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Abstract
Kiwifruit is purchased by consumers worldwide and is increasing in demand. Unfortunately, kiwifruit is susceptible to postharvest decay caused by a variety of fungal pathogens, including Botrytis cinerea, Penicillium expansum, Alternaria alternata, Botryosphaeria dothidea, and Diaporthe spp. Among these pathogens, B. cinerea is the most prevalent and devastating. Infections by these fungal pathogens result in a deterioration in fruit quality and a reduction in marketable yield. Eco-friendly methods to control kiwifruit postharvest decay have been explored as alternatives to the use of synthetic fungicides. In this review, we provide an overview and discuss the virulence and pathogenesis of fungi that are causal agents of kiwifruit decay, especially B. cinerea, including recent molecular and genomic studies. Advances in pre- and postharvest measures for postharvest decay management, including biological control, physical applications, the use of natural compounds and plant hormones, and the use of combined methods, are also reviewed. Eco-friendly control measures are a critical component of an integrated management approach for sustainable production of kiwifruit. The need for further research on the use of microbial consortia for the management of postharvest diseases of kiwifruit is also discussed.
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Affiliation(s)
- Yuan Dai
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jinsong Leng
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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52
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Kapoore RV, Padmaperuma G, Maneein S, Vaidyanathan S. Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing. Crit Rev Biotechnol 2021; 42:46-72. [PMID: 33980092 DOI: 10.1080/07388551.2021.1921691] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The application of microbial co-cultures is now recognized in the fields of biotechnology, ecology, and medicine. Understanding the biological interactions that govern the association of microorganisms would shape the way in which artificial/synthetic co-cultures or consortia are developed. The ability to accurately predict and control cell-to-cell interactions fully would be a significant enabler in synthetic biology. Co-culturing method development holds the key to strategically engineer environments in which the co-cultured microorganism can be monitored. Various approaches have been employed which aim to emulate the natural environment and gain access to the untapped natural resources emerging from cross-talk between partners. Amongst these methods are the use of a communal liquid medium for growth, use of a solid-liquid interface, membrane separation, spatial separation, and use of microfluidics systems. Maximizing the information content of interactions monitored is one of the major challenges that needs to be addressed by these designs. This review critically evaluates the significance and drawbacks of the co-culturing approaches used to this day in biotechnological applications, relevant to biomanufacturing. It is recommended that experimental results for a co-cultured species should be validated with different co-culture approaches due to variations in interactions that could exist as a result of the culturing method selected.
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Affiliation(s)
- Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Gloria Padmaperuma
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Supattra Maneein
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Pharmaceutical, Chemical & Environmental Sciences, The University of Greenwich, Kent, UK
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53
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Shahrtash M, Brown SP. A Path Forward: Promoting Microbial-Based Methods in the Control of Invasive Plant Species. Plants (Basel) 2021; 10:943. [PMID: 34065068 PMCID: PMC8151036 DOI: 10.3390/plants10050943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 01/18/2023]
Abstract
In this review, we discuss the unrealized potential of incorporating plant-microbe and microbe-microbe interactions into invasive plant management strategies. While the development of this as a viable strategy is in its infancy, we argue that incorporation of microbial components into management plans should be a priority and has great potential for diversifying sustainable control options. We advocate for increased research into microbial-mediated phytochemical production, microbial controls to reduce the competitiveness of invasive plants, microbial-mediated increases of herbicidal tolerance of native plants, and to facilitate increased pathogenicity of plant pathogens of invasive plants.
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Affiliation(s)
| | - Shawn P. Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN 38152, USA;
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54
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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55
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Petch JE, Gurnani P, Yilmaz G, Mastrotto F, Alexander C, Heeb S, Cámara M, Mantovani G. Combining Inducible Lectin Expression and Magnetic Glyconanoparticles for the Selective Isolation of Bacteria from Mixed Populations. ACS Appl Mater Interfaces 2021; 13:19230-19243. [PMID: 33852268 DOI: 10.1021/acsami.1c00907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial bioreactors. Selective isolation techniques are generally limited to the confinement of small populations in defined locations, may be unable to target specific bacteria, or rely on immunomagnetic separation, which is not universally applicable. In this proof-of-concept work, we describe a novel strategy combining inducible bacterial lectin expression with magnetic glyconanoparticles (MGNPs) as a platform technology to enable selective bacterial isolation from cocultures. An inducible mutant of the type 1 fimbriae, displaying the mannose-specific lectin FimH, was constructed in Escherichia coli allowing for "on-demand" glycan-binding protein presentation following external chemical stimulation. Binding to glycopolymers was only observed upon fimbrial induction and was specific for mannosylated materials. A library of MGNPs was produced via the grafting of well-defined catechol-terminal glycopolymers prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization to magnetic nanoparticles. Thermal analysis revealed high functionalization (≥85% polymer by weight). Delivery of MGNPs to cocultures of fluorescently labeled bacteria followed by magnetic extraction resulted in efficient depletion of type 1 fimbriated target cells from wild-type or afimbriate E. coli. Extraction efficiency was found to be dependent on the molecular weight of the glycopolymers utilized to engineer the nanoparticles, with MGNPs decorated with shorter Dopa-(ManAA)50 mannosylated glycopolymers found to perform better than those assembled from a longer Dopa-(ManAA)200 analogue. The extraction efficiency of fimbriated E. coli was also improved when the counterpart strain did not harbor the genetic apparatus for the expression of the type 1 fimbriae. Overall, this work suggests that the modulation of the genetic apparatus encoding bacterial surface-associated lectins coupled with capture through MGNPs could be a versatile tool for the extraction of bacteria from mixed populations.
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Affiliation(s)
- Joshua E Petch
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Pratik Gurnani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Gokhan Yilmaz
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Cameron Alexander
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Stephan Heeb
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Miguel Cámara
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Giuseppe Mantovani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
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56
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Baleeiro FCF, Kleinsteuber S, Sträuber H. Hydrogen as a Co-electron Donor for Chain Elongation With Complex Communities. Front Bioeng Biotechnol 2021; 9:650631. [PMID: 33898406 PMCID: PMC8059637 DOI: 10.3389/fbioe.2021.650631] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Electron donor scarcity is seen as one of the major issues limiting economic production of medium-chain carboxylates from waste streams. Previous studies suggest that co-fermentation of hydrogen in microbial communities that realize chain elongation relieves this limitation. To better understand how hydrogen co-feeding can support chain elongation, we enriched three different microbial communities from anaerobic reactors (A, B, and C with ascending levels of diversity) for their ability to produce medium-chain carboxylates from conventional electron donors (lactate or ethanol) or from hydrogen. In the presence of abundant acetate and CO2, the effects of different abiotic parameters (pH values in acidic to neutral range, initial acetate concentration, and presence of chemical methanogenesis inhibitors) were tested along with the enrichment. The presence of hydrogen facilitated production of butyrate by all communities and improved production of i-butyrate and caproate by the two most diverse communities (B and C), accompanied by consumption of acetate, hydrogen, and lactate/ethanol (when available). Under optimal conditions, hydrogen increased the selectivity of conventional electron donors to caproate from 0.23 ± 0.01 mol e-/mol e- to 0.67 ± 0.15 mol e-/mol e- with a peak caproate concentration of 4.0 g L-1. As a trade-off, the best-performing communities also showed hydrogenotrophic methanogenesis activity by Methanobacterium even at high concentrations of undissociated acetic acid of 2.9 g L-1 and at low pH of 4.8. According to 16S rRNA amplicon sequencing, the suspected caproate producers were assigned to the family Anaerovoracaceae (Peptostreptococcales) and the genera Megasphaera (99.8% similarity to M. elsdenii), Caproiciproducens, and Clostridium sensu stricto 12 (97-100% similarity to C. luticellarii). Non-methanogenic hydrogen consumption correlated to the abundance of Clostridium sensu stricto 12 taxa (p < 0.01). If a robust methanogenesis inhibition strategy can be found, hydrogen co-feeding along with conventional electron donors can greatly improve selectivity to caproate in complex communities. The lessons learned can help design continuous hydrogen-aided chain elongation bioprocesses.
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Affiliation(s)
- Flávio C F Baleeiro
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Technical Biology, Institute of Process Engineering in Life Science II, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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57
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Foster C, Charubin K, Papoutsakis ET, Maranas CD. Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture. mSystems 2021; 6:e01325-20. [PMID: 33622858 DOI: 10.1128/mSystems.01325-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum-evolved H2 and through acquisition of C. acetobutylicum-native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community.IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum/C. ljungdahlii culture is a novel observation that has not been explored in silico The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.
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58
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Tabacchioni S, Passato S, Ambrosino P, Huang L, Caldara M, Cantale C, Hett J, Del Fiore A, Fiore A, Schlüter A, Sczyrba A, Maestri E, Marmiroli N, Neuhoff D, Nesme J, Sørensen SJ, Aprea G, Nobili C, Presenti O, Giovannetti G, Giovannetti C, Pihlanto A, Brunori A, Bevivino A. Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms 2021; 9:426. [PMID: 33669534 DOI: 10.3390/microorganisms9020426] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 01/28/2023] Open
Abstract
A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.
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59
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Noonan AJC, Qiu Y, Ho JCH, Ocampo J, Vreugdenhil KA, Marr RA, Zhao Z, Yoshikuni Y, Hallam SJ. CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli. Synth Biol (Oxf) 2021; 5:ysaa015. [PMID: 33381654 PMCID: PMC7751189 DOI: 10.1093/synbio/ysaa015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/06/2020] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Here, we develop an experimental high-throughput co-culture system to measure and model the relationship between fluorescence and cell abundance, combining chassis-independent recombinase-assisted genome engineering (CRAGE) and whole-cell biosensing with a PemrR-green fluorescent protein (GFP) monoaromatic reporter used in plate-based functional screening. CRAGE was used to construct Escherichia coli EPI300 strains constitutively expressing red fluorescent protein (RFP) and the relationship between RFP expression and optical density (OD600) was determined throughout the EPI300 growth cycle. A linear equation describing the increase of normalized RFP fluorescence during deceleration phase was derived and used to predict biosensor strain dynamics in co-culture. Measured and predicted values were compared using flow cytometric detection methods. Induction of the biosensor lead to increased GFP fluorescence normalized to biosensor cell abundance, as expected, but a significant decrease in relative abundance of the biosensor strain in co-culture and a decrease in bulk GFP fluorescence. Taken together, these results highlight sensitivity of population dynamics to variations in metabolic activity in co-culture and the potential effect of these dynamics on the performance of functional screens in plate-based formats. The engineered strains and model used to evaluate these dynamics provide a framework for optimizing growth of synthetic co-cultures used in screening, testing and pathway engineering applications.
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Affiliation(s)
- Avery J C Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yilin Qiu
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joe C H Ho
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jewel Ocampo
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - K A Vreugdenhil
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - R Alexander Marr
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Hallam
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Ray P, Lakshmanan V, Labbé JL, Craven KD. Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Front Microbiol 2020; 11:622926. [PMID: 33408712 PMCID: PMC7779556 DOI: 10.3389/fmicb.2020.622926] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.
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Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK, United States
| | | | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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61
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Banderas A, Le Bec M, Cordier C, Hersen P. Autonomous and Assisted Control for Synthetic Microbiology. Int J Mol Sci 2020; 21:E9223. [PMID: 33287299 DOI: 10.3390/ijms21239223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
The control of microbes and microbial consortia to achieve specific functions requires synthetic circuits that can reliably cope with internal and external perturbations. Circuits that naturally evolved to regulate biological functions are frequently robust to alterations in their parameters. As the complexity of synthetic circuits increases, synthetic biologists need to implement such robust control "by design". This is especially true for intercellular signaling circuits for synthetic consortia, where robustness is highly desirable, but its mechanisms remain unclear. Cybergenetics, the interface between synthetic biology and control theory, offers two approaches to this challenge: external (computer-aided) and internal (autonomous) control. Here, we review natural and synthetic microbial systems with robustness, and outline experimental approaches to implement such robust control in microbial consortia through population-level cybergenetics. We propose that harnessing natural intercellular circuit topologies with robust evolved functions can help to achieve similar robust control in synthetic intercellular circuits. A "hybrid biology" approach, where robust synthetic microbes interact with natural consortia and-additionally-with external computers, could become a useful tool for health and environmental applications.
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62
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Li Y, Chen X, Shu G, Ma W. Screening of gamma-aminobutyric acid-producing lactic acid bacteria and its application in Monascus-fermented rice production. Acta Sci Pol Technol Aliment 2020; 19:387-394. [PMID: 33179479 DOI: 10.17306/j.afs.0868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Gamma-aminobutyric acid (GABA), with an antidepressant effect, and Monacolin K, with a cholesterol-lowering effect, are the main bioactive ingredients in Monascus-fermented rice (MFR). The simultaneous enrichment of both ingredients can effectively enhance the health benefits of MFR. However, the capacity of Monascus spp. to produce GABA is limited. METHODS Seventeen lactic acid bacteria (LAB) strains were preliminarily screened for GABA-producing by whole-cells bioconversion of L-glutamate, followed by rescreening through fermentation with the addition of the precursor L-glutamic acid. Subsequently, the bioconversion conditions (temperature, metal ions, and pH) for the conversion of L-monosodium glutamate (MSG) were investigated. Additionally, the GABA-producing LAB was co-inoculated with a monacolin K producing strain Monascus anka 20-2, and the ratio of M. anka 20-2 to LAB in microbial consortia was optimized for MFR production. RESULTS The strain Lactobacillus plantarum 8014 was screened out for its ability to produce GABA. At an optimal temperature of 33°C and pH 7.5, with the addition of 0.05 g/L ZnSO4, the strain showed an L-glutamate conversion rate of 100%. The ratio optimization of M. anka 20-2 to L. plantarum 8014 in microbial consortia showed that when the dry cell ratio was 2:1, the content of monacolin K and GABA in the MFR simultaneously reached 2.22 mg/g and 29.9 mg/g, respectively. CONCLUSIONS A two-stage fermentation using microbial consortia containing M. anka 20-2 and L. plantarum 8014 was developed for the production of bioactive MFR, in which the active ingredients monacolin K and GABA were simultaneously enriched, with good consumer acceptability due to the aromatic scent produced by lactic acid bacteria.
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Affiliation(s)
- Yijing Li
- Sweet Cherry Technology Innovation Center of Gansu Province, Tianshui Engineering Research Center for Agricultural Products, Deep Processing, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Xia Chen
- Sweet Cherry Technology Innovation Center of Gansu Province, Tianshui Engineering Research Center for Agricultural Products, Deep Processing, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Guowei Shu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Weichao Ma
- Sweet Cherry Technology Innovation Center of Gansu Province, Tianshui Engineering Research Center for Agricultural Products, Deep Processing, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
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63
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Xu P. Dynamics of microbial competition, commensalism, and cooperation and its implications for coculture and microbiome engineering. Biotechnol Bioeng 2020; 118:199-209. [PMID: 32915459 PMCID: PMC7821011 DOI: 10.1002/bit.27562] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022]
Abstract
Microbial consortium is a complex adaptive system with higher‐order dynamic characteristics that are not present by individual members. To accurately predict the social interactions, we formulate a set of unstructured kinetic models to quantitatively capture the dynamic interactions of multiple microbial species. By introducing an interaction coefficient, we analytically derived the steady‐state solutions for the interacting species and the substrate‐depleting profile in the chemostat. We analyzed the stability of the possible coexisting states defined by competition, parasitism, amensalism, commensalism, and cooperation. Our model predicts that only parasitism, commensalism, and cooperation could lead to stable coexisting states. We also determined the optimal social interaction criteria of microbial coculture when sequential metabolic reactions are compartmentalized into two distinct species. Coupled with Luedeking–Piret and Michaelis–Menten equations, accumulation of metabolic intermediates in one species and formation of end‐product in another species could be derived and assessed. We discovered that parasitism consortia disfavor the bioconversion of intermediate to final product; and commensalism consortia could efficiently convert metabolic intermediates to final product and maintain metabolic homeostasis with a broad range of operational conditions (i.e., dilution rates); whereas cooperative consortia leads to highly nonlinear pattern of precursor accumulation and end‐product formation. The underlying dynamics and emergent properties of microbial consortia may provide critical knowledge for us to understand ecological coexisting states, engineer efficient bioconversion process, deliver effective gut therapeutics as well as elucidate probiotic‐pathogen or tumor‐host interactions in general.
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Affiliation(s)
- Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
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64
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Kowalska J, Tyburski J, Matysiak K, Tylkowski B, Malusá E. Field Exploitation of Multiple Functions of Beneficial Microorganisms for Plant Nutrition and Protection: Real Possibility or Just a Hope? Front Microbiol 2020; 11:1904. [PMID: 32849475 PMCID: PMC7419637 DOI: 10.3389/fmicb.2020.01904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/20/2020] [Indexed: 02/01/2023] Open
Abstract
Bioproducts, i.e., microbial based pesticides or fertilizers (biopesticides and biofertilizers), should be expected to play an ever-increasing role and application in agricultural practices world-wide in the effort to implement policies concerned with sustainable agriculture. However, several microbial strains have proven the capacity to augment plant productivity by enhancing crop nutrition and functioning as biopesticides, or vice-versa. This multifunctionality is an issue that is still not included as a concept and possibility in any legal provision regarding the placing on the market of bioproducts, and indicates difficulties in clearly classifying the purpose of their suitability. In this review, we overview the current understanding of the mechanisms in plant-microbe interactions underlining the dual function of microbial strains toward plant nutrition and protection. The prospects of market development for multifunctional bioproducts are then considered in view of the current regulatory approach in the European Union, in an effort that wants to stimulate a wider adoption of the new knowledge on the role played by microorganisms in crop production.
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Affiliation(s)
| | - Józef Tyburski
- Department of Agroecosystems, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | | | | | - Eligio Malusá
- Research Institute of Horticulture, Skierniewice, Poland
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Karkaria BD, Treloar NJ, Barnes CP, Fedorec AJH. From Microbial Communities to Distributed Computing Systems. Front Bioeng Biotechnol 2020; 8:834. [PMID: 32793576 PMCID: PMC7387671 DOI: 10.3389/fbioe.2020.00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
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Affiliation(s)
- Behzad D. Karkaria
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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Zavala-Díaz de la Serna FJ, Contreras-López R, Lerma-Torres LP, Ruiz-Terán F, Rocha-Gutiérrez BA, Pérez-Vega SB, Elías-Ogaz LR, Salmerón I. Understanding the Biosynthetic Changes that Give Origin to the Distinctive Flavor of Sotol: Microbial Identification and Analysis of the Volatile Metabolites Profiles During Sotol ( Dasylirion sp.) Must Fermentation. Biomolecules 2020; 10:E1063. [PMID: 32708695 DOI: 10.3390/biom10071063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/02/2022] Open
Abstract
In northern Mexico, the distilled spirit sotol with a denomination of origin is made from species of Dasylirion. The configuration of the volatile metabolites produced during the spontaneous fermentation of Dasylirion sp. must is insufficiently understood. In this study, the aim was to investigate the composition of the microbial consortia, describe the variation of volatile metabolites, and relate such profiles with their particular flavor attributes during the fermentation of sotol (Dasylirion sp.) must. Ascomycota was the phylum of most strains identified with 75% of total abundance. The genus of fermenting yeasts constituted of 101 Pichia strains and 13 Saccharomyces strains. A total of 57 volatile metabolites were identified and grouped into ten classes. The first stage of fermentation was composed of diesel, green, fruity, and cheesy attributes due to butyl 2-methylpropanoate, octan-1-ol, ethyl octanoate, and butanal, respectively, followed by a variation to pungent and sweet descriptors due to 3-methylbutan-1-ol and butyl 2-methylpropanoate. The final stage was described by floral, ethereal-winey, and vinegar attributes related to ethyl ethanimidate, 2-methylpropan-1-ol, and 2-hydroxyacetic acid. Our results improve the knowledge of the variations of volatile metabolites during the fermentation of sotol must and their contribution to its distinctive flavor.
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Vinale F, Sivasithamparam K. Beneficial effects of Trichoderma secondary metabolites on crops. Phytother Res 2020; 34:2835-2842. [PMID: 32578292 DOI: 10.1002/ptr.6728] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022]
Abstract
Selected microbial strains used as active ingredients of biopesticides for agricultural management practices (e.g., IPM, Integrated Pest Management) are known for their ability to control phytopathogens, promote plant growth, and/or induce disease resistance. Microbes belonging to the Trichoderma genus are considered as an appropriate example of beneficial microbes and are model organisms to study plant-microbe interactions. Several Trichoderma strains are marketed as biocontrol agents and are known to increase plant growth, stress tolerance, and nutrient availability. These effects have sometimes been related to the production of effector metabolites that beneficial microbes produce during the interaction with plant and other microbes. Secondary metabolites (SMs) comprise different classes of natural compounds with low molecular weight and having numerous biological roles, especially in the interactions among organisms. Metabolomic analysis of the interactions between plants, phytopathogens, and beneficial fungi aided in the identification of several bioactive fungal SMs that positively affect plant metabolism. Some of these compounds showed direct activity against phytopathogens, but also increased disease resistance by triggering the plant defence system, and/or enhanced vegetative growth. A new generation of bioformulations based on microbial metabolites and living consortia responsible for the desired beneficial effects on crops may overcome the difficulties associated with the use of a single living microbial strain.
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Affiliation(s)
- Francesco Vinale
- Department of Veterinary Medicine and Animal Production, University of Naples 'Federico II', Naples, Italy.,CNR Institute for Sustainable Plant Protection, Portici, Italy
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68
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Altermann E, Hickey WJ. Grand Challenges in Microbiotechnology: Through the Prism of Microbiotechnology. Front Microbiol 2020; 11:430. [PMID: 32265872 PMCID: PMC7099634 DOI: 10.3389/fmicb.2020.00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
- Eric Altermann
- AgResearch, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - William J Hickey
- Department of Soil Science, University of Wisconsin, Madison, WI, United States
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Tusher TR, Shimizu T, Inoue C, Chien MF. Enrichment and Analysis of Stable 1,4-dioxane-Degrading Microbial Consortia Consisting of Novel Dioxane-Degraders. Microorganisms 2019; 8:microorganisms8010050. [PMID: 31881778 PMCID: PMC7022751 DOI: 10.3390/microorganisms8010050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 12/11/2022] Open
Abstract
Biodegradation of 1,4-dioxane, a water contaminant of emerging concern, has drawn substantial attention over the last two decades. A number of dioxane-degraders have been identified, though many of them are unable to metabolically utilize 1,4-dioxane. Moreover, it is considered more preferable to use microbial consortia rather than the pure strains, especially in conventional bioreactors for industrial wastewater treatment. In the present study, a stable 1,4-dioxane-degrading microbial consortium was enriched, namely 112, from industrial wastewater by nitrate mineral salt medium (NMSM). The consortium 112 is capable of utilizing 1,4-dioxane as a sole carbon and energy source, and can completely degrade 1,4-dioxane up to 100 mg/L. From the consortium 112, two 1,4-dioxane-degrading bacterial strains were isolated and identified, in which the Variovorax sp. TS13 was found to be a novel 1,4-dioxane-degrader that can utilize 100 mg/L of 1,4-dioxane. The efficacy of the consortium 112 was increased significantly when we cultured the consortium with mineral salt medium (MSM). The new consortium, N112, could utilize 1,4-dioxane at a rate of 1.67 mg/L·h. The results of the ribosomal RNA intergenic spacer analysis (RISA) depicted that changes in the microbial community structure of consortium 112 was the reason behind the improved degradation efficiency of consortium N112, which was exhibited as a stable and effective microbial consortium with a high potential for bioremediation of the dioxane-impacted sites and contaminated industrial wastewater.
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70
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Singh R, Ryu J, Kim SW. Microbial consortia including methanotrophs: some benefits of living together. J Microbiol 2019; 57:939-952. [PMID: 31659683 DOI: 10.1007/s12275-019-9328-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/30/2019] [Accepted: 09/25/2019] [Indexed: 01/13/2023]
Abstract
With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph-heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with co-cultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.
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Affiliation(s)
- Rajendra Singh
- Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea
| | - Jaewon Ryu
- Department of Energy Convergence, Chosun University, Gwangju, 61452, Republic of Korea
| | - Si Wouk Kim
- Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea. .,Department of Energy Convergence, Chosun University, Gwangju, 61452, Republic of Korea.
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71
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Wang S, Zhang T, Bao M, Su H, Xu P. Microbial Production of Hydrogen by Mixed Culture Technologies: A Review. Biotechnol J 2019; 15:e1900297. [PMID: 31556225 DOI: 10.1002/biot.201900297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/05/2019] [Indexed: 12/18/2022]
Abstract
With its high energy content and clean combustion, hydrogen is recognized as a renewable clean energy source with enormous potential. Biological hydrogen production is a promising alternative with significant advantages over conventional petroleum-derived chemical processes. Sustainable hydrogen production from renewable resources such as cassava, wastewater, and other agricultural waste is economically feasible for industrial applications. So far, the major bottlenecks in large-scale biological hydrogen production are the low production rate and yield. This review discusses the various factors that affect the metabolic pathways of dark hydrogen production, and highlights the state-of-the-art development of mixed culture technology. The aim of this review is to provide suggestions for the future directions of mixed culture technology, as well as by-product valorization in dark fermentation.
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Affiliation(s)
- Shaojie Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Ting Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Meidan Bao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Haijia Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
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72
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Gilmore SP, Lankiewicz TS, Wilken SE, Brown JL, Sexton JA, Henske JK, Theodorou MK, Valentine DL, O’Malley MA. Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation. ACS Synth Biol 2019; 8:2174-2185. [PMID: 31461261 DOI: 10.1021/acssynbio.9b00271] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.
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Affiliation(s)
- Sean P. Gilmore
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - St. Elmo Wilken
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jennifer L. Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - John K. Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael K. Theodorou
- Harper Adams University, Agriculture Centre for Sustainable Energy Systems, Newport, Shropshire TF10 8NB, United Kingdom
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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73
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Alnahhas RN, Winkle JJ, Hirning AJ, Karamched B, Ott W, Josić K, Bennett MR. Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices. ACS Synth Biol 2019; 8:2051-2058. [PMID: 31361464 PMCID: PMC6754295 DOI: 10.1021/acssynbio.9b00146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell-cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia cocultured in microfluidic devices. To do this, we grew two different strains of Escherichia coli in microfluidic devices with cell-trapping regions (traps) of several different designs. We found that the size of the traps is a critical determinant of spatiotemporal dynamics. In small traps, cells can easily signal one another, but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by increasing the initial seeding of cells in larger traps. We also built a mathematical model, which suggests that increasing the number of seed cells can also increase the strain ratio variability due to an increased number of strain interfaces in the trap. These results help elucidate the complex behaviors of synthetic microbial consortia in microfluidic traps and provide a means of analysis to help remedy the spatial heterogeneity inherent to different trap types.
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Affiliation(s)
- Razan N Alnahhas
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - James J Winkle
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Andrew J Hirning
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Bhargav Karamched
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - William Ott
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - Krešimir Josić
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- 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
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Truskewycz A, Gundry TD, Khudur LS, Kolobaric A, Taha M, Aburto-Medina A, Ball AS, Shahsavari E. Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems-Fate and Microbial Responses. Molecules 2019; 24:molecules24183400. [PMID: 31546774 PMCID: PMC6767264 DOI: 10.3390/molecules24183400] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
Petroleum hydrocarbons represent the most frequent environmental contaminant. The introduction of petroleum hydrocarbons into a pristine environment immediately changes the nature of that environment, resulting in reduced ecosystem functionality. Natural attenuation represents the single, most important biological process which removes petroleum hydrocarbons from the environment. It is a process where microorganisms present at the site degrade the organic contaminants without the input of external bioremediation enhancers (i.e., electron donors, electron acceptors, other microorganisms or nutrients). So successful is this natural attenuation process that in environmental biotechnology, bioremediation has developed steadily over the past 50 years based on this natural biodegradation process. Bioremediation is recognized as the most environmentally friendly remediation approach for the removal of petroleum hydrocarbons from an environment as it does not require intensive chemical, mechanical, and costly interventions. However, it is under-utilized as a commercial remediation strategy due to incomplete hydrocarbon catabolism and lengthy remediation times when compared with rival technologies. This review aims to describe the fate of petroleum hydrocarbons in the environment and discuss their interactions with abiotic and biotic components of the environment under both aerobic and anaerobic conditions. Furthermore, the mechanisms for dealing with petroleum hydrocarbon contamination in the environment will be examined. When petroleum hydrocarbons contaminate land, they start to interact with its surrounding, including physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) interactions. As microorganism (including bacteria and fungi) play an important role in the degradation of petroleum hydrocarbons, investigations into the microbial communities within contaminated soils is essential for any bioremediation project. This review highlights the fate of petroleum hydrocarbons in tertial environments, as well as the contributions of different microbial consortia for optimum petroleum hydrocarbon bioremediation potential. The impact of high-throughput metagenomic sequencing in determining the underlying degradation mechanisms is also discussed. This knowledge will aid the development of more efficient, cost-effective commercial bioremediation technologies.
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Affiliation(s)
- Adam Truskewycz
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Taylor D Gundry
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Leadin S Khudur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Adam Kolobaric
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Mohamed Taha
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
- Department of Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Toukh, Qaliuobia 13736, Egypt.
| | - Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
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Wang F, Wang M, Zhao Q, Niu K, Liu S, He D, Liu Y, Xu S, Fang X. Exploring the Relationship Between Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17. Front Microbiol 2019; 10:2035. [PMID: 31551972 PMCID: PMC6746925 DOI: 10.3389/fmicb.2019.02035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Characterizing and engineering microbial communities for lignocellulosic biofuel production has received widespread attention. Previous research has established that Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17 coculture significantly improves overall cellulosic biofuel production efficiency. Here, we investigated this interaction and revealed the mechanism underlying the improved efficiency observed. In contrast to the previously reported mutualistic relationship, a harmful effect toward C. thermocellum JN4 was observed in these microbial consortia. Although T. thermosaccharolyticum GD17 relieves the carbon catabolite repression of C. thermocellum JN4 regarding obtaining more cellobiose or glucose released from lignocellulose, T. thermosaccharolyticum GD17 significantly hampers the growth of C. thermocellum JN4 in coculture. The increased formation of end products is due to the strong competitive metabolic advantage of T. thermosaccharolyticum GD17 over C. thermocellum JN4 in the conversion of glucose or cellobiose into final products. The possibility of controlling and rebalancing these microbial consortia to modulate cellulose degradation was achieved by adding T. thermosaccharolyticum GD17 stimulants into the system. As cellulolytic bacteria are usually at a metabolic disadvantage, these discoveries may apply to a large proportion of cellulosic biofuel-producing microbial consortia. These findings provide a reference for engineering efficient and modular microbial consortia for modulating cellulosic conversion.
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Affiliation(s)
- Fangzhong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shasha Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Didi He
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yan Liu
- College of Life Science, Qufu Normal University, Qufu, China
| | - Shiping Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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76
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Bradáčová K, Sittinger M, Tietz K, Neuhäuser B, Kandeler E, Berger N, Ludewig U, Neumann G. Maize Inoculation with Microbial Consortia: Contrasting Effects on Rhizosphere Activities, Nutrient Acquisition and Early Growth in Different Soils. Microorganisms 2019; 7:microorganisms7090329. [PMID: 31500269 PMCID: PMC6780557 DOI: 10.3390/microorganisms7090329] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 12/18/2022] Open
Abstract
The benefit of plant growth-promoting microorganisms (PGPMs) as plant inoculants is influenced by a wide range of environmental factors. Therefore, microbial consortia products (MCPs) based on multiple PGPM strains with complementary functions, have been proposed as superior, particularly under challenging environmental conditions and for restoration of beneficial microbial communities in disturbed soil environments. To test this hypothesis, the performance of a commercial MCP inoculant based on 22 PGPM strains was investigated in greenhouse experiments with maize on three soils with contrasting pH, organic matter content and microbial activity, under different P and N fertilization regimes. Interestingly, the MCP inoculant stimulated root and shoot growth and improved the acquisition of macronutrients only on a freshly collected field soil with high organic matter content, exclusively in combination with stabilized ammonium fertilization. This was associated with transiently increased expression of AuxIAA5 in the root tissue, a gene responsive to exogenous auxin supply, suggesting root growth promotion by microbial auxin production as a major mode of action of the MCP inoculant. High microbial activity was indicated by intense expression of soil enzyme activities involved in C, N and P cycling in the rhizosphere (cellulase, leucine peptidase, alkaline and acid phosphatases) but without MCP effects. By contrast, the MCP inoculation did not affect maize biomass production or nutrient acquisition on soils with very little Corg and low microbial activity, although moderate stimulation of rhizosphere enzymes involved in N and P cycling was recorded. There was also no indication for MCP-induced solubilization of Ca-phosphates on a calcareous sub-soil fertilized with rock-phosphate. The results demonstrate that the combination of multiple PGPM strains with complementary properties as MCP inoculants does not necessarily translate into plant benefits in challenging environments. Thus, a better understanding of the conditions determining successful MCP application is mandatory.
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Affiliation(s)
- Klára Bradáčová
- Institute of Crop Science (340h), Universität Hohenheim, Fruwirthstraße 20, 70593 Stuttgart, Germany.
| | - Maximilian Sittinger
- Julius Kühn-Institut, Institute for Biological Control, Heinrichstraße 243, 64287 Darmstadt, Germany.
| | - Katharina Tietz
- Institute of Crop Science (340h), Universität Hohenheim, Fruwirthstraße 20, 70593 Stuttgart, Germany.
| | - Benjamin Neuhäuser
- Institute of Crop Science (340h), Universität Hohenheim, Fruwirthstraße 20, 70593 Stuttgart, Germany.
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Department, Universität Hohenheim, Emil-Wolff-Straße 27, 70593 Stuttgart, Germany.
| | | | - Uwe Ludewig
- Institute of Crop Science (340h), Universität Hohenheim, Fruwirthstraße 20, 70593 Stuttgart, Germany.
| | - Günter Neumann
- Institute of Crop Science (340h), Universität Hohenheim, Fruwirthstraße 20, 70593 Stuttgart, Germany.
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77
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Abstract
Synthetic microbial consortia are a rapidly growing area of synthetic biology. So far, most consortia are designed without considering their environments; however, in nature, microbial interactions are constantly modulated by cellular contexts, which, in principle, can dramatically alter community behaviors. Here we present the construction, validation, and characterization of an engineered bacterial predator-prey consortium that involves a chloramphenicol (CM)-mediated, context-dependent cellular interaction. We show that varying the CM level in the environment can induce success in the ecosystem with distinct patterns from predator dominance to prey-predator crossover to ecosystem collapse. A mathematical model successfully captures the essential dynamics of the experimentally observed patterns. We also illustrate that such a dependence enriches community dynamics under different initial conditions and further test the resistance of the consortium to invasion with engineered bacterial strains. This work exemplifies the role of the context dependence of microbial interactions in modulating ecosystem dynamics, underscoring the importance of including contexts into the design of engineered ecosystems for synthetic biology applications.
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Affiliation(s)
- Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Junwen Mao
- Department of Physics, Huzhou University, Huzhou 313000, China
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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78
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Ziesack M, Gibson T, Oliver JKW, Shumaker AM, Hsu BB, Riglar DT, Giessen TW, DiBenedetto NV, Bry L, Way JC, Silver PA, Gerber GK. Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium. mSystems 2019; 4:e00352-19. [PMID: 31409662 PMCID: PMC6697442 DOI: 10.1128/msystems.00352-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/23/2019] [Indexed: 01/15/2023] Open
Abstract
In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.
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Affiliation(s)
- Marika Ziesack
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Travis Gibson
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John K W Oliver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew M Shumaker
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Bryan B Hsu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - David T Riglar
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas V DiBenedetto
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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79
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Burow K, Grawunder A, Harpke M, Pietschmann S, Ehrhardt R, Wagner L, Voigt K, Merten D, Büchel G, Kothe E. Microbiomes in an acidic rock-water cave system. FEMS Microbiol Lett 2019; 366:fnz167. [PMID: 31365079 DOI: 10.1093/femsle/fnz167] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/23/2019] [Indexed: 01/01/2023] Open
Abstract
Belowground ecosystems are accessible by mining, where a specific microbial community can be discovered. The biodiversity of a former alum mine rich in carbon, but with a low pH of 2.6-3.7, was evaluated by DNA- and cultivation-dependent methods using samples of the black slate rock material, secondary mineralization phases and seepage water. Pyrite oxidation within the low-grade metamorphic Silurian black slate established high concentrations of Fe and $\rm{SO}_4^{2-}$ forming the extreme conditions visible with acidophilic and Fe-oxidizing microorganisms. In addition, an unexpected predominance of fungi in this C-rich and acidic cave ecosystem, including high numbers of Mucoromycota and Mortierellomycota, was detected. Therefore, fungal cultures were obtained, mainly from the secondary mineral phases that are iron phosphates. Hence, the fungi might well have been involved in phosphate mobilization there. The rock material itself is rich in organic carbon that can be used by oxidase activity. The cultivation setup mimicked the cave conditions (low temperature, low pH, oxic conditions), with one oligotrophic and one medium rich in nutrients that allowed for isolation of different fungal (and eutrophic bacterial) groups. The acidic conditions prevented the occurrence of many basidiomycetes, while the isolated fungi could survive these adverse conditions.
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Affiliation(s)
- Katja Burow
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, D-07743 Jena, Germany
- Institute for Geosciences, Applied Geology, Friedrich Schiller University Jena, Burgweg 11, D-07749 Jena, Germany
| | - Anja Grawunder
- Institute for Geosciences, Applied Geology, Friedrich Schiller University Jena, Burgweg 11, D-07749 Jena, Germany
| | - Marie Harpke
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, D-07743 Jena, Germany
| | - Sebastian Pietschmann
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, D-07743 Jena, Germany
| | - Ralf Ehrhardt
- Institute for Geosciences, Applied Geology, Friedrich Schiller University Jena, Burgweg 11, D-07749 Jena, Germany
| | - Lysett Wagner
- National Reference Center for Invasive Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Beutenbergstraße 11a, D-07745 Jena, Germany
| | - Kerstin Voigt
- National Reference Center for Invasive Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Beutenbergstraße 11a, D-07745 Jena, Germany
- Jena Microbial Resource Collection, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 24/25, D-07743 Jena, Germany
| | - Dirk Merten
- Institute for Geosciences, Applied Geology, Friedrich Schiller University Jena, Burgweg 11, D-07749 Jena, Germany
| | - Georg Büchel
- Institute for Geosciences, Applied Geology, Friedrich Schiller University Jena, Burgweg 11, D-07749 Jena, Germany
| | - Erika Kothe
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, D-07743 Jena, Germany
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80
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Zegeye EK, Brislawn CJ, Farris Y, Fansler SJ, Hofmockel KS, Jansson JK, Wright AT, Graham EB, Naylor D, McClure RS, Bernstein HC. Selection, Succession, and Stabilization of Soil Microbial Consortia. mSystems 2019; 4:e00055-19. [PMID: 31098394 DOI: 10.1128/mSystems.00055-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/24/2019] [Indexed: 12/25/2022] Open
Abstract
Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.
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81
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Li F, An X, Wu D, Xu J, Chen Y, Li W, Cao Y, Guo X, Lin X, Li C, Liu S, Song H. Engineering Microbial Consortia for High-Performance Cellulosic Hydrolyzates-Fed Microbial Fuel Cells. Front Microbiol 2019; 10:409. [PMID: 30936852 PMCID: PMC6432859 DOI: 10.3389/fmicb.2019.00409] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial fuel cells (MFCs) are eco-friendly bio-electrochemical reactors that use exoelectrogens as biocatalyst for electricity harvest from organic biomass, which could also be used as biosensors for long-term environmental monitoring. Glucose and xylose, as the primary ingredients from cellulose hydrolyzates, is an appealing substrate for MFC. Nevertheless, neither xylose nor glucose can be utilized as carbon source by well-studied exoelectrogens such as Shewanella oneidensis. In this study, to harvest the electricity by rapidly harnessing xylose and glucose from corn stalk hydrolysate, we herein firstly designed glucose and xylose co-fed engineered Klebsiella pneumoniae-S. oneidensis microbial consortium, in which K. pneumoniae as the fermenter converted glucose and xylose into lactate to feed the exoelectrogens (S. oneidensis). To produce more lactate in K. pneumoniae, we eliminated the ethanol and acetate pathway via deleting pta (phosphotransacetylase gene) and adhE (alcohol dehydrogenase gene) and further constructed a synthesis and delivery system through expressing ldhD (lactate dehydrogenase gene) and lldP (lactate transporter gene). To facilitate extracellular electron transfer (EET) of S. oneidensis, a biosynthetic flavins pathway from Bacillus subtilis was expressed in a highly hydrophobic S. oneidensis CP-S1, which not only improved direct-contacted EET via enhancing S. oneidensis adhesion to the carbon electrode but also accelerated the flavins-mediated EET via increasing flavins synthesis. Furthermore, we optimized the ratio of glucose and xylose concentration to provide a stable carbon source supply in MFCs for higher power density. The glucose and xylose co-fed MFC inoculated with the recombinant consortium generated a maximum power density of 104.7 ± 10.0 mW/m2, which was 7.2-folds higher than that of the wild-type consortium (12.7 ± 8.0 mW/m2). Lastly, we used this synthetic microbial consortium in the corn straw hydrolyzates-fed MFC, obtaining a power density 23.5 ± 6.0 mW/m2.
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Affiliation(s)
- Feng Li
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xingjuan An
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Renhuai, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
| | - Jing Xu
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yuanyuan Chen
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Wenchao Li
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yingxiu Cao
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xuewu Guo
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
| | - Xue Lin
- College of Food Science and Technology, Hainan University, Haikou, China
| | - Congfa Li
- College of Food Science and Technology, Hainan University, Haikou, China
| | - Sixin Liu
- College of Food Science and Technology, Hainan University, Haikou, China
| | - Hao Song
- Key Laboratory of Systems Bioengineering (MOE), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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82
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McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
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Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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83
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Wang J, Lu X, Ying H, Ma W, Xu S, Wang X, Chen K, Ouyang P. A Novel Process for Cadaverine Bio-Production Using a Consortium of Two Engineered Escherichia coli. Front Microbiol 2018; 9:1312. [PMID: 29971056 PMCID: PMC6018084 DOI: 10.3389/fmicb.2018.01312] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/29/2018] [Indexed: 01/03/2023] Open
Abstract
Bio-production of cadaverine from cheap carbon sources for synthesizing bio-based polyamides is becoming more common. Here, a novel fermentation process for cadaverine bio-production from glucose was implemented by using a microbial consortium of two engineered Escherichia coli strains to relieve the toxic effect of cadaverine on fermentation efficiency. To achieve controllable growth of strains in the microbial consortium, two engineered E. coli strains grown separately on different carbon sources were first constructed. The strains were, an L-lysine-producing E. coli NT1004 with glucose as carbon source, and a cadaverine-producing E. coli CAD03 with glucose metabolism deficiency generated by modifying the PTSGlc system with CRISPR-Cas9 technology and inactivating cadaverine degradation pathways. Co-culturing these two engineered E. coli strains with a mixture of glucose and glycerol led to successful production of cadaverine. After optimizing cultivation conditions, a cadaverine titer of 28.5 g/L was achieved with a multi-stage constant-speed feeding strategy.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiaolu Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanxiao Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Weichao Ma
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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84
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Abstract
Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.
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Affiliation(s)
- Shashi Kant Bhatia
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
| | - Ravi Kant Bhatia
- c Department of Biotechnology , Himachal Pradesh University , Shimla , India
| | - Yong-Keun Choi
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Eunsung Kan
- d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Yun-Gon Kim
- e Department of Chemical Engineering , Soongsil University , Seoul , South Korea
| | - Yung-Hun Yang
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
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85
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Matyjaszkiewicz A, Fiore G, Annunziata F, Grierson CS, Savery NJ, Marucci L, di Bernardo M. BSim 2.0: An Advanced Agent-Based Cell Simulator. ACS Synth Biol 2017; 6:1969-1972. [PMID: 28585809 DOI: 10.1021/acssynbio.7b00121] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modeling approaches, permitting incorporation of great detail and realism into simulations, allowing in silico tracking of single-cell behaviors and correlation of these with emergent effects at the macroscopic level. In this study we present BSim 2.0, a radically new version of BSim, a computational ABM framework for modeling dynamics of bacteria in typical experimental environments including microfluidic chemostats. This is facilitated through the implementation of new methods including cells with capsular geometry that are able to physically and chemically interact with one another, a realistic model of cellular growth, a delay differential equation solver, and realistic environmental geometries.
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Affiliation(s)
- Antoni Matyjaszkiewicz
- Department of Engineering
Mathematics, University of Bristol, Merchant Venturers’ Building,
Woodland Road, Bristol BS8 1UB, U.K
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
| | - Gianfranco Fiore
- Department of Engineering
Mathematics, University of Bristol, Merchant Venturers’ Building,
Woodland Road, Bristol BS8 1UB, U.K
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
| | - Fabio Annunziata
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Claire S. Grierson
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Nigel J. Savery
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Lucia Marucci
- Department of Engineering
Mathematics, University of Bristol, Merchant Venturers’ Building,
Woodland Road, Bristol BS8 1UB, U.K
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
| | - Mario di Bernardo
- Department of Engineering
Mathematics, University of Bristol, Merchant Venturers’ Building,
Woodland Road, Bristol BS8 1UB, U.K
- BrisSynBio, Life Sciences Building, Tyndall
Avenue, Bristol BS8 1TQ, U.K
- Department
of Electrical Engineering and Information Technology, University of Naples Federico II, 80125 Naples, Italy
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86
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Cortes-Tolalpa L, Salles JF, van Elsas JD. Bacterial Synergism in Lignocellulose Biomass Degradation - Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source. Front Microbiol 2017; 8:1628. [PMID: 29067002 PMCID: PMC5641323 DOI: 10.3389/fmicb.2017.01628] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/10/2017] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass (LCB) is an attractive source of carbon for the production of sugars and other chemicals. Due to its inherent complexity and heterogeneity, efficient biodegradation requires the actions of different types of hydrolytic enzymes. In nature, complex microbial communities that work efficiently and often synergistically accomplish degradation. Studying such synergisms in LCB degradation is fundamental for the establishment of an optimal biological degradation process. Here, we examine the wheat straw degradation potential of synthetic microbial consortia composed of bacteria and fungi. Growth of, and enzyme secretion by, monocultures of degrader strains were studied in aerobic cultures using wheat straw as the sole carbon and energy source. To investigate synergism, co-cultures were constructed from selected strains and their performance was tested in comparison with the respective monocultures. In monoculture, each organism – with a typical enzymatic profile – was found to mainly consume the cellulose part of the substrate. One strain, Flavobacterium ginsengisoli so9, displayed an extremely high degradation capacity, as measured by its secreted enzymes. Among 13 different co-cultures, five presented synergisms. These included four bacterial bicultures and one bacterial–fungal triculture. The highest level of synergism was found in a Citrobacter freundii/Sphingobacterium multivorum biculture, which revealed an 18.2-fold increase of the produced biomass. As compared to both monocultures, this bacterial pair showed significantly increased enzymatic activities, in particular of cellobiohydrolases, mannosidases, and xylosidases. Moreover, the synergism was unique to growth on wheat straw, as it was completely absent in glucose-grown bicultures. Spent supernatants of either of the two partners were found to stimulate the growth on wheat straw of the counterpart organism, in a directional manner. Thus, the basis of the LCB-specific synergism might lie in the specific release of compounds or agents by S. multivorum w15 that promote the activity of C. freundii so4 and vice versa.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana F Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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87
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Xiong JQ, Kurade MB, Jeon BH. Can Microalgae Remove Pharmaceutical Contaminants from Water? Trends Biotechnol 2018; 36:30-44. [PMID: 28993012 DOI: 10.1016/j.tibtech.2017.09.003] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/10/2017] [Accepted: 09/12/2017] [Indexed: 11/23/2022]
Abstract
The increase in worldwide water contamination with numerous pharmaceutical contaminants (PCs) has become an emerging environmental concern due to their considerable ecotoxicities and associated health issues. Microalgae-mediated bioremediation of PCs has recently gained scientific attention, as microalgal bioremediation is a solar-power driven, ecologically comprehensive, and sustainable reclamation strategy. In this review, we comprehensively describe the current research on the possible roles and applications of microalgae for removing PCs from aqueous media. We summarize several novel approaches including constructing microbial consortia, acclimation, and cometabolism for enhanced removal of PCs by microalgae, which would improve practical feasibility of these technologies. Some novel concepts for degrading PCs using integrated processes and genetic modifications to realize algal-based bioremediation technologies are also recommended.
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88
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Abstract
Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we used exometabolite profiling to follow the resource processing by a microbial co-culture of two biotechnologically relevant microbes, the bacterial cellulose degrader Cellulomonas fimi, and the oleaginous yeast Yarrowia lipolytica. We characterized the substrate preferences of the two strains on compounds typically found in lignocellulose hydrolysates. This allowed prediction that specific sugars resulting from hemicellulose polysaccharide degradation by C. fimi may serve as a cross-feeding metabolites to Y. lipolytica in co-culture. We also showed that products of ionic liquid-treated switchgrass lignocellulose degradation by C. fimi were channeled to Y. lipolytica in a co-culture. Additionally, we observed metabolites, such as shikimic acid accumulating in the co-culture supernatants, suggesting the potential for producing interesting co-products. Insights gained from characterizing the exometabolite profiles of individual and co-cultures of the two strains can help to refine this interaction, and guide strategies for making this an industrially viable co-culture to produce valuable products from lignocellulose material.
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Affiliation(s)
- Andrea Lubbe
- Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley 94720, CA, USA.
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley 94720, CA, USA.
| | - Trent Northen
- Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley 94720, CA, USA.
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89
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Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD. Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. Trends Microbiol 2017. [PMID: 28648267 DOI: 10.1016/j.tim.2017.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Francisco Dini-Andreote
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003-9298, USA
| | - Steven W Singer
- Joint BioEnergy Institute,5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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90
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Abstract
The ability to stably and specifically conjugate recombinant proteins to one another is a powerful approach for engineering multifunctional enzymes, protein therapeutics, and novel biological materials. While many of these applications have been illustrated through in vitro and in vivo intracellular protein conjugation methods, extracellular self-assembly of protein conjugates offers unique advantages: simplifying purification, reducing toxicity and burden, and enabling tunability. Exploiting the recently described SpyTag-SpyCatcher system, we describe here how enzymes and structural proteins can be genetically encoded to covalently conjugate in culture media following programmable secretion from Bacillus subtilis. Using this approach, we demonstrate how self-conjugation of a secreted industrial enzyme, XynA, dramatically increases its resilience to boiling, and we show that cellular consortia can be engineered to self-assemble functional protein-protein conjugates with tunable composition. This novel genetically encoded modular system provides a flexible strategy for protein conjugation harnessing the substantial advantages of extracellular self-assembly.
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Affiliation(s)
- Charlie Gilbert
- Centre
for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, U.K
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Colin R. Harwood
- Centre
for Bacterial Cell Biology, Baddiley-Clark Building, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K
| | - Tom Ellis
- Centre
for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, U.K
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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91
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Abstract
The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.
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Affiliation(s)
- Sami Ben Said
- Department of Environmental Systems Science, Soil and Terrestrial Environmental Physics, ETH ZürichZürich, Switzerland
| | - Dani Or
- Department of Environmental Systems Science, Soil and Terrestrial Environmental Physics, ETH ZürichZürich, Switzerland
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92
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Abstract
Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria.
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Affiliation(s)
- Danillo O Alvarenga
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP)Jaboticabal, Brazil.,Centro de Energia Nuclear na Agricultura, Universidade de São Paulo (USP)Piracicaba, Brazil
| | - Marli F Fiore
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo (USP)Piracicaba, Brazil
| | - Alessandro M Varani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP)Jaboticabal, Brazil
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93
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Jiang L, Zhou J, Wang X, Sun Y, Xiu Z. [Progress in chemicals production by microbial consortia]. Sheng Wu Gong Cheng Xue Bao 2016; 32:1496-1506. [PMID: 29034620 DOI: 10.13345/j.cjb.160113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using cheap biomass resources is a hotspot of research on industrial biotechnology. It is difficult for traditional fermentations with single strain to treat so complex components and more impurities, which becomes the key problem in industrialization. In this review, some existing industrial bioprocesses involving microbial consortia were described. Comparison of 1,3-propanediol production by microbial consortia and pure cultures were then introduced and the relationship between cells in microbial consortia were summarized. Finally, the perspective was also addressed to design and apply microbial consortia in the future.
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Affiliation(s)
- Lili Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Jinjie Zhou
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Xudong Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Yaqin Sun
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Zhilong Xiu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, Liaoning, China
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94
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Jeanbille M, Gury J, Duran R, Tronczynski J, Agogué H, Ben Saïd O, Ghiglione JF, Auguet JC. Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats. Front Microbiol 2016; 7:1637. [PMID: 27790213 PMCID: PMC5061854 DOI: 10.3389/fmicb.2016.01637] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.
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Affiliation(s)
- Mathilde Jeanbille
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'Adour Pau, France
| | - Jérôme Gury
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'Adour Pau, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'Adour Pau, France
| | - Jacek Tronczynski
- Laboratoire Biogéochimie des Contaminants Organiques, Unité Biogéochimie et Ecotoxicologie, Département Ressources Biologiques et Environnement, Ifremer Centre Atlantique Nantes, France
| | - Hélène Agogué
- Littoral, Environnement et Sociétés, UMR 7266 Centre National de la Recherche Scientifique - Université de La Rochelle La Rochelle, France
| | - Olfa Ben Saïd
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 Centre National de la Recherche Scientifique - Université de Pau et des Pays de L'AdourPau, France; Laboratoire de Bio-surveillance de l'Environnement, Faculté des Sciences de BizerteZarzouna, Tunisie
| | - Jean-François Ghiglione
- Laboratoire d'Océanographie Microbienne, Sorbonne Universités, UMR 7621, Centre National de la Recherche Scientifique-University Pierre and Marie Curie Banyuls sur mer, France
| | - Jean-Christophe Auguet
- Marine Biodiversity, Exploitation and Conservation, UMR Centre National de la Recherche Scientifique 9190 Montpellier, France
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95
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Abstract
The power of a single engineered organism is limited by its capacity for genetic modification. To circumvent the constraints of any singular microbe, a new frontier in synthetic biology is emerging: synthetic ecology, or the engineering of microbial consortia. Here we develop communication systems for such consortia in an effort to allow for complex social behavior across different members of a community. We posit that such communities will outpace monocultures in their ability to perform complicated tasks if communication among and between members of the community is well regulated. Quorum sensing was identified as the most promising candidate for precise control of engineered microbial ecosystems, due to its large diversity and established utility in synthetic biology. Through promoter and protein modification, we engineered two quorum sensing systems (rpa and tra) to add to the extensively used lux and las systems. By testing the cross-talk between all systems, we thoroughly characterized many new inducible systems for versatile control of engineered communities. Furthermore, we've identified several system pairs that exhibit useful types of orthogonality. Most notably, the tra and rpa systems were shown to have neither signal crosstalk nor promoter crosstalk for each other, making them completely orthogonal in operation. Overall, by characterizing the interactions between all four systems and their components, these circuits should lend themselves to higher-level genetic circuitry for use in microbial consortia.
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Affiliation(s)
- Spencer R. Scott
- Department of Bioengineering, ‡Molecular Biology
Section, Division of Biological
Science, and ¶BioCircuits Institute, University of California, San Diego, La Jolla, California 92093, United States
| | - Jeff Hasty
- Department of Bioengineering, ‡Molecular Biology
Section, Division of Biological
Science, and ¶BioCircuits Institute, University of California, San Diego, La Jolla, California 92093, United States
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96
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Abstract
The intestinal microbiota has long been known to play an important role in the maintenance of health. In addition, alterations of the intestinal microbiota have recently been associated with a range of immune-mediated and metabolic disorders. Characterizing the composition and functionality of the intestinal microbiota, unravelling relevant microbe-host interactions, and identifying disease-relevant microbes are therefore currently of major interest in scientific and medical communities. Experimental animal models for the respective diseases of interest are pivotal in order to address functional questions on microbe-host interaction and to clarify the clinical relevance of microbiome alterations associated with disease initiation and development. This review presents an overview of the outcomes of highly sophisticated experimental studies on microbe-host interaction in animal models of inflammatory diseases, with a focus on inflammatory bowel disease (IBD). We will address the advantages and drawbacks of analyzing microbe-host interaction in complex colonized animal models compared with gnotobiotic animal models using monoassociation, simplified microbial consortia (SMC), or microbial humanization.
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Affiliation(s)
- G Hörmannsperger
- Gabriele Hörmannsperger, PhD, is a molecular biologist researcher, Monika Schaubeck, MSc, is a PhD student, and Dirk Haller, PhD, is full professor and head of the Chair of Nutrition and Immunology at the Technische Universität München, Freising-Weihenstephan, Germany
| | - M Schaubeck
- Gabriele Hörmannsperger, PhD, is a molecular biologist researcher, Monika Schaubeck, MSc, is a PhD student, and Dirk Haller, PhD, is full professor and head of the Chair of Nutrition and Immunology at the Technische Universität München, Freising-Weihenstephan, Germany
| | - D Haller
- Gabriele Hörmannsperger, PhD, is a molecular biologist researcher, Monika Schaubeck, MSc, is a PhD student, and Dirk Haller, PhD, is full professor and head of the Chair of Nutrition and Immunology at the Technische Universität München, Freising-Weihenstephan, Germany
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97
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Abstract
BACKGROUND Discharge of textile dyes into the environment poses a significant threat. They are poorly biodegradable and toxic due to their complex composition and aromatic structures. In the search for alternatives to physical and chemical treatments, biodegradation of synthetic dyes by various microbes is emerging as an effective and promising approach. OBJECTIVES The decolorization of synthetic dyes by yeast co-cultures and consortia from leaves and fruit peels was assessed at a 50 μg/mL dye concentration. METHODS Yeasts isolates from leaves and fruit peels were screened for potential decolorization of synthetic dyes at 25-50 μg/mL. Decolorization parameters were optimized for synergistic properties and development of yeast co-cultures and consortium. Possible decolorization reactions were initially assessed by cell immobilization, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and Fourier transform infrared spectroscopy (FTIR) analysis. RESULTS A total of 16 organisms were isolated from rose, mango, and pineapple leaves and pineapple fruit peels. Only 4 organisms showed high decolorization of four synthetic dyes: Direct Pink B, Disperse Yellow 5G, Direct Fast Orange S, and Reactive Turquoise Blue G. The optimum condition for best decolorizers of selected dyes at 50 μg/mL were Candida guilliermondii (Y011) for Direct Pink B at pH 9, 37°C; C. dubliniensis (Y014) for Disperse Yellow 5G at pH 4, 25°C; C. guilliermondii (Y004) for Direct Fast Orange S at pH 7, 25°C, and C. famata (Y003) for Reactive Turquoise Blue G at pH 4, 35°C. None of the 4 yeast isolates showed any antagonistic activity when subjected to the lawn-spotting method for the formation of co-cultures and consortium. The best co-cultures obtained 61% decolorization of Direct Pink B, 65% decolorization of Disperse Yellow 5G, 41% decolorization of Direct Fast Orange S, and 50-51% decolorization of Reactive Turquoise Blue G. Immobilized yeast cells were active in decolorizing the dyes and SDS-PAGE analysis confirmed the presence of an extracellular protein. The results of FTIR also showed changes in the functional group of Direct Pink B, but minimal changes in the functional groups of Reactive Turquoise Blue G, indicating a different decolorization pathway. CONCLUSIONS Yeasts in co-cultures and consortia can decolorize toxic synthetic dyes through different decolorization pathways such as enzyme degradation and bioaccumulation. This technique may have a use in the treatment of wastewater systems.
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Affiliation(s)
- Anna Christina R. Ngo
- The Graduate School, University of Santo Tomas
- Research Center for the Natural and Applied Sciences, University of Santo Tomas
| | - Mark Kevin P. Devanadera
- The Graduate School, University of Santo Tomas
- Research Center for the Natural and Applied Sciences, University of Santo Tomas
| | - Gina R. Dedeles
- The Graduate School, University of Santo Tomas
- Research Center for the Natural and Applied Sciences, University of Santo Tomas
- Department of Biological Sciences, College of Science, University of Santo Tomas, España, Manila, 1015 Philippines
- Corresponding Author: Gina Rio Dedeles, Laboratory of Pure and Applied Microbiology, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Complex University of Santo Tomas, Manila, 1008 Philippines, Tel. +63-(2)-4061611 loc. 8297,
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98
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Abstract
This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed.
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Affiliation(s)
- Marc Ereshefsky
- Department of Philosophy, University of Calgary, Calgary, AB, Canada T2N 1N4;
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99
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Escalante AE, Rebolleda-Gómez M, Benítez M, Travisano M. Ecological perspectives on synthetic biology: insights from microbial population biology. Front Microbiol 2015; 6:143. [PMID: 25767468 PMCID: PMC4341553 DOI: 10.3389/fmicb.2015.00143] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/07/2015] [Indexed: 11/13/2022] Open
Abstract
The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems.
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Affiliation(s)
- Ana E. Escalante
- Department of Ecology, Evolution and Behavior, University of MinnesotaSt. Paul, MN, USA
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - María Rebolleda-Gómez
- Department of Ecology, Evolution and Behavior, University of MinnesotaSt. Paul, MN, USA
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of MinnesotaSt. Paul, MN, USA
- BioTechnology Institute, University of MinnesotaSt. Paul, MN, USA
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Abstract
Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions.
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Affiliation(s)
- Lisa Goers
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Paul Freemont
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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