1
|
Shin J, Liao S, Kuanyshev N, Xin Y, Kim C, Lu T, Jin YS. Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium. Nat Commun 2024; 15:781. [PMID: 38278783 PMCID: PMC10817915 DOI: 10.1038/s41467-024-45011-w] [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: 08/31/2022] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.
Collapse
Affiliation(s)
- Jonghyeok Shin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Siqi Liao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongping Xin
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chanwoo Kim
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
2
|
Hosoda K, Seno S, Murakami N, Matsuda H, Osada Y, Kamiura R, Kondoh M. Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach. Biosystems 2024; 235:105087. [PMID: 37989470 DOI: 10.1016/j.biosystems.2023.105087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Simultaneous understanding of both population and ecosystem dynamics is crucial in an era marked by the degradation of ecosystem services. Experimental ecosystems are a powerful tool for understanding these dynamics; however, they often face technical challenges, typically falling into two categories: "complex but with limited replicability microcosms" and "highly replicable but overly simplistic microcosms." Herein, we present a high-throughput synthetic microcosm system comprising 12 functionally and phylogenetically diverse microbial species. These species are axenically culturable, cryopreservable, and can be measured noninvasively via microscopy, aided by machine learning. This system includes prokaryotic and eukaryotic producers and decomposers, and eukaryotic consumers to ensure functional redundancy. Our model system exhibited key features of a complex ecosystem: (i) various positive and negative interspecific interactions, (ii) higher-order interactions beyond two-species dynamics, (iii) probabilistic dynamics leading to divergent outcomes, and (iv) stable nonlinear transitions. We identified several conditions under which at least one species from each of the three functional groups-producers, consumers, and decomposers-and one functionally redundant species, persisted for over six months. These conditions set the stage for detailed investigations in the future. Given its designability and experimental replicability, our model ecosystem offers a promising platform for deeper insights integrating both population and ecosystem dynamics.
Collapse
Affiliation(s)
- Kazufumi Hosoda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan; Center for Information and Neural Networks (CiNet), National Institute of Information and Communications Technology (NICT), Osaka, Japan; Institute for Transdisciplinary Graduate Degree Programs, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan; Life and Medical Sciences Area, Health Sciences Discipline, Kobe University, Tomogaoka 7-10-2, Suma-ku, Kobe, Hyogo, 654-0142, Japan.
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naomi Murakami
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Rikuto Kamiura
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| |
Collapse
|
3
|
Benninghaus L, Schwardmann LS, Jilg T, Wendisch VF. Establishment of synthetic microbial consortia with Corynebacterium glutamicum and Pseudomonas putida: Design, construction, and application to production of γ-glutamylisopropylamide and l-theanine. Microb Biotechnol 2024; 17:e14400. [PMID: 38206115 PMCID: PMC10832564 DOI: 10.1111/1751-7915.14400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Microbial synthetic consortia are a promising alternative to classical monoculture for biotechnological applications and fermentative processes. Their versatile use offers advantages in the degradation of complex substrates, the allocation of the metabolic burden between individual partners, or the division of labour in energy utilisation, substrate supply or product formation. Here, stable synthetic consortia between the two industrially relevant production hosts, Pseudomonas putida KT2440 and Corynebacterium glutamicum ATCC13032, were established for the first time. By applying arginine auxotrophy/overproduction and/or formamidase-based utilisation of the rare nitrogen source formamide, different types of interaction were realised, such as commensal relationships (+/0 and 0/+) and mutualistic cross-feeding (+/+). These consortia did not only show stable growth but could also be used for fermentative production of the γ-glutamylated amines theanine and γ-glutamyl-isopropylamide (GIPA). The consortia produced up to 2.8 g L-1 of GIPA and up to 2.6 g L-1 of theanine, a taste-enhancing constituent of green tea leaves. Thus, the advantageous approach of using synthetic microbial consortia for fermentative production of value-added compounds was successfully demonstrated.
Collapse
Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
| | - Lynn S. Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
- Present address:
Aminoverse B.V.Daelderweg 9Nuth6361 HKthe Netherlands
| | - Tatjana Jilg
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
- Present address:
Symrise AGMühlenfeldstraße 1Holzminden37603Germany
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
| |
Collapse
|
4
|
Zong DM, Sadeghpour M, Molinari S, Alnahhas RN, Hirning AJ, Giannitsis C, Ott W, Josić K, Bennett MR. Tunable Dynamics in a Multistrain Transcriptional Pulse Generator. ACS Synth Biol 2023; 12:3531-3543. [PMID: 38016068 DOI: 10.1021/acssynbio.3c00434] [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] [Indexed: 11/30/2023]
Abstract
One challenge in synthetic biology is the tuning of regulatory components within gene circuits to elicit a specific behavior. This challenge becomes more difficult in synthetic microbial consortia since each strain's circuit must function at the intracellular level and their combination must operate at the population level. Here we demonstrate that circuit dynamics can be tuned in synthetic consortia through the manipulation of strain fractions within the community. To do this, we construct a microbial consortium comprised of three strains of engineered Escherichia coli that, when cocultured, use homoserine lactone-mediated intercellular signaling to create a multistrain incoherent type-1 feedforward loop (I1-FFL). Like naturally occurring I1-FFL motifs in gene networks, this engineered microbial consortium acts as a pulse generator of gene expression. We demonstrate that the amplitude of the pulse can be easily tuned by adjusting the relative population fractions of the strains. We also develop a mathematical model for the temporal dynamics of the microbial consortium. This model allows us to identify population fractions that produced desired pulse characteristics, predictions that were confirmed for all but extreme fractions. Our work demonstrates that intercellular gene circuits can be effectively tuned simply by adjusting the starting fractions of each strain in the consortium.
Collapse
Affiliation(s)
- David M Zong
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Mehdi Sadeghpour
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
| | - Sara Molinari
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Andrew J Hirning
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Charilaos Giannitsis
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
5
|
van Aalst ACA, van der Meulen IS, Jansen MLA, Mans R, Pronk JT. Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield. Metab Eng 2023; 80:151-162. [PMID: 37751790 DOI: 10.1016/j.ymben.2023.09.010] [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: 06/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023]
Abstract
Glycerol is the major organic byproduct of industrial ethanol production with the yeast Saccharomyces cerevisiae. Improved ethanol yields have been achieved with engineered S. cerevisiae strains in which heterologous pathways replace glycerol formation as the predominant mechanism for anaerobic re-oxidation of surplus NADH generated in biosynthetic reactions. Functional expression of heterologous phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes enables yeast cells to couple a net oxidation of NADH to the conversion of glucose to ethanol. In another strategy, NADH-dependent reduction of exogenous acetate to ethanol is enabled by introduction of a heterologous acetylating acetaldehyde dehydrogenase (A-ALD). This study explores potential advantages of co-cultivating engineered PRK-RuBisCO-based and A-ALD-based strains in anaerobic bioreactor batch cultures. Co-cultivation of these strains, which in monocultures showed reduced glycerol yields and improved ethanol yields, strongly reduced the formation of acetaldehyde and acetate, two byproducts that were formed in anaerobic monocultures of a PRK-RuBisCO-based strain. In addition, co-cultures on medium with low acetate-to-glucose ratios that mimicked those in industrial feedstocks completely removed acetate from the medium. Kinetics of co-cultivation processes and glycerol production could be optimized by tuning the relative inoculum sizes of the two strains. Co-cultivation of a PRK-RuBisCO strain with a Δgpd1 Δgpd2 A-ALD strain, which was unable to grow in the absence of acetate and evolved for faster anaerobic growth in acetate-supplemented batch cultures, further reduced glycerol formation but led to extended fermentation times. These results demonstrate the potential of using defined consortia of engineered S. cerevisiae strains for high-yield, minimal-waste ethanol production.
Collapse
Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Igor S van der Meulen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX, Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| |
Collapse
|
6
|
Jiang Y, Wu R, Zhang W, Xin F, Jiang M. Construction of stable microbial consortia for effective biochemical synthesis. Trends Biotechnol 2023; 41:1430-1441. [PMID: 37330325 DOI: 10.1016/j.tibtech.2023.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.
Collapse
Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China.
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
| |
Collapse
|
7
|
Bao T, Qian Y, Xin Y, Collins JJ, Lu T. Engineering microbial division of labor for plastic upcycling. Nat Commun 2023; 14:5712. [PMID: 37752119 PMCID: PMC10522701 DOI: 10.1038/s41467-023-40777-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/09/2023] [Indexed: 09/28/2023] Open
Abstract
Plastic pollution is rapidly increasing worldwide, causing adverse impacts on the environment, wildlife and human health. One tempting solution to this crisis is upcycling plastics into products with engineered microorganisms; however, this remains challenging due to complexity in conversion. Here we present a synthetic microbial consortium that efficiently degrades polyethylene terephthalate hydrolysate and subsequently produces desired chemicals through division of labor. The consortium involves two Pseudomonas putida strains, specializing in terephthalic acid and ethylene glycol utilization respectively, to achieve complete substrate assimilation. Compared with its monoculture counterpart, the consortium exhibits reduced catabolic crosstalk and faster deconstruction, particularly when substrate concentrations are high or crude hydrolysate is used. It also outperforms monoculture when polyhydroxyalkanoates serves as a target product and confers flexible tuning through population modulation for cis-cis muconate synthesis. This work demonstrates engineered consortia as a promising, effective platform that may facilitate polymer upcycling and environmental sustainability.
Collapse
Affiliation(s)
- Teng Bao
- 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
| | - Yuanchao Qian
- 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
| | - Yongping Xin
- 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
| | - James J Collins
- Department of Biological Engineering and Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Longwood, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 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.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- National Center for Supercomputing Applications, Urbana, IL, 61801, USA.
| |
Collapse
|
8
|
Pan R, Yang X, Qiu M, Jiang W, Zhang W, Jiang Y, Xin F, Jiang M. Construction of Coculture System Containing Escherichia coli with Different Microbial Species for Biochemical Production. ACS Synth Biol 2023; 12:2208-2216. [PMID: 37506399 DOI: 10.1021/acssynbio.3c00329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Microbial synthesis of target chemicals usually involves multienzymatic reactions in vivo, especially for compounds with a long metabolic pathway. However, when various genes are introduced into one single strain, it leads to a heavy metabolic burden. In contrast, the microbial coculture system can allocate metabolic pathways into different hosts, which will relieve the metabolic burdens. Escherichia coli is the most used chassis to synthesize biofuels and chemicals owing to its well-known genetics, high transformation efficiency, and easy cultivation. Accordingly, cocultures containing the cooperative E. coli with other microbial species have received great attention. In this review, the individual applications and boundedness of different combinations will be summarized. Additionally, the strategies for the self-regulation of population composition, which can help enhance the stability of a coculture system, will also be discussed. Finally, perspectives for the cocultures will be proposed.
Collapse
Affiliation(s)
- Runze Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Xinyi Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| |
Collapse
|
9
|
Zhou M, Guan X, Deng T, Hu R, Qian L, Yang X, Wu B, Li J, He Q, Shu L, Yan Q, He Z. Synthetic phylogenetically diverse communities promote denitrification and stability. ENVIRONMENTAL RESEARCH 2023; 231:116184. [PMID: 37207729 DOI: 10.1016/j.envres.2023.116184] [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: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.
Collapse
Affiliation(s)
- Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
10
|
Martínez C, Cinquemani E, Jong HD, Gouzé JL. Optimal protein production by a synthetic microbial consortium: coexistence, distribution of labor, and syntrophy. J Math Biol 2023; 87:23. [PMID: 37395814 DOI: 10.1007/s00285-023-01935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/22/2022] [Accepted: 05/17/2023] [Indexed: 07/04/2023]
Abstract
The bacterium E. coli is widely used to produce recombinant proteins such as growth hormone and insulin. One inconvenience with E. coli cultures is the secretion of acetate through overflow metabolism. Acetate inhibits cell growth and represents a carbon diversion, which results in several negative effects on protein production. One way to overcome this problem is the use of a synthetic consortium of two different E. coli strains, one producing recombinant proteins and one reducing the acetate concentration. In this paper, we study a mathematical model of such a synthetic community in a chemostat where both strains are allowed to produce recombinant proteins. We give necessary and sufficient conditions for the existence of a coexistence equilibrium and show that it is unique. Based on this equilibrium, we define a multi-objective optimization problem for the maximization of two important bioprocess performance metrics, process yield and productivity. Solving numerically this problem, we find the best available trade-offs between the metrics. Under optimal operation of the mixed community, both strains must produce the protein of interest, and not only one (distribution instead of division of labor). Moreover, in this regime acetate secretion by one strain is necessary for the survival of the other (syntrophy). The results thus illustrate how complex multi-level dynamics shape the optimal production of recombinant proteins by synthetic microbial consortia.
Collapse
Affiliation(s)
- Carlos Martínez
- Université Côte d' Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, Sophia Antipolis, France.
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
| | | | - Hidde de Jong
- Univ. Grenoble Alpes, Inria, 38000, Grenoble, France
| | - Jean-Luc Gouzé
- Université Côte d' Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, Sophia Antipolis, France
| |
Collapse
|
11
|
López-Gálvez J, Schiessl K, Besmer MD, Bruckmann C, Harms H, Müller S. Development of an Automated Online Flow Cytometry Method to Quantify Cell Density and Fingerprint Bacterial Communities. Cells 2023; 12:1559. [PMID: 37371029 DOI: 10.3390/cells12121559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/09/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Cell density is an important factor in all microbiome research, where interactions are of interest. It is also the most important parameter for the operation and control of most biotechnological processes. In the past, cell density determination was often performed offline and manually, resulting in a delay between sampling and immediate data processing, preventing quick action. While there are now some online methods for rapid and automated cell density determination, they are unable to distinguish between the different cell types in bacterial communities. To address this gap, an online automated flow cytometry procedure is proposed for real-time high-resolution analysis of bacterial communities. On the one hand, it allows for the online automated calculation of cell concentrations and, on the other, for the differentiation between different cell subsets of a bacterial community. To achieve this, the OC-300 automation device (onCyt Microbiology, Zürich, Switzerland) was coupled with the flow cytometer CytoFLEX (Beckman Coulter, Brea, USA). The OC-300 performs the automatic sampling, dilution, fixation and 4',6-diamidino-2-phenylindole (DAPI) staining of a bacterial sample before sending it to the CytoFLEX for measurement. It is demonstrated that this method can reproducibly measure both cell density and fingerprint-like patterns of bacterial communities, generating suitable data for powerful automated data analysis and interpretation pipelines. In particular, the automated, high-resolution partitioning of clustered data into cell subsets opens up the possibility of correlation analysis to identify the operational or abiotic/biotic causes of community disturbances or state changes, which can influence the interaction potential of organisms in microbiomes or even affect the performance of individual organisms.
Collapse
Affiliation(s)
- Juan López-Gálvez
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | | | - Michael D Besmer
- onCyt Microbiology AG, Marchwartstrasse 61, 8038 Zürich, Switzerland
| | - Carmen Bruckmann
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| |
Collapse
|
12
|
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.
Collapse
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:
| |
Collapse
|
13
|
Dolinšek J, Ramoneda J, Johnson DR. Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability. ISME COMMUNICATIONS 2022; 2:77. [PMID: 37938324 PMCID: PMC9723679 DOI: 10.1038/s43705-022-00160-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 06/19/2023]
Abstract
Multi-step substrate consumption pathways can promote microbial biodiversity via cross-feeding. If one cell type preferentially consumes a primary substrate rather than the subsequently formed intermediates, then other cell types can specialize in consuming the intermediates. While this mechanism for promoting biodiversity is established, predicting the long-term persistence of such cross-feeding interactions remains challenging. Under what conditions will the interaction (and thus biodiversity) persist or disappear? To address this question, we propagated co-cultures of two isogenic strains of the bacterium Pseudomonas stutzeri. One completely reduces nitrate to nitrogen gas but preferentially reduces nitrate rather than nitrite (referred to as the generalist), while the other only reduces nitrite to nitrogen gas (referred to as the specialist). We found that the two strains coexist via nitrite cross-feeding when grown together, but the initial ratio of specialist-to-generalist (rS/G) determines the long-term dynamics of the co-culture. Co-cultures with large initial rS/Gs converge to the same rS/G and persist thereafter. Co-cultures with small initial rS/Gs also converge to the same rS/G but then become increasingly dominated by the generalist. The likely cause of these different dynamics is that the initial rS/G determines the initial environment, which in turn determines the initial selection pressures and phenotypes acquired by the generalist. Our results demonstrate that initial community composition controls the long-term dynamics and persistence of a cross-feeding interaction, and is therefore an important factor for community development and for engineering communities to achieve desired outcomes.
Collapse
Affiliation(s)
- Jan Dolinšek
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH), 8092, Zürich, Switzerland
| | - Josep Ramoneda
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland.
| |
Collapse
|
14
|
Gao L, Zhou J, He G. Effect of microbial interaction on flavor quality in Chinese baijiu fermentation. Front Nutr 2022; 9:960712. [PMID: 35990321 PMCID: PMC9381987 DOI: 10.3389/fnut.2022.960712] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/11/2022] [Indexed: 11/14/2022] Open
Abstract
Chinese baijiu brewing is an open, complex, and synergetic functional microbiota fermentation process. Microbial interaction is pivotal for the regulation of microbial structure and function in the brewing microecosystem, consequently affecting the flavor and quality of baijiu. This article mainly summarizes the effect of microbial interactions among functional microbiota on the growth performance, flavor formation, and safe quality of baijiu fermentation process. In addition, the review specifically emphasizes on the microbial interactions for the regulation of “Ethyl Caproate-Increasing and Ethyl Lactate-Decreasing” in Chinese strong-flavor baijiu. Furthermore, the construction of synthetic microbiota by metabolic characteristics of the functional microbes and their interactions for regulating and controlling flavor quality of Chinese baijiu is also reviewed and prospected.
Collapse
Affiliation(s)
- Lei Gao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Jian Zhou
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Guiqiang He
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| |
Collapse
|
15
|
Ding Q, Li Z, Guo L, Song W, Wu J, Chen X, Liu L, Gao C. Engineering Escherichia coli asymmetry distribution-based synthetic consortium for shikimate production. Biotechnol Bioeng 2022; 119:3230-3240. [PMID: 35982023 DOI: 10.1002/bit.28211] [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: 05/17/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022]
Abstract
Microbial consortia constitute a promising tool for achieving high-value chemical bio-production. However, customizing the consortium ratio remains challenging. Herein, an asymmetry distribution-based synthetic consortium (ADSC) was developed to switch cell phenotypes using shikimate synthesis for proof of concept. First, the cell pole-organizing protein PopZ was screened as a mediator of asymmetric protein distribution in Escherichia coli. The ADSC was then constructed to incorporate PopZ-mediated asymmetry distribution and a TetR-based transcription repression switch to achieve the dynamical control of microbial population ratio. Finally, the ADSC was used to decouple cell growth from shikimate synthesis by effectively coordinating the ratio of growing cells and production cells at the consortium level, thereby increasing shikimate titer to 30.1 g/L in the 7.5-L bioreactor with a minimal medium. This titer was further improved to 82.5 g/L when using rich medium fermentation. Our results illustrate a novel approach to control consortium structure through ADSC-mediated regulation, highlighting its potential as an efficient strategy for controlling metabolic state in microbes. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.,School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network. Biosystems 2022; 213:104608. [DOI: 10.1016/j.biosystems.2022.104608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/07/2021] [Accepted: 01/11/2022] [Indexed: 01/12/2023]
|
18
|
Liang Y, Ma A, Zhuang G. Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles. Front Microbiol 2022; 13:829717. [PMID: 35283862 PMCID: PMC8905317 DOI: 10.3389/fmicb.2022.829717] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 01/30/2023] Open
Abstract
In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.
Collapse
Affiliation(s)
- Yu Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
19
|
Zhang G, Yang X, Zhao Z, Xu T, Jia X. Artificial Consortium of Three E. coli BL21 Strains with Synergistic Functional Modules for Complete Phenanthrene Degradation. ACS Synth Biol 2022; 11:162-175. [PMID: 34914358 DOI: 10.1021/acssynbio.1c00349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic and persistent organic pollutions that can accumulate in the environment. In this study, an aromatic ring cleavage module, a salicylic acid synthesis module, and a catechol metabolism module were respectively constructed in three Escherichia coli BL21 strains. Subsequently, the engineered strains were cocultured as an artificial consortium for the biodegradation of phenanthrene, a typical PHA. Single factor experiments and response surface methodology were used to identify the optimal degradation conditions, including an inoculation interval of 6 h, inoculation ratio of 1:1:1, and IPTG concentration of 2 mM. Under these conditions, the 7-day degradation ratio of 100 mg/L phenanthrene reached 72.67%. Moreover, the engineered Escherichia coli BL21 strains showed good phenanthrene degradation ability at substrate concentrations 10 mg/L up to 500 mg/L. Enzyme activity assays combined with gas chromatography-mass spectrometry measurements confirmed that the three engineered strains behaved as a synergistic consortium in the phenanthrene degradation process. Based on the analysis of the key metabolites, the engineered bacteria were supplemented at 7-day intervals in batches so that each engineered strain maintained its optimal degradation ability. The 21-day degradation ratio finally reached 90.66%, which was much higher than what was observed with simultaneous inoculation. These findings suggest that the three engineered strains with separate modules constructed in this study offer an attractive solution for removing PAHs from the environment.
Collapse
Affiliation(s)
- Guangbao Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaohui Yang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhenhua Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tao Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| |
Collapse
|
20
|
Lindane removal in contaminated soil by defined microbial consortia and evaluation of its effectiveness by bioassays and cytotoxicity studies. Int Microbiol 2022; 25:365-378. [PMID: 35032229 DOI: 10.1007/s10123-022-00232-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/05/2021] [Accepted: 12/31/2021] [Indexed: 12/29/2022]
Abstract
Lindane contamination in different environmental matrices has been a global concern for long. Bacterial consortia consisting of Paracoccus sp. NITDBR1, Rhodococcus rhodochrous NITDBS9, Ochrobactrum sp. NITDBR3, NITDBR4 and NITDBR5 were used for the bioremediation of soil artificially contaminated with lindane. The bacteria, Paracoccus sp. NITDBR1 and Rhodococcus rhodochrous NITDBS9, have been selected based on their lindane degrading capacity in liquid culture conditions (~80-90 %). The remaining three bacteria were chosen for their auxiliary properties for plant growth promotion, such as nitrogen fixation, phosphate solubilization, indole-3-acetic acid production and ammonia production under in vitro conditions. In this study, market wastes, mainly vegetable wastes, were added to the soil as a biostimulant to form a biomixture for assisting the degradation of lindane by bioaugmentation. Residual lindane was measured at regular intervals of 7 days to monitor the biodegradation process. It was observed that the consortium could degrade ~80% of 50 mg kg-1 lindane in soil which was further increased in the biomixture after six weeks of incubation. Bioassays performed on plant seeds and cytotoxicity studies performed on human skin fibroblast and HCT116 cell lines revealed that the groups contaminated with lindane and treated with the bacterial consortium showed lower toxicity than their respective controls without any bacteria. Hence, the use of both pesticide degrading and plant growth-promoting bacteria in a consortium can be a promising strategy for improved bioremediation against chemical pesticides, particularly in soil and agricultural fields, simultaneously enhancing crop productivity in those contaminated soil.
Collapse
|
21
|
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.
Collapse
|
22
|
Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication. Microb Cell Fact 2021; 20:215. [PMID: 34819093 PMCID: PMC8611841 DOI: 10.1186/s12934-021-01703-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/06/2021] [Indexed: 12/04/2022] Open
Abstract
Background Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01703-2.
Collapse
|
23
|
Aparicio JD, Espíndola D, Montesinos VN, Litter MI, Donati E, Benimeli CS, Polti MA. Evaluation of the sequential coupling of a bacterial treatment with a physicochemical process for the remediation of wastewater containing Cr and organic pollutants. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126307. [PMID: 34130164 DOI: 10.1016/j.jhazmat.2021.126307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
A restoration strategy was developed for the treatment of two artificial liquid systems (Minimal Medium, MM, and Water Carbon Nitrogen, WCN) contaminated with Cr(VI), lindane (γ-HCH), phenanthrene (Phe), and reactive black 5 (RB5), through the use of an actinobacteria consortium, coupled with a physicochemical treatment using a column filled with nano-scale zero valent iron particles immobilized on dried Macrocystis pyrifera algae biomass. The Sequential Treatment A (STA: physicochemical followed by biological method) removed the three organic compounds with different effectiveness; however, it was very ineffective for Cr(VI) removal. The Sequential Treatment B (STB: biological followed by the physicochemical method) removed the four compounds with variable efficiencies. The removal of γ-HCH, Phe, and RB5 in both effluents did not present significant differences, regardless of the sequential treatment used. The highest removal of Cr(VI) and total Cr was observed in MM and WCN, respectively. Ecotoxicity tests (L. sativa) of the effluents treated with both methodological couplings demonstrated that the toxicity of WCN only decreased at the end of STA, while that of MM decreased at all stages of both sequential treatments. Therefore, MM would be more appropriate to perform both treatments.
Collapse
Affiliation(s)
- Juan Daniel Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 Tucumán, Argentina
| | - Diego Espíndola
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 Tucumán, Argentina
| | - Víctor Nahuel Montesinos
- Gerencia Química, Centro Atómico Constituyentes, CNEA, Av. Gral. Paz 1499, 1650 San Martín, Prov. de Buenos Aires, Argentina
| | - Marta Irene Litter
- IIIA (CONICET-UNSAM), Universidad Nacional de General San Martín, Campus Miguelete, Av. 25 de Mayo y Francia, 1650 San Martín, Prov. de Buenos Aires, Argentina
| | - Edgardo Donati
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Claudia Susana Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Av. Belgrano 300, 4700 Catamarca, Argentina.
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina.
| |
Collapse
|
24
|
Liu H, Dai L, Yao J, Mei Y, Hrynsphan D, Tatsiana S, Chen J. Efficient biotransformation of sulfide in anaerobic sequencing batch reactor by composite microbial agent: performance optimization and microbial community analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:48718-48727. [PMID: 33913111 DOI: 10.1007/s11356-021-12717-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Sulfur-containing wastewater is very common as an industrial waste, yet a high-efficiency composite microbial agent for sulfur-containing wastewater treatment is still lacking. In this work, three novel and efficient desulfurizing bacteria were isolated from the sewage treatment tank of Zhejiang Satellite Energy Co., Ltd. They were identified as Brucella melitensis (S1), Ochrobactrum oryzae (S8), and Achromobacter xylosoxidans (S9). These three strains of bacteria were responsible for the oxidative metabolism of sodium sulfide via a similar polythionate pathway, which could be expressed as follows: S2-→S2O32-/S0→SO32-→SO42-. Activated carbon, wheat bran, and diatomite at 1:1:1 ratio are used as carriers to construct a composite microbial agent containing the three bacteria. The desulfurization efficiency of 95% was predicted by response surface methodology under the following optimum conditions: the dosage of the inoculum was 3 g/L, pH 7.86, and temperature of 39 °C. Additionally, the impact resistance was studied in the anaerobic sequencing batch reactor. The removal capacity of microbial agent reached 98%. High-throughput analysis showed that composite microbial agent increased bacterial evenness and diversity, and the relative abundance of Brucellaceae increased from 5.04 to 8.79% in the reactor. In the process of industrial wastewater transformation, the transformation rate of sulfide by composite microbial agent was maintained between 70 and 81%. The composite microbial agent had potential for the treatment of sulfur-containing wastewater.
Collapse
Affiliation(s)
- Huan Liu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Luyao Dai
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Jiachao Yao
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 30021, People's Republic of China
| | - Yu Mei
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 30021, People's Republic of China
| | - Dzmitry Hrynsphan
- Research Institute of Physical and Chemical Problems, Blearusian State University, 220030, Minsk, Belarus
| | - Savitskaya Tatsiana
- Research Institute of Physical and Chemical Problems, Blearusian State University, 220030, Minsk, Belarus
| | - Jun Chen
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 30021, People's Republic of China.
| |
Collapse
|
25
|
Tang Q, Huang J, Zhang S, Qin H, Dong Y, Wang C, Li D, Zhou R. Keystone microbes affect the evolution and ecological coexistence of the community via species/strain specificity. J Appl Microbiol 2021; 132:1227-1238. [PMID: 34427980 DOI: 10.1111/jam.15255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 02/02/2023]
Abstract
AIM Microbial communities exhibit different diversity and fluctuations in the ecological functions due to time and environmental migration. Despite a long history of research and a plethora of data, the factors determining the biodiversity and stability of ecosystems is still elusive. METHODS AND RESULTS Here, the Chinese Xiaoqu fermentation system was used as a template to explore the mechanism in which the species specificity and strain in the initial phase affect the community structure and metabolites in the subsequent micro-ecosystem. The micro-ecosystem has been applied for hundreds of years, and the main metabolic function can be reproduced and traced. CONCLUSIONS The result proved that Rhizopus spp. is a keystone microbe with a species/strain specificity affecting the trophic interaction niche and function of modules in the complex community through glucose. The fungal community was demonstrated to have a high sealing and stability, while the bacterial community was generally found to change the community structure, physiological function, and interaction relationship, producing strains with connector functions to adapt to fluctuations. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows that the taxonomic level of key microbial strains can be changed to affect the evolution of coexistence and functional realisation of the community.
Collapse
Affiliation(s)
- Qiuxiang Tang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Suyi Zhang
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Hui Qin
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Yi Dong
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Chao Wang
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Delin Li
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,National Engineering Research Centre of Solid-State Brewing, Luzhou, China
| |
Collapse
|
26
|
Patel A, Carlson RP, Henson MA. In silico analysis of synthetic multispecies biofilms for cellobiose-to-isobutanol conversion reveals design principles for stable and productive communities. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
27
|
Du R, Li C, Pan P, Sze Ki Lin C, Yan J. Characterization and evaluation of a natural derived bacterial consortium for efficient lignocellulosic biomass valorization. BIORESOURCE TECHNOLOGY 2021; 329:124909. [PMID: 33684842 DOI: 10.1016/j.biortech.2021.124909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 05/26/2023]
Abstract
A consortium (HPP) with improved ability in biomass conversion was achieved by adjusting the proportion of Pseudoxanthomonas taiwanensis in a natural consortium (HP), but the mechanism behind was unknown. Herein, the diversities of microbial community structure and gene functions of the consortia were analyzed first, and found that HPP had a more balanced microbial structure with enriched gene pathways related to cellular processes, environmental information processing and metabolism. Then, key genes responsible for biomass conversion were further analyzed, finding that their abundance and distribution contributed to HPP's efficient biomass conversion. Finally, consolidated bioprocessing of agricultural wastes by HPP was carried out to verify its enhanced ability, and ethanol with the highest yield that was ever reported was achieved at 0.28 g/g. This is the first study which reported the underlying mechanisms for synergistic effects of microbial consortia, and will guide the artificial construction of complex microbial consortium for specific purpose.
Collapse
Affiliation(s)
- Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peipei Pan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| |
Collapse
|
28
|
Grandel NE, Reyes Gamas K, Bennett MR. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol 2021; 29:1095-1105. [PMID: 33966922 DOI: 10.1016/j.tim.2021.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.
Collapse
Affiliation(s)
- Nicolas E Grandel
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Kiara Reyes Gamas
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA.
| |
Collapse
|
29
|
Pacheco AR, Osborne ML, Segrè D. Non-additive microbial community responses to environmental complexity. Nat Commun 2021; 12:2365. [PMID: 33888697 PMCID: PMC8062479 DOI: 10.1038/s41467-021-22426-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental composition is a major, though poorly understood, determinant of microbiome dynamics. Here we ask whether general principles govern how microbial community growth yield and diversity scale with an increasing number of environmental molecules. By assembling hundreds of synthetic consortia in vitro, we find that growth yield can remain constant or increase in a non-additive manner with environmental complexity. Conversely, taxonomic diversity is often much lower than expected. To better understand these deviations, we formulate metrics for epistatic interactions between environments and use them to compare our results to communities simulated with experimentally-parametrized consumer resource models. We find that key metabolic and ecological factors, including species similarity, degree of specialization, and metabolic interactions, modulate the observed non-additivity and govern the response of communities to combinations of resource pools. Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems.
Collapse
Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Melisa L Osborne
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
| |
Collapse
|
30
|
Qi M, Liang B, Zhang L, Ma X, Yan L, Dong W, Kong D, Zhang L, Zhu H, Gao SH, Jiang J, Liu SJ, Corvini PFX, Wang A. Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3270-3282. [PMID: 33566597 DOI: 10.1021/acs.est.0c06687] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.
Collapse
Affiliation(s)
- Mengyuan Qi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodan Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenchen Dong
- Department of Civil and Natural Resources Engineering, University of Canterbury, Christchurch 8140, New Zealand
| | - Deyong Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liying Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Haizhen Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| |
Collapse
|
31
|
Simonet C, McNally L. Kin selection explains the evolution of cooperation in the gut microbiota. Proc Natl Acad Sci U S A 2021; 118:e2016046118. [PMID: 33526674 PMCID: PMC8017935 DOI: 10.1073/pnas.2016046118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Through the secretion of "public goods" molecules, microbes cooperatively exploit their habitat. This is known as a major driver of the functioning of microbial communities, including in human disease. Understanding why microbial species cooperate is therefore crucial to achieve successful microbial community management, such as microbiome manipulation. A leading explanation is that of Hamilton's inclusive-fitness framework. A cooperator can indirectly transmit its genes by helping the reproduction of an individual carrying similar genes. Therefore, all else being equal, as relatedness among individuals increases, so should cooperation. However, the predictive power of relatedness, particularly in microbes, is surrounded by controversy. Using phylogenetic comparative analyses across the full diversity of the human gut microbiota and six forms of cooperation, we find that relatedness is predictive of the cooperative gene content evolution in gut-microbe genomes. Hence, relatedness is predictive of cooperation over broad microbial taxonomic levels that encompass variation in other life-history and ecology details. This supports the generality of Hamilton's central insights and the relevance of relatedness as a key parameter of interest to advance microbial predictive and engineering science.
Collapse
Affiliation(s)
- Camille Simonet
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
| | - Luke McNally
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| |
Collapse
|
32
|
Schlembach I, Grünberger A, Rosenbaum MA, Regestein L. Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes. Trends Biotechnol 2021; 39:1093-1109. [PMID: 33573846 PMCID: PMC7612867 DOI: 10.1016/j.tibtech.2021.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial mixed cultures are gaining increasing attention as biotechnological production systems, since they offer a large but untapped potential for future bioprocesses. Effects of secondary metabolite induction and advantages of labor division for the degradation of complex substrates offer new possibilities for process intensification. However, mixed cultures are highly complex, and, consequently, many biotic and abiotic parameters are required to be identified, characterized, and ideally controlled to establish a stable bioprocess. In this review, we discuss the advantages and disadvantages of existing measurement techniques for identifying, characterizing, monitoring, and controlling mixed cultures and highlight promising examples. Moreover, existing challenges and emerging technologies are discussed, which lay the foundation for novel analytical workflows to monitor mixed-culture bioprocesses.
Collapse
Affiliation(s)
- Ivan Schlembach
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Lars Regestein
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
| |
Collapse
|
33
|
Krieger AG, Zhang J, Lin XN. Temperature regulation as a tool to program synthetic microbial community composition. Biotechnol Bioeng 2021; 118:1381-1392. [PMID: 33399224 DOI: 10.1002/bit.27662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/07/2022]
Abstract
Engineering of synthetic microbial communities is emerging as a powerful new paradigm for performing various industrially, medically, and environmentally important processes. To reach the fullest potential, however, this approach requires further development in many aspects, a key one being regulating the community composition. Here we leverage well-established mechanisms in ecology which govern the relative abundance of multispecies ecosystems and develop a new tool for programming the composition of synthetic microbial communities. Using a simple model system consisting of two microorganisms Escherichia coli and Pseudomonas putida, which occupy different but partially overlapping thermal niches, we demonstrated that temperature regulation could be used to enable coexistence and program the community composition. We first investigated a constant temperature regime and showed that different temperatures led to different community compositions. Next, we invented a new cycling temperature regime and showed that it can dynamically tune the microbial community, achieving a wide range of compositions depending on parameters that are readily manipulatable. Our work provides conclusive proof of concept that temperature regulation is a versatile and powerful tool capable of programming compositions of synthetic microbial communities.
Collapse
Affiliation(s)
- Adam G Krieger
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Jiahao Zhang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiaoxia N Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
34
|
Sharma B, Shukla P. Futuristic avenues of metabolic engineering techniques in bioremediation. Biotechnol Appl Biochem 2020; 69:51-60. [PMID: 33242354 DOI: 10.1002/bab.2080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/22/2020] [Indexed: 12/15/2022]
Abstract
Bioremediation is a promising technology for the treatment of environmental contaminants and paving new avenues for the betterment of the environment. Over the last some years, several approaches have been employed to optimize the genetic machinery of microorganisms relevant to bioremediation. Metabolic engineering is one of them that provides a new insight for bioremediation. This review envisages the critical role of these techniques toward exploring the possibilities of the creation of a new pathway, leading to pathway expansion to new substrates by assembling of catabolic modules from different origins in the same microbial cell. The recombinant DNA technology and gene editing tools were also explored for the construction of metabolically engineered microbial strains for the degradation of complex pollutants. Moreover, the importance of CRISPR-Cas system for knock-in and knock-out of genes was described by using recent studies. Further, the idea of the cocultivation of more than one metabolic engineered microbial communities is also discussed, which can be crucial in the bioremediation of multiple and complex pollutants. Finally, this review also elucidates the effective application of metabolic engineering in bioremediation through these techniques and tools.
Collapse
Affiliation(s)
- Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| |
Collapse
|
35
|
Ding Q, Diao W, Gao C, Chen X, Liu L. Microbial cell engineering to improve cellular synthetic capacity. Biotechnol Adv 2020; 45:107649. [PMID: 33091485 DOI: 10.1016/j.biotechadv.2020.107649] [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: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Rapid technological progress in gene assembly, biosensors, and genetic circuits has led to reinforce the cellular synthetic capacity for chemical production. However, overcoming the current limitations of these techniques in maintaining cellular functions and enhancing the cellular synthetic capacity (e.g., catalytic efficiency, strain performance, and cell-cell communication) remains challenging. In this review, we propose a strategy for microbial cell engineering to improve the cellular synthetic capacity by utilizing biotechnological tools along with system biology methods to regulate cellular functions during chemical production. Current strategies in microbial cell engineering are mainly focused on the organelle, cell, and consortium levels. This review highlights the potential of using biotechnology to further develop the field of microbial cell engineering and provides guidance for utilizing microorganisms as attractive regulation targets.
Collapse
Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wenwen Diao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
36
|
Chang CY, Osborne ML, Bajic D, Sanchez A. Artificially selecting bacterial communities using propagule strategies. Evolution 2020; 74:2392-2403. [PMID: 32888315 PMCID: PMC7942404 DOI: 10.1111/evo.14092] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/21/2020] [Accepted: 08/29/2020] [Indexed: 02/06/2023]
Abstract
Artificial selection is a promising approach to manipulate microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both used "propagule" selection strategies, whereby the best-performing communities are used as the inocula to form a new generation of communities. Both experiments were contrasted to a random selection control. The first experiment used a defined set of strains as the starting inoculum, and the function under selection was the amylolytic activity of the consortia. The second experiment used multiple soil communities as the starting inocula, and the function under selection was the communities' cross-feeding potential. In both experiments, the selected communities reached a higher mean function than the control. In the first experiment, this was caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, this response was fueled by the large initial variance in function across communities, and stopped when the top-performing community "fixed" in the metacommunity. Our results are in agreement with basic expectations from breeding theory, pointing to some of the limitations of community-level selection experiments that can inform the design of future studies.
Collapse
Affiliation(s)
- Chang-Yu Chang
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA
| | - Melisa L. Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.,Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA.,The Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.,Corresponding author:
| |
Collapse
|
37
|
Perez G, Debernardis F, Boido E, Carrau F. Simultaneous identification to monitor consortia strain dynamics of four biofuel yeast species during fermentation. J Ind Microbiol Biotechnol 2020; 47:1133-1140. [PMID: 32965544 DOI: 10.1007/s10295-020-02310-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/07/2020] [Indexed: 11/28/2022]
Abstract
Mixed strain dynamics are still not well or easily monitored although recently molecular identification methods have improved our knowledge. This study used a chromogenic differential plating medium that allows the discrimination of four of the main selected biofuel strains that are currently under development for ethanol production from cellulosic hydrolysates. Complete fermentation of hexoses and xylose was obtained with a yeast consortium composed of Spathaspora passalidarum, Scheffersomyces stipitis, Candida akabanensis and Saccharomyces cerevisiae. The results showed that C.akabanensis excessively dominated consortium balance. Reducing its inoculum from 33 to 4.8% improved population strain balance and fermentation efficiency. Comparison of the consortia with single strain fermentations showed that it optimize sugar consumption and ethanol yields. This simple and cheap method also has advantages compared with molecular methods, as the yeast strains do not need to be genetically marked and identified cell proportions are probably active in the fermentation system as compared to DNA determination methods.
Collapse
Affiliation(s)
- Gabriel Perez
- Área Enología y Biotecnología de la Fermentación, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica, 11800, Montevideo, Uruguay
| | - Florencia Debernardis
- Área Enología y Biotecnología de la Fermentación, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica, 11800, Montevideo, Uruguay
| | - Eduardo Boido
- Área Enología y Biotecnología de la Fermentación, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica, 11800, Montevideo, Uruguay
| | - Francisco Carrau
- Área Enología y Biotecnología de la Fermentación, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica, 11800, Montevideo, Uruguay.
| |
Collapse
|
38
|
Canon F, Nidelet T, Guédon E, Thierry A, Gagnaire V. Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures. Front Microbiol 2020; 11:2088. [PMID: 33013761 PMCID: PMC7500094 DOI: 10.3389/fmicb.2020.02088] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms grow in concert, both in natural communities and in artificial or synthetic co-cultures. Positive interactions between associated microbes are paramount to achieve improved substrate conversion and process performance in biotransformation and fermented food production. The mechanisms underlying such positive interactions have been the focus of numerous studies in recent decades and are now starting to be well characterized. Lactic acid bacteria (LAB) contribute to the final organoleptic, nutritional, and health properties of fermented food products. However, interactions in LAB co-cultures have been little studied, apart from the well-characterized LAB co-culture used for yogurt manufacture. LAB are, however, multifunctional microorganisms that display considerable potential to create positive interactions between them. This review describes why LAB co-cultures are of such interest, particularly in foods, and how their extensive nutritional requirements can be used to favor positive interactions. In that respect, our review highlights the benefits of co-cultures in different areas of application, details the mechanisms underlying positive interactions and aims to show how mechanisms based on nutritional interactions can be exploited to create efficient LAB co-cultures.
Collapse
Affiliation(s)
| | - Thibault Nidelet
- SPO, INRAE, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | | | | |
Collapse
|
39
|
Van Landuyt J, Cimmino L, Dumolin C, Chatzigiannidou I, Taveirne F, Mattelin V, Zhang Y, Vandamme P, Scoma A, Williamson A, Boon N. Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders. FEMS Microbiol Ecol 2020; 96:5841521. [PMID: 32436568 DOI: 10.1093/femsec/fiaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/20/2020] [Indexed: 11/12/2022] Open
Abstract
Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.
Collapse
Affiliation(s)
- Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Charles Dumolin
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ioanna Chatzigiannidou
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Felix Taveirne
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, 800 Dongchuan Rd, 200240 Shanghai, China
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Alberto Scoma
- Engineered Microbial Systems (EMS) Laboratory, Section of Biological and Chemical Engineering (BCE), Department of Engineering, Aarhus University, Hangøvej 2, 8200 Aarhus, Denmark
| | - Adam Williamson
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| |
Collapse
|
40
|
Stephens K, Bentley WE. Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia. Trends Microbiol 2020; 28:633-643. [DOI: 10.1016/j.tim.2020.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022]
|
41
|
Antoniewicz MR. A guide to deciphering microbial interactions and metabolic fluxes in microbiome communities. Curr Opin Biotechnol 2020; 64:230-237. [PMID: 32711357 DOI: 10.1016/j.copbio.2020.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 01/21/2023]
Abstract
Microbiomes occupy nearly all environments on Earth. These communities of interacting microorganisms are highly complex, dynamic biological systems that impact and reshape the molecular composition of their habitats by performing complex biochemical transformations. The structure and function of microbiomes are influenced by local environmental stimuli and spatiotemporal changes. In order to control the dynamics and ultimately the function of microbiomes, we need to develop a mechanistic and quantitative understanding of the ecological, molecular, and evolutionary driving forces that govern these systems. Here, we describe recent advances in developing computational and experimental approaches that can promote a more fundamental understanding of microbial communities through comprehensive model-based analysis of heterogeneous data types across multiple scales, from intracellular metabolism, to metabolite cross-feeding interactions, to the emergent macroscopic behaviors. Ultimately, harnessing the full potential of microbiomes for practical applications will require developing new predictive modeling approaches and better tools to manipulate microbiome interactions.
Collapse
Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
42
|
Lu J, Peng W, Lv Y, Jiang Y, Xu B, Zhang W, Zhou J, Dong W, Xin F, Jiang M. Application of Cell Immobilization Technology in Microbial Cocultivation Systems for Biochemicals Production. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01867] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiasheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, P. R. China
| | - Yang Lv
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Bin Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| |
Collapse
|
43
|
Alnahhas RN, Sadeghpour M, Chen Y, Frey AA, Ott W, Josić K, Bennett MR. Majority sensing in synthetic microbial consortia. Nat Commun 2020; 11:3659. [PMID: 32694598 PMCID: PMC7374166 DOI: 10.1038/s41467-020-17475-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/25/2020] [Indexed: 01/26/2023] Open
Abstract
As synthetic biocircuits become more complex, distributing computations within multi-strain microbial consortia becomes increasingly beneficial. However, designing distributed circuits that respond predictably to variation in consortium composition remains a challenge. Here we develop a two-strain gene circuit that senses and responds to which strain is in the majority. This involves a co-repressive system in which each strain produces a signaling molecule that signals the other strain to down-regulate production of its own, orthogonal signaling molecule. This co-repressive consortium links gene expression to ratio of the strains rather than population size. Further, we control the cross-over point for majority via external induction. We elucidate the mechanisms driving these dynamics by developing a mathematical model that captures consortia response as strain fractions and external induction are varied. These results show that simple gene circuits can be used within multicellular synthetic systems to sense and respond to the state of the population.
Collapse
Affiliation(s)
| | - Mehdi Sadeghpour
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Mathematics, University of Houston, Houston, TX, USA
| | - Ye Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Alexis A Frey
- Department of Biosciences, Rice University, Houston, TX, USA
| | - William Ott
- Department of Mathematics, University of Houston, Houston, TX, USA
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
| |
Collapse
|
44
|
Consortium Growth of Filamentous Fungi and Microalgae: Evaluation of Different Cultivation Strategies to Optimize Cell Harvesting and Lipid Accumulation. ENERGIES 2020. [DOI: 10.3390/en13143648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study aims to evaluate the potential of consortium biomass formation between Mucor circinelloides, an oleaginous filamentous fungal species, and Chlorella vulgaris, in order to promote a straightforward approach to harvest microalgal cells and to evaluate the lipid production in the consortium system. A synthetic medium with glucose (2 g·L−1) and mineral nutrients essential for both fungi and algae was selected. Four different inoculation strategies were assessed, considering the effect of simultaneous vs. separate development of fungal spores and algae cells, and the presence of a supporting matrix aiming at the higher recovery of algae cell rates. The results were evaluated in terms of consortium biomass composition, demonstrating that the strategy using a mature fungal mycelium with a higher algae count may provide biomass samples with up to 79% of their dry weight as algae, still promoting recovery rates greater than 97%. The findings demonstrate a synergistic effect on the lipid accumulation by the fungal strain, at around a fourfold increase when compared to the axenic control, with values in the range of 23% of dry biomass weight. Furthermore, the fatty acid profile from the samples presents a balance between saturated and unsaturated fatty acids that is likely to present an adequate balance for applications such as biodiesel production.
Collapse
|
45
|
Liang L, Liu R, Freed EF, Eckert CA. Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2-C6 Bioalcohol Production. Front Bioeng Biotechnol 2020; 8:710. [PMID: 32719784 PMCID: PMC7347752 DOI: 10.3389/fbioe.2020.00710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022] Open
Abstract
Biofuel production from renewable and sustainable resources is playing an increasingly important role within the fuel industry. Among biofuels, bioethanol has been most widely used as an additive for gasoline. Higher alcohols can be blended at a higher volume compared to ethanol and generate lower greenhouse gas (GHG) emissions without a need to change current fuel infrastructures. Thus, these fuels have the potential to replace fossil fuels in support of more environmentally friendly processes. This review summarizes the efforts to enhance bioalcohol production in engineered Escherichia coli over the last 5 years and analyzes the current challenges for increasing productivities for industrial applications.
Collapse
Affiliation(s)
- Liya Liang
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| |
Collapse
|
46
|
Decoding social behaviors in a glycerol dependent bacterial consortium during Reactive Blue 28 degradation. Braz J Microbiol 2020; 51:1837-1851. [PMID: 32483666 DOI: 10.1007/s42770-020-00303-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/18/2020] [Indexed: 10/24/2022] Open
Abstract
Biodegradation of reactive azo dyes has been an arduous problem for decades. Several efficient biosystems have been proposed for dye degradation, but most of them are dependent on the availability of costly co-substrates such as peptone, yeast extract, and/or glucose. The present study describes the azo dye degradation by a bacterial consortium using glycerol as a sole co-substrate. The consortium was developed from a mixed bacterial culture obtained upon enrichment of soil sediment for Reactive Blue 28 (RB28) decolorization in the presence of glycerol (0.1%; v/v). The consortium with three bacterial species, i.e., Stenotrophomonas acidaminiphila APG1, Cellulomonas sp. APG4, and Pseudomonas stutzeri APG2, designated as "SCP," decolorized 92% of 100 ppm dye in 96 h. The intricacies of the interactions existing within the members of the consortium were resolved by a simple and unique analysis called "BSocial." Among all the members, Cellulomonas sp. APG4 exerted a net-positive impact for decolorization (%) on the consortium. The net fitness of the community increased when all the three species were present, and thus, all of them were selected for further analysis. Moreover, APG4 seemed to be central in the reductive decolorization as it possessed the highest reductase activity. The dye degradation by the consortium was demonstrated by UV-Visible spectroscopy, HPTLC, and FTIR spectroscopy of control and decolorized cell-free supernatant. The LC-ESI-MS analysis of metabolites extracted from decolorized cell-free medium led to the identification of degradation products, thus leading us to propose the plausible pathway for degradation of RB28 by bacterial consortium.
Collapse
|
47
|
Whitehead TA, Banta S, Bentley WE, Betenbaugh MJ, Chan C, Clark DS, Hoesli CA, Jewett MC, Junker B, Koffas M, Kshirsagar R, Lewis A, Li CT, Maranas C, Terry Papoutsakis E, Prather KLJ, Schaffer S, Segatori L, Wheeldon I. The importance and future of biochemical engineering. Biotechnol Bioeng 2020; 117:2305-2318. [PMID: 32343367 DOI: 10.1002/bit.27364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023]
Abstract
Today's Biochemical Engineer may contribute to advances in a wide range of technical areas. The recent Biochemical and Molecular Engineering XXI conference focused on "The Next Generation of Biochemical and Molecular Engineering: The role of emerging technologies in tomorrow's products and processes". On the basis of topical discussions at this conference, this perspective synthesizes one vision on where investment in research areas is needed for biotechnology to continue contributing to some of the world's grand challenges.
Collapse
Affiliation(s)
- Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California
| | - Corinne A Hoesli
- Department of Chemical Engineering & Department of Biological and Biomedical Engineering, McGill University, Montreal, Québec, Canada
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois
| | - Beth Junker
- BioProcess Advantage LLC, Middesex, New Jersey
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | | | | | - Chien-Ting Li
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - E Terry Papoutsakis
- Department of Chemical & Biomolecular Engineering & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Laura Segatori
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, California
| |
Collapse
|
48
|
Qian X, Chen L, Sui Y, Chen C, Zhang W, Zhou J, Dong W, Jiang M, Xin F, Ochsenreither K. Biotechnological potential and applications of microbial consortia. Biotechnol Adv 2020; 40:107500. [DOI: 10.1016/j.biotechadv.2019.107500] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
|
49
|
Mauri M, Gouzé JL, de Jong H, Cinquemani E. Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs. PLoS Comput Biol 2020; 16:e1007795. [PMID: 32282794 PMCID: PMC7179936 DOI: 10.1371/journal.pcbi.1007795] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/23/2020] [Accepted: 03/18/2020] [Indexed: 01/20/2023] Open
Abstract
Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A first E. coli strain, producing a heterologous protein, is sided by a second E. coli strain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species. In nature, microorganisms occur in communities comprising a variety of mutually interacting species. Established through evolution, these interactions allow for the survival and growth of microorganisms in their natural environment, and give rise to complex dynamics that could not be exhibited by any of the species in isolation. The richness of microbial community dynamics has been leveraged to outperform individual species in biotechnological production processes and other processes of high societal value. Yet, in view of their complexity, natural communities are difficult to study and control. In order to overcome these issues, a rapidly growing research field concerns the rational design and engineering of synthetic microbial consortia. Despite the great potential of synthetic microbial consortia, and significant efforts devoted to their mathematical modelling and analysis, a detailed understanding of how enhanced production can be achieved, and at what cost, is still unavailable. In this work, based on a quantitative model of a prototypical synthetic microbial consortium, we determine precise conditions under which a consortium outperforms individual species in the production of a recombinant protein. Moreover, we identify the inherent trade-offs between productivity and efficiency of substrate utilization.
Collapse
Affiliation(s)
- Marco Mauri
- Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
| | - Jean-Luc Gouzé
- University Côte d’Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, 06902 Sophia-Antipolis, France
| | - Hidde de Jong
- Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
- * E-mail: (HdJ); (EC)
| | - Eugenio Cinquemani
- Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
- * E-mail: (HdJ); (EC)
| |
Collapse
|
50
|
Wen Z, Ledesma‐Amaro R, Lu M, Jiang Y, Gao S, Jin M, Yang S. Combined evolutionary engineering and genetic manipulation improve low pH tolerance and butanol production in a synthetic microbial
Clostridium
community. Biotechnol Bioeng 2020; 117:2008-2022. [DOI: 10.1002/bit.27333] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/14/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology Nanjing China
| | | | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology Nanjing China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological SciencesChinese Academy of Sciences Zhejiang China
- Shanghai TaoYuSheng Biotechnology Co., Ltd. Shanghai China
| | - Shuliang Gao
- Zhejiang Huarui Biotechnology Co., Ltd. Zhejiang China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology Nanjing China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological SciencesChinese Academy of Sciences Zhejiang China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of Sciences Shanghai China
| |
Collapse
|