us identify key species that are missing from commercial starter cultures to reproduce the flavor compounds and nutrients of traditional Fuet FSs. IFSs, inoculated with P. pentosaceus, P. acidilactici, S. xylosus, S. carnosus (SBM-52) or P. pentosaceus, and S. xylosus (THM-17), were deficient in reproducing the volatilome profile (in particular esters, methyl aldehydes, and methyl ketones) of traditional Fuet FSs because of the lack of diverse Staphylococci (S. carnosus, S. xylosus, S. equorum, and S. saprophyticus). Moreover, the combination of Pediococcus and Staphylococcus were positively associated with amino acid, fatty acid, l-anserine, and l-carnosine levels. Pyridoxal and indolelactic acid levels were significantly increased in IFSs with the addition of P. acidilactici and S. carnosus, which were positively associated with vitamin B6 and tryptophan metabolic pathways.
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Affiliation(s)
- Peng Yang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China
| | - Guixia Zhong
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China
| | - Juanchun Yang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China
| | - Linyu Zhao
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China
| | - Ding Sun
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China
| | - Yaqin Tian
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China
| | - Ruren Li
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China.
| | - Liangyan Rong
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, 121013, China.
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14
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Noto Guillen M, Rosener B, Sayin S, Mitchell A. Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods. Cell Syst 2021; 12:1064-1078.e7. [PMID: 34469744 PMCID: PMC8602757 DOI: 10.1016/j.cels.2021.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/18/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022]
Abstract
Metabolic cross-feeding frequently underlies mutualistic relationships in natural microbial communities and is often exploited to assemble synthetic microbial consortia. We systematically identified all single-gene knockouts suitable for imposing cross-feeding in Escherichia coli and used this information to assemble syntrophic communities. Most strains benefiting from shared goods were dysfunctional in biosynthesis of amino acids, nucleotides, and vitamins or mutants in central carbon metabolism. We tested cross-feeding potency in 1,444 strain pairs and mapped the interaction network between all functional groups of mutants. This network revealed that auxotrophs for vitamins are optimal cooperators. Lastly, we monitored how assemblies composed of dozens of auxotrophs change over time and observed that they rapidly and repeatedly coalesced to seven strain consortia composed primarily from vitamin auxotrophs. The composition of emerging consortia suggests that they were stabilized by multiple cross-feeding interactions. We conclude that vitamins are ideal shared goods since they optimize consortium growth while still imposing member co-dependence.
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Affiliation(s)
- Mariana Noto Guillen
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Brittany Rosener
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Serkan Sayin
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Amir Mitchell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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15
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Giri S, Oña L, Waschina S, Shitut S, Yousif G, Kaleta C, Kost C. Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria. Curr Biol 2021; 31:5547-5557.e6. [PMID: 34731676 DOI: 10.1016/j.cub.2021.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 09/01/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022]
Abstract
The exchange of metabolites among different bacterial genotypes profoundly impacts the structure and function of microbial communities. However, the factors governing the establishment of these cross-feeding interactions remain poorly understood. While shared physiological features may facilitate interactions among more closely related individuals, a lower relatedness should reduce competition and thus increase the potential for synergistic interactions. Here, we investigate how the relationship between a metabolite donor and recipient affects the propensity of strains to engage in unidirectional cross-feeding interactions. For this, we performed pairwise cocultivation experiments between four auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients grew in the vast majority of pairs tested (63%), suggesting metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient and the dissimilarity of their metabolic networks were positively associated with the growth of auxotrophic recipients. Analyzing the co-growth of species from a gut microbial community in silico also revealed that recipient genotypes benefitted more from interacting with metabolically dissimilar partners, thus corroborating the empirical results. Together, our work identifies the metabolic dissimilarity between bacterial genotypes as a key factor determining the establishment of metabolic cross-feeding interactions in microbial communities.
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Affiliation(s)
- Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Nutriinformatics, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Ghada Yousif
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany; Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
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Abstract
Bioremediation is a sustainable remediation technology as it utilizes microorganisms to convert hazardous compounds into their less toxic or non-toxic constituent elements. This technology has achieved some success in the past decades; however, factors involving microbial consortia, such as microbial assembly, functional interactions, and the role of member species, hinder its development. Microbial consortia may be engineered to reconfigure metabolic pathways and reprogram social interactions to get the desired function, thereby providing solutions to its inherent problems. The engineering of microbial consortia is commonly applied for the commercial production of biomolecules. However, in the field of bioremediation, the engineering of microbial consortia needs to be emphasized. In this review, we will discuss the molecular and ecological mechanisms of engineering microbial consortia with a particular focus on metabolic cross-feeding within species and the transfer of metabolites. We also discuss the advantages and limitations of top-down and bottom-up approaches of engineering microbial consortia and their applications in bioremediation.
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17
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Yamagishi JF, Saito N, Kaneko K. Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem. PLoS Comput Biol 2021; 17:e1009143. [PMID: 34161322 PMCID: PMC8260005 DOI: 10.1371/journal.pcbi.1009143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/06/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023] Open
Abstract
Microbial communities display remarkable diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. Based on theoretical results indicating that cells can enhance their own growth rate by leaking even essential metabolites, we show that such "leaker" cells can establish an asymmetric form of mutualism with "consumer" cells that consume the leaked chemicals: the consumer cells benefit from the uptake of the secreted metabolites, while the leaker cells also benefit from such consumption, as it reduces the metabolite accumulation in the environment and thereby enables further secretion, resulting in frequency-dependent coexistence of multiple microbial species. As supported by extensive simulations, such symbiotic relationships generally evolve when each species has a complex reaction network and adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations. Accordingly, symbiotic ecosystems with diverse cell species that leak and exchange many metabolites with each other are shaped by cell-level adaptation of leakiness of metabolites. Moreover, the resultant ecosystems with entangled metabolite exchange are resilient against structural and environmental perturbations. Thus, we present a theory for the origin of resilient ecosystems with diverse microbes mediated by secretion and exchange of essential chemicals.
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Affiliation(s)
- Jumpei F. Yamagishi
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Nen Saito
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
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18
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Borchert E, Hammerschmidt K, Hentschel U, Deines P. Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology. Trends Microbiol 2021; 29:908-918. [PMID: 33812769 DOI: 10.1016/j.tim.2021.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022]
Abstract
Environmental accumulation of anthropogenic pollutants is a pressing global issue. The biodegradation of these pollutants by microbes is an emerging field but is hampered by inefficient degradation rates and a limited knowledge of potential enzymes and pathways. Here, we advocate the view that significant progress can be achieved by harnessing artificial community selection for a desired biological process, an approach that makes use of eco-evolutionary principles. The selected communities can either be directly used in bioremediation applications or further be analyzed and modified, for instance through a combination of systems biology, synthetic biology, and genetic engineering. This knowledge can then inform machine learning and enhance the discovery of novel biodegradation pathways.
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Affiliation(s)
- Erik Borchert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany; University of Kiel, Kiel, Germany
| | - Peter Deines
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
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19
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Rosero-Chasoy G, Rodríguez-Jasso RM, Aguilar CN, Buitrón G, Chairez I, Ruiz HA. Microbial co-culturing strategies for the production high value compounds, a reliable framework towards sustainable biorefinery implementation - an overview. BIORESOURCE TECHNOLOGY 2021; 321:124458. [PMID: 33338739 DOI: 10.1016/j.biortech.2020.124458] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The microbial co-cultures or consortia are a natural set of microorganisms formed from different species or the same species but different strains, in which members can interact with each other. The co-culture systems have wide variety of technological applications such as the production of foods, treatment of wastewater, removal of toxic substances, environmental recovery, and all these without the need to work in sterile conditions. Therefore, the need of understanding communication mechanisms between cell-to-cell within co-culture will allow to construct and to program their biological behavior from the use of complex substrates to produce biocompounds. The technology of co-culture systems enables the development of biorefinery platforms to obtain biofuels, and high value compounds through biomass transformation by sustainable process. This review focuses on understanding the roles of consortia microbial to design and built co-culture systems to produce high value compounds in terms a sustainable biorefinery.
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Affiliation(s)
- Gilver Rosero-Chasoy
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico
| | - Rosa M Rodríguez-Jasso
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico.
| | - Cristóbal N Aguilar
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico
| | - Germán Buitrón
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Queretaro 76230, Mexico
| | - Isaac Chairez
- Unidad Profesional Interdisciplinaria de Biotecnología, UPIBI, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Héctor A Ruiz
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico.
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21
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Autonomous and Assisted Control for Synthetic Microbiology. Int J Mol Sci 2020; 21:ijms21239223. [PMID: 33287299 PMCID: PMC7731081 DOI: 10.3390/ijms21239223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
The control of microbes and microbial consortia to achieve specific functions requires synthetic circuits that can reliably cope with internal and external perturbations. Circuits that naturally evolved to regulate biological functions are frequently robust to alterations in their parameters. As the complexity of synthetic circuits increases, synthetic biologists need to implement such robust control "by design". This is especially true for intercellular signaling circuits for synthetic consortia, where robustness is highly desirable, but its mechanisms remain unclear. Cybergenetics, the interface between synthetic biology and control theory, offers two approaches to this challenge: external (computer-aided) and internal (autonomous) control. Here, we review natural and synthetic microbial systems with robustness, and outline experimental approaches to implement such robust control in microbial consortia through population-level cybergenetics. We propose that harnessing natural intercellular circuit topologies with robust evolved functions can help to achieve similar robust control in synthetic intercellular circuits. A "hybrid biology" approach, where robust synthetic microbes interact with natural consortia and-additionally-with external computers, could become a useful tool for health and environmental applications.
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22
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Shibasaki S, Mitri S. Controlling evolutionary dynamics to optimize microbial bioremediation. Evol Appl 2020; 13:2460-2471. [PMID: 33005234 PMCID: PMC7513707 DOI: 10.1111/eva.13050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 06/03/2020] [Accepted: 06/22/2020] [Indexed: 12/24/2022] Open
Abstract
Some microbes have a fascinating ability to degrade compounds that are toxic for humans in a process called bioremediation. Although these traits help microbes survive the toxins, carrying them can be costly if the benefit of detoxification is shared by all surrounding microbes, whether they detoxify or not. Detoxification can thereby be seen as a public goods game, where nondegrading mutants can sweep through the population and collapse bioremediation. Here, we constructed an evolutionary game theoretical model to optimize bioremediation in a chemostat initially containing "cooperating" (detoxifying) microbes. We consider two types of mutants: "cheaters" that do not detoxify, and mutants that become resistant to the toxin through private mechanisms that do not benefit others. By manipulating the concentration and flow rate of a toxin into the chemostat, we identified conditions where cooperators can exclude cheaters that differ in their private resistance. However, eventually, cheaters are bound to invade. To overcome this inevitable outcome and maximize detoxification efficiency, cooperators can be periodically reinoculated into the population. Our study investigates the outcome of an evolutionary game combining both public and private goods and demonstrates how environmental parameters can be used to control evolutionary dynamics in practical applications.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Sara Mitri
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
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23
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Baltrus DA. Bacterial dispersal and biogeography as underappreciated influences on phytobiomes. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:37-46. [PMID: 32278259 DOI: 10.1016/j.pbi.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 06/11/2023]
Abstract
Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.
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Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson AZ, USA; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.
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24
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Augelletti F, Jousset A, Agathos SN, Stenuit B. Diversity Manipulation of Psychrophilic Bacterial Consortia for Improved Biological Treatment of Medium-Strength Wastewater at Low Temperature. Front Microbiol 2020; 11:1490. [PMID: 32793129 PMCID: PMC7393979 DOI: 10.3389/fmicb.2020.01490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/08/2020] [Indexed: 11/13/2022] Open
Abstract
Psychrophilic bacteria are valuable biocatalysts to develop robust bioaugmentation formulations for enhanced wastewater treatment at low temperatures or fluctuating temperature conditions. Here, using different biodiversity indices [based on species richness (SR), phylogenetic diversity (PD) and functional diversity (FD)], we studied the effects of microbial diversity of artificial bacterial consortia on the biomass gross yields (measured through OD600) and removal efficiency of soluble chemical oxygen demand (mg sCOD removed/mg sCOD introduced) in synthetic, medium-strength wastewater. We built artificial consortia out of one to six bacterial strains isolated at 4°C through combinatorial biodiversity experiments. Increasing species richness resulted in improved sCOD removal efficiency (i.e., 0.266 ± 0.146, 0.542 ± 0.155, 0.742 ± 0.136, 0.822 ± 0.019 for mono-, tri-, penta-and hexacultures, respectively) and higher biomass gross yields (i.e., 0.065 ± 0.052, 0.132 ± 0.046, 0.173 ± 0.049, 0.216 ± 0.019 for mono-, tri-, penta,- and hexacultures, respectively). This positive relationship between biodiversity, sCOD removal and biomass gross yield was also observed when considering metabolic profiling (functional diversity) or evolutionary relationships (phylogenetic diversity). The positive effect of biodiversity on sCOD removal efficiency could be attributed to the selection of a particular, best-performing species (i.e., Pedobacter sp.) as well as complementary use of carbon resources among consortia members (i.e., complementarity effects). Among the biodiversity indices, PD diversity metrics explained higher variation in sCOD removal than SR and FD diversity metrics. For a more effective bioaugmentation, our results stress the importance of using phylogenetically diverse consortia, with an increased degradation ability, instead of single pure cultures. Moreover, PD could be used as an assembly rule to guide the composition of mixed cultures for wastewater bioaugmentation under psychrophilic conditions.
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Affiliation(s)
- Floriana Augelletti
- Laboratory of Bioengineering, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Spiros N Agathos
- Laboratory of Bioengineering, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Benoit Stenuit
- Joint Research Unit of Agropolymer Engineering and Emerging Technologies (IATE, UMR 1208), Polytech Montpellier, University of Montpellier, Montpellier, France
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25
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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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