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Kim YJ, Choi HS, Park DH. Persistence and viable but non-culturable state induced by streptomycin in Erwinia amylovora. Front Microbiol 2024; 15:1346300. [PMID: 38450169 PMCID: PMC10914980 DOI: 10.3389/fmicb.2024.1346300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
Persister cell and viable but non-culturable (VBNC) state of bacteria are survival strategies against antibiotics and various environmental stresses, respectively, but they tend to be ignored in agriculture fields, even though bacteria can regain their abilities to survive and produce disease once those stresses disappear. This study was carried out to determine whether persister cell and VBNC state in Erwinia amylovora are present after exposures to streptomycin, the length of their persistence, and the steps needed to decrease the inoculum. Persister cells were observed using biphasic killed growth curve for 4-8 h when the late stationary phase cells of E. amylovora were cultured in liquid medium containing streptomycin. This state was maintained for up to 12 h based on the colony forming units (CFUs) of the colonies that grew on the mannitol glutamate yeast extract (MGY) medium after streptomycin was removed. The CFUs on the MGY medium were lower than the total count determined using the LIVE/DEAD Kit, suggesting that persister cells and VBNC state might co-exist for up to 12 h after exposure to streptomycin. However, after 12 h, E. amylovora cells did not continue to grow on the medium for 9 days, suggesting that they entered a VBNC state at that time and remained in a persistent state. In addition, based on the Redox Sensor Green staining method, the presence of both states was confirmed for up to 12 h, and only then did the VBNC state became apparent. Furthermore, persister cells were observed for up to 24 h, and damaged cells reduced when E. amylovora cells were culture in distilled water with streptomycin, indicating that the uptake of lower nutrients in E. amylovora led to prolonged persister cells and VBNC state, which are more likely to survive after streptomycin treatments. The addition of sucrose and oxytetracycline to distilled water containing streptomycin reduced persister cells than other sources did. Thus, to inhibit the spread of fire blight, management techniques must consider the hazards of using streptomycin treatments that induce dormancy, such as persister cells and VBNC state, beyond the development of resistant strain.
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Affiliation(s)
- Yeon Ju Kim
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon-si, Republic of Korea
| | - Hyun Seo Choi
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon-si, Republic of Korea
| | - Duck Hwan Park
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon-si, Republic of Korea
- Plant Medicine Program, Division of Bioresource Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon-si, Republic of Korea
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Hoang MD, Riessner S, Oropeza Vargas JE, von den Eichen N, Heins AL. Influence of Varying Pre-Culture Conditions on the Level of Population Heterogeneity in Batch Cultures with an Escherichia coli Triple Reporter Strain. Microorganisms 2023; 11:1763. [PMID: 37512936 PMCID: PMC10384452 DOI: 10.3390/microorganisms11071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
When targeting robust, high-yielding bioprocesses, phenomena such as population heterogeneity have to be considered. Therefore, the influence of the conditions which the cells experience prior to the main culture should also be evaluated. Here, the influence of a pre-culture medium (complex vs. minimal medium), optical density for inoculation of the main culture (0.005, 0.02 and 0.0125) and harvest time points of the pre-culture in exponential growth phase (early, mid and late) on the level of population heterogeneity in batch cultures of the Escherichia coli triple reporter strain G7BL21(DE3) in stirred-tank bioreactors was studied. This strain allows monitoring the growth (rrnB-EmGFP), general stress response (rpoS-mStrawberry) and oxygen limitation (nar-TagRFP657) of single cells through the expression of fluorescent proteins. Data from batch cultivations with varying pre-culture conditions were analysed with principal component analysis. According to fluorescence data, the pre-culture medium had the largest impact on population heterogeneities during the bioprocess. While a minimal medium as a pre-culture medium elevated the differences in cellular growth behaviour in the subsequent batch process, a complex medium increased the general stress response and led to a higher population heterogeneity. The latter was promoted by an early harvest of the cells with low inoculation density. Seemingly, nar-operon expression acted independently of the pre-culture conditions.
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Affiliation(s)
- Manh Dat Hoang
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Sophi Riessner
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Jose Enrique Oropeza Vargas
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Nikolas von den Eichen
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Anna-Lena Heins
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
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Hang Z, Tong P, Zhao P, He Z, Shao L, Jia Y, Wang XC, Li Z. Hierarchical stringent response behaviors of activated sludge system to stressed conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161832. [PMID: 36716870 DOI: 10.1016/j.scitotenv.2023.161832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
The stringent response of activated sludge systems to either stressed or harmful environments is important for the stable operation of activated sludge, which is examined by taking copper ion (Cu2+) as a stress model in this study. When weak stress was employed (Cu2+ ≤ 2.5 mg/L), the N-acyl-homoserine lactones (AHLs) of C6-, C8-, and C10-HSL increased by 30 %, 13 %, and 127 %, respectively, while the redox sensor green (RSG) intensity decreased by 28 %. Encountering the increased stress (2.5 mg/L < Cu2+ ≤ 5 mg/L), bacteria concentration in the supernatant increased by 87 %. However, the respiration rates of autotrophic and heterotrophic bacteria (SOURa and SOURh) and adenosine triphosphate decreased by 52 %, 18 %, and 27 %, respectively, and the flocs disintegrated with a diameter decreasing from 57 to 51 μm. When the stress became more serious (Cu2+ > 5 mg/L), the respiration rates continued to decline, but the quasi-endogenous respiration ratio (Rq/t) increased from 31 % to 47 %. Negligible changes occurred in the endogenous respiration rate (SOURe), adenosine diphosphate, and adenosine monophosphate. Based on these results, a hierarchical stringent response model of the activated sludge system to stressed conditions was proposed, and these responses were evaluated by respirogram. The initial response to weak stress was related to the most sensitive signals of quorum sensing and RSG intensity, well described by the quasi-endogenous respiration rate. The adaptive response to increased stress was the proactive migrations of low- and high-nucleic-acid bacteria to the supernatant, causing the looseness and even disintegration of sludge flocs, well described by SOURa, SOURh, and Rq/t. The lethal response to lethal stress was related to endogenous metabolic processes, well described by SOURe. This work provides new insights into understanding the stringent response of activated sludge systems to some stressed conditions. It helps to regulate the stability of activated sludge systems with respirogram technology.
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Affiliation(s)
- Zhenyu Hang
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Peipei Tong
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Pian Zhao
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhangwei He
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Linjun Shao
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yanru Jia
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiaochang C Wang
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhihua Li
- Key Laboratory of Northwest Water Resource, Environment, and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Xi'an Key Laboratory of Intelligent Equipment Technology in Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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Zhao P, Zhao S, Wang HG, Lu M, Li ZH. Encapsulation of bacteria in different stratified extracellular polymeric substances and its implications for performance enhancement and resource recovery. WATER RESEARCH 2022; 220:118684. [PMID: 35661510 DOI: 10.1016/j.watres.2022.118684] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 05/06/2023]
Abstract
Simultaneous recovery of biopolymers and enhanced bio-reactor performance are promising options for sustainable wastewater treatment, and the bioactivity of sludge after biopolymer extraction is thus critical for the performance of the system. To this end, stratified extracellular polymeric substances (EPS), including slime, loosely bound EPS (LB-EPS), and tightly bound EPS (TB-EPS), were extracted, and the bioactivities of the consequent extraction residues were assessed using aerobic respirogram, kinetic, and flow cytometry (FCM). After the initial weak extraction of slime, the particle size distribution of the sludge significantly decreased, and subsequent extractions of LB-EPS and TB-EPS produced an equivalent size distribution. In contrast, the fractal dimension decreased after each extraction, suggesting that LB-EPS and TB-EPS affected the compactness of flocs rather than the size. The aerobic bacteria distribution estimated using respirogram shows that slime mainly encapsulated heterotrophs while LB-EPS mainly encapsulated nitrifiers. In addition, the ammonia-nitrogen affinity coefficient decreased from 1.79 to 0.28 mg/L when slime was removed, thereby encouraging the activities of autotrophic nitrifiers. Further removal of LB-EPS induced high energy dispersion as the maintenance coefficient m and the metabolic dispersion index μ/m increased from 0.11 to 0.22 and 0.44 to 0.63, respectively. Meanwhile, the yield rate decreased from 0.77 to 0.66. Although pellets that resulted from TB-EPS extraction were not aerobically active as described by respirogram and growth curves, they were still metabolically active as measured by live/dead cell counting and redox sensor green signal. These pellets used more energy for maintenance as indicated by the high maintenance coefficient than those residual after either slime or LB-EPS extraction. In addition, the variation in bacteria community distribution across flocs was related to the variation in temperatures, suggesting that the inner part of a floc might be hotter than the outer side. Therefore, compared to bacteria in the raw sludge, the viable bacteria bounded in LB-EPS and TB-EPS convert more energy to heat rather than growth. These results indicate that energy was dispersed as metabolic heat for the LB-EPS extracted sludge, and removal of LB-EPS favored thermogenesis and sludge reduction. Based on the above findings, a simultaneously EPS-recovery and performance enhancement configuration is thus proposed, which holds great promise for the integration of next-generation wastewater treatment plants.
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Affiliation(s)
- Pian Zhao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Song Zhao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hai-Guang Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Meng Lu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhi-Hua Li
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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Fifani B, Steels S, Helmus C, Delacuvellerie A, Deracinois B, Phalip V, Delvigne F, Jacques P. Coculture of Trichoderma harzianum and Bacillus velezensis Based on Metabolic Cross-Feeding Modulates Lipopeptide Production. Microorganisms 2022; 10:microorganisms10051059. [PMID: 35630500 PMCID: PMC9148127 DOI: 10.3390/microorganisms10051059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol of plant diseases: the fungus Trichoderma harzianum IHEM5437 and the bacterium Bacillus velezensis GA1 (a strong antifungal lipopeptide producing strain). While the Bacillus overgrew the Trichoderma in a rich medium due to its antifungal lipopeptide production, a drastically different trend was observed in a medium in which a nitrogen nutritional dependency was imposed. Indeed, in this minimum medium containing nitrate as the sole nitrogen source, cooperation between the bacterium and the fungus was established. This is reflected by the growth of both species as well as the inhibition of the expression of Bacillus genes encoding lipopeptide synthetases. Interestingly, the growth of the bacterium in the minimum medium was enabled by the amendment of the culture by the fungal supernatant, which, in this case, ensures a high production yield of lipopeptides. These results highlight, for the first time, that Trichoderma harzianum and Bacillus velezensis are able, in specific environmental conditions, to adapt their metabolisms in order to grow together.
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Affiliation(s)
- Barbara Fifani
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Sebastien Steels
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Catherine Helmus
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | | | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Vincent Phalip
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Frank Delvigne
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Philippe Jacques
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- Correspondence:
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Bouchat R, Vélard F, Audonnet S, Rioult D, Delvigne F, Rémond C, Rakotoarivonina H. Xylanase production by Thermobacillus xylanilyticus is impaired by population diversification but can be mitigated based on the management of cheating behavior. Microb Cell Fact 2022; 21:39. [PMID: 35292016 PMCID: PMC8922903 DOI: 10.1186/s12934-022-01762-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Background The microbial production of hemicellulasic cocktails is still a challenge for the biorefineries sector and agro-waste valorization. In this work, the production of hemicellulolytic enzymes by Thermobacillus xylanilyticus has been considered. This microorganism is of interest since it is able to produce an original set of thermostable hemicellulolytic enzymes, notably a xylanase GH11, Tx-xyn11. However, cell-to-cell heterogeneity impairs the production capability of the whole microbial population. Results Sequential cultivations of the strain on xylan as a carbon source has been considered in order to highlight and better understand this cell-to-cell heterogeneity. Successive cultivations pointed out a fast decrease of xylanase activity (loss of ~ 75%) and Tx-xyn11 gene expression after 23.5 generations. During serial cultivations on xylan, flow cytometry analyses pointed out that two subpopulations, differing at their light-scattering properties, were present. An increase of the recurrence of the subpopulation exhibiting low forward scatter (FSC) signal was correlated with a progressive loss of xylanase activity over several generations. Cell sorting and direct observation of the sorted subpopulations revealed that the low-FSC subpopulation was not sporulating, whereas the high-FSC subpopulation contained cells at the onset of the sporulation stage. The subpopulation differences (growth and xylanase activity) were assessed during independent growth. The low-FSC subpopulation exhibited a lag phase of 10 h of cultivation (and xylanase activities from 0.15 ± 0.21 to 3.89 ± 0.14 IU/mL along the cultivation) and the high-FSC subpopulation exhibited a lag phase of 5 h (and xylanase activities from 0.52 ± 0.00 to 4.43 ± 0.61 over subcultivations). Serial cultivations on glucose, followed by a switch to xylan led to a ~ 1.5-fold to ~ 15-fold improvement of xylanase activity, suggesting that alternating cultivation conditions could lead to an efficient population management strategy for the production of xylanase. Conclusions Taken altogether, the data from this study point out that a cheating behavior is responsible for the progressive reduction in xylanase activity during serial cultivations of T. xylanilyticus. Alternating cultivation conditions between glucose and xylan could be used as an efficient strategy for promoting population stability and higher enzymatic productivity from this bacterium. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01762-z.
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Affiliation(s)
- Romain Bouchat
- INRAE, FARE, UMR A 614, Chaire AFERE, Université de Reims Champagne Ardenne, 51097, Reims, France.,Laboratory of Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté 2B, B140, 5030, Gembloux, Belgium
| | - Frédéric Vélard
- BIOS EA 4691 "Biomatériaux et Inflammation en site osseux", Université de Reims Champagne Ardenne, 51097, Reims, France
| | - Sandra Audonnet
- URCACyt, Flow Cytometry Technical Platform, Université de Reims Champagne-Ardenne, 51096, Reims, France
| | - Damien Rioult
- Plateau Technique Mobile de Cytométrie Environnementale MOBICYTE, Université de Reims Champagne-Ardenne, 51097, Reims, France
| | - Frank Delvigne
- Laboratory of Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté 2B, B140, 5030, Gembloux, Belgium
| | - Caroline Rémond
- INRAE, FARE, UMR A 614, Chaire AFERE, Université de Reims Champagne Ardenne, 51097, Reims, France
| | - Harivony Rakotoarivonina
- INRAE, FARE, UMR A 614, Chaire AFERE, Université de Reims Champagne Ardenne, 51097, Reims, France.
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Goes A, Vidakovic L, Drescher K, Fuhrmann G. Interaction of myxobacteria-derived outer membrane vesicles with biofilms: antiadhesive and antibacterial effects. NANOSCALE 2021; 13:14287-14296. [PMID: 34477714 DOI: 10.1039/d1nr02583j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial biofilms are widespread in nature and in medical settings and display a high tolerance to antibiotics and disinfectants. Extracellular vesicles have been increasingly studied to characterise their origins and assess their potential for use as a versatile drug delivery system; however, it remains unclear whether they also have antibiofilm effects. Outer membrane vesicles are lipid vesicles shed by Gram-negative bacteria and, in the case of myxobacteria, carry natural antimicrobial compounds produced by these microorganisms. In this study, we demonstrate that vesicles derived from the myxobacteria Cystobacter velatus Cbv34 and Cystobacter ferrugineus Cbfe23 are highly effective at inhibiting the formation and disrupting biofilms by different bacterial species.
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Affiliation(s)
- Adriely Goes
- Helmholtz Centre for Infection Research (HZI), Biogenic Nanotherapeutics Group (BION), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany.
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Patel RR, Kandel PP, Traverso E, Hockett KL, Triplett LR. Pseudomonas syringae pv. phaseolicola Uses Distinct Modes of Stationary-Phase Persistence To Survive Bacteriocin and Streptomycin Treatments. mBio 2021; 12:e00161-21. [PMID: 33849974 PMCID: PMC8092213 DOI: 10.1128/mbio.00161-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/11/2021] [Indexed: 02/08/2023] Open
Abstract
Antimicrobial treatment of bacteria often results in a small population of surviving tolerant cells, or persisters, that may contribute to recurrent infection. Antibiotic persisters are metabolically dormant, but the basis of their persistence in the presence of membrane-disrupting biological compounds is less well understood. We previously found that the model plant pathogen Pseudomonas syringae pv. phaseolicola 1448A (Pph) exhibits persistence to tailocin, a membrane-disrupting biocontrol compound with potential for sustainable disease control. Here, we compared physiological traits associated with persistence to tailocin and to the antibiotic streptomycin and established that both treatments leave similar frequencies of persisters. Microscopic profiling of treated populations revealed that while tailocin rapidly permeabilizes most cells, streptomycin treatment results in a heterogeneous population in the redox and membrane permeability state. Intact cells were sorted into three fractions according to metabolic activity, as indicated by a redox-sensing reporter dye. Streptomycin persisters were cultured from the fraction associated with the lowest metabolic activity, but tailocin persisters were cultured from a fraction associated with an active metabolic signal. Cells from culturable fractions were able to infect host plants, while the nonculturable fractions were not. Tailocin and streptomycin were effective in eliminating all persisters when applied sequentially, in addition to eliminating cells in other viable states. This study identifies distinct metabolic states associated with antibiotic persistence, tailocin persistence, and loss of virulence and demonstrates that tailocin is highly effective in eliminating dormant cells.IMPORTANCE Populations of genetically identical bacteria encompass heterogeneous physiological states. The small fraction of bacteria that are dormant can help the population survive exposure to antibiotics and other stresses, potentially contributing to recurring infection cycles in animal or plant hosts. Membrane-disrupting biological control treatments are effective in killing dormant bacteria, but these treatments also leave persister-like survivors. The current work demonstrates that in Pph, persisters surviving treatment with membrane-disrupting tailocin proteins have an elevated redox state compared to that of dormant streptomycin persisters. Combination treatment was effective in killing both persister types. Culturable persisters corresponded closely with infectious cells in each treated population, whereas the high-redox and unculturable fractions were not infectious. In linking redox states to heterogeneous phenotypes of tailocin persistence, streptomycin persistence, and infection capability, this work will inform the search for mechanisms and markers for each phenotype.
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Affiliation(s)
- Ravikumar R Patel
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Prem P Kandel
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Eboni Traverso
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Kevin L Hockett
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lindsay R Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
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9
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Heins AL, Reyelt J, Schmidt M, Kranz H, Weuster-Botz D. Development and characterization of Escherichia coli triple reporter strains for investigation of population heterogeneity in bioprocesses. Microb Cell Fact 2020; 19:14. [PMID: 31992282 PMCID: PMC6988206 DOI: 10.1186/s12934-020-1283-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/12/2020] [Indexed: 12/17/2022] Open
Abstract
Background Today there is an increasing demand for high yielding robust and cost efficient biotechnological production processes. Although cells in these processes originate from isogenic cultures, heterogeneity induced by intrinsic and extrinsic influences is omnipresent. To increase understanding of this mechanistically poorly understood phenomenon, advanced tools that provide insights into single cell physiology are needed. Results Two Escherichia coli triple reporter strains have been designed based on the industrially relevant production host E. coli BL21(DE3) and a modified version thereof, E. coli T7E2. The strains carry three different fluorescence proteins chromosomally integrated. Single cell growth is followed with EmeraldGFP (EmGFP)-expression together with the ribosomal promoter rrnB. General stress response of single cells is monitored by expression of sigma factor rpoS with mStrawberry, whereas expression of the nar-operon together with TagRFP657 gives information about oxygen limitation of single cells. First, the strains were characterized in batch operated stirred-tank bioreactors in comparison to wildtype E. coli BL21(DE3). Afterwards, applicability of the triple reporter strains for investigation of population heterogeneity in bioprocesses was demonstrated in continuous processes in stirred-tank bioreactors at different growth rates and in response to glucose and oxygen perturbation simulating gradients on industrial scale. Population and single cell level physiology was monitored evaluating general physiology and flow cytometry analysis of fluorescence distributions of the triple reporter strains. Although both triple reporter strains reflected physiological changes that were expected based on the expression characteristics of the marker proteins, the triple reporter strain based on E. coli T7E2 showed higher sensitivity in response to environmental changes. For both strains, noise in gene expression was observed during transition from phases of non-growth to growth. Apparently, under some process conditions, e.g. the stationary phase in batch cultures, the fluorescence response of EmGFP and mStrawberry is preserved, whereas TagRFP657 showed a distinct response. Conclusions Single cell growth, general stress response and oxygen limitation of single cells could be followed using the two triple reporter strains developed in this study. They represent valuable tools to study population heterogeneity in bioprocesses significantly increasing the level of information compared to the use of single reporter strains.
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Affiliation(s)
- Anna-Lena Heins
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Jan Reyelt
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Marlen Schmidt
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Harald Kranz
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Dirk Weuster-Botz
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
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10
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Jaén KE, Velazquez D, Delvigne F, Sigala JC, Lara AR. Engineering E. coli for improved microaerobic pDNA production. Bioprocess Biosyst Eng 2019; 42:1457-1466. [PMID: 31079222 DOI: 10.1007/s00449-019-02142-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/20/2019] [Accepted: 05/02/2019] [Indexed: 02/08/2023]
Abstract
Escherichia coli strains W3110 and BL21 were engineered for the production of plasmid DNA (pDNA) under aerobic and transitions to microaerobic conditions. The gene coding for recombinase A (recA) was deleted in both strains. In addition, the Vitreoscilla hemoglobin (VHb) gene (vgb) was chromosomally inserted and constitutively expressed in each E. coli recA mutant and wild type. The recA inactivation increased the supercoiled pDNA fraction (SCF) in both strains, while VHb expression improved the pDNA production in W3110, but not in BL21. Therefore, a codon-optimized version of vgb was inserted in strain BL21recA-, which, together with W3110recA-vgb+, was tested in cultures with shifts from aerobic to oxygen-limited regimes. VHb expression lowered the accumulation of fermentative by-products in both strains. VHb-expressing cells displayed higher oxidative activity as indicated by the Redox Sensor Green fluorescence, which was more intense in BL21 than in W3110. Furthermore, VHb expression did not change pDNA production in W3110, but decreased it in BL21. These results are useful for understanding the physiological effects of VHb expression in two industrially relevant E. coli strains, and for the selection of a host for pDNA production.
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Affiliation(s)
- Karim E Jaén
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico
| | - Daniela Velazquez
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico
| | - Frank Delvigne
- Gembloux Agro-Bio Tech, TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), University of Liege, Gembloux, Belgium
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, 05348, Mexico City, Mexico.
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11
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Heins AL, Lundin L, Nunes I, Gernaey KV, Sørensen SJ, Lantz AE. The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures. Biotechnol Prog 2019; 35:e2796. [PMID: 30816011 DOI: 10.1002/btpr.2796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/07/2019] [Accepted: 02/22/2019] [Indexed: 01/14/2023]
Abstract
Acetate as the major by-product in industrial-scale bioprocesses with Escherichia coli is found to decrease process efficiency as well as to be toxic to cells, which has several effects like a significant induction of cellular stress responses. However, the underlying phenomena are poorly explored. Therefore, we studied time-resolved population heterogeneity of the E. coli growth reporter strain MG1655/pGS20PrrnBGFPAAV expressing destabilized green fluorescent protein during batch growth on acetate and glucose as sole carbon sources. Additionally, we applied five fluorescent stains targeting different cellular properties (viability as well as metabolic and respiratory activity). Quantitative analysis of flow cytometry data verified that bacterial populations in the bioreactor are more heterogeneous in growth as well as stronger metabolically challenged during growth on acetate as sole carbon source, compared to growth on glucose or acetate after diauxic shift. Interestingly, with acetate as sole carbon source, significant subpopulations were found with some cells that seem to be more robust than the rest of the population. In conclusion, following batch cultures population heterogeneity was evident in all measured parameters. Our approach enabled a deeper study of heterogeneity during growth on the favored substrate glucose as well as on the toxic by-product acetate. Using a combination of activity fluorescent dyes proved to be an accurate and fast alternative as well as a supplement to the use of a reporter strain. However, the choice of combination of stains should be well considered depending on which population traits to aim for.
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Affiliation(s)
- Anna-Lena Heins
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.,Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Luisa Lundin
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.,Division of Scientific Support, Becton-Dickison biosciences, Erembodegem, Belgium
| | - Inês Nunes
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Eliasson Lantz
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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12
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Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A. Engineering Robust Production Microbes for Large-Scale Cultivation. Trends Microbiol 2019; 27:524-537. [PMID: 30819548 DOI: 10.1016/j.tim.2019.01.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/11/2019] [Accepted: 01/23/2019] [Indexed: 11/27/2022]
Abstract
Systems biology and synthetic biology are increasingly used to examine and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these approaches. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in large-scale production.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | | | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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13
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Fragoso-Jiménez JC, Baert J, Nguyen TM, Liu W, Sassi H, Goormaghtigh F, Van Melderen L, Gaytán P, Hernández-Chávez G, Martinez A, Delvigne F, Gosset G. Growth-dependent recombinant product formation kinetics can be reproduced through engineering of glucose transport and is prone to phenotypic heterogeneity. Microb Cell Fact 2019; 18:26. [PMID: 30710996 PMCID: PMC6359759 DOI: 10.1186/s12934-019-1073-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Background Escherichia coli W3110 and a group of six isogenic derivatives, each displaying distinct specific rates of glucose consumption were characterized to determine levels of GFP production and population heterogeneity. These strains have single or combinatory deletions in genes encoding phosphoenolpyruvate:sugar phosphotransferase system (PTS) permeases as PtsG and ManX, as well as common components EI, Hpr protein and EIIA, also the non-PTS Mgl galactose/glucose ABC transporter. They have been transformed for expressing GFP based on a lac-based expression vector, which is subject to bistability. Results These strains displayed specific glucose consumption and growth rates ranging from 1.75 to 0.45 g/g h and 0.54 to 0.16 h−1, respectively. The rate of acetate production was strongly reduced in all mutant strains when compared with W3110/pV21. In bioreactor cultures, wild type W3110/pV21 produced 50.51 mg/L GFP, whereas strains WG/pV21 with inactive PTS IICBGlc and WGM/pV21 with the additional inactivation of PTS IIABMan showed the highest titers of GFP, corresponding to 342 and 438 mg/L, respectively. Moreover, we showed experimentally that bistable expression systems, as lac-based ones, induce strong phenotypic segregation among microbial populations. Conclusions We have demonstrated that reduction on glucose consumption rate in E. coli leads to an improvement of GFP production. Furthermore, from the perspective of phenotypic heterogeneity, we observed in this case that heterogeneous systems are also the ones leading to the highest performance. This observation suggests reconsidering the generally accepted proposition stating that phenotypic heterogeneity is generally unwanted in bioprocess applications.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1073-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Carlos Fragoso-Jiménez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jonathan Baert
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Thai Minh Nguyen
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Wenzheng Liu
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Hosni Sassi
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Frédéric Goormaghtigh
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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14
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González-Cabaleiro R, Mitchell AM, Smith W, Wipat A, Ofiţeru ID. Heterogeneity in Pure Microbial Systems: Experimental Measurements and Modeling. Front Microbiol 2017; 8:1813. [PMID: 28970826 PMCID: PMC5609101 DOI: 10.3389/fmicb.2017.01813] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/05/2017] [Indexed: 01/02/2023] Open
Abstract
Cellular heterogeneity influences bioprocess performance in ways that until date are not completely elucidated. In order to account for this phenomenon in the design and operation of bioprocesses, reliable analytical and mathematical descriptions are required. We present an overview of the single cell analysis, and the mathematical modeling frameworks that have potential to be used in bioprocess control and optimization, in particular for microbial processes. In order to be suitable for bioprocess monitoring, experimental methods need to be high throughput and to require relatively short processing time. One such method used successfully under dynamic conditions is flow cytometry. Population balance and individual based models are suitable modeling options, the latter one having in particular a good potential to integrate the various data collected through experimentation. This will be highly beneficial for appropriate process design and scale up as a more rigorous approach may prevent a priori unwanted performance losses. It will also help progressing synthetic biology applications to industrial scale.
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Affiliation(s)
- Rebeca González-Cabaleiro
- School of Engineering, Chemical Engineering, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Anca M Mitchell
- School of Engineering, Chemical Engineering, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Wendy Smith
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of ComputingNewcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of ComputingNewcastle University, Newcastle upon Tyne, United Kingdom
| | - Irina D Ofiţeru
- School of Engineering, Chemical Engineering, Newcastle UniversityNewcastle upon Tyne, United Kingdom
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15
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Delvigne F, Baert J, Sassi H, Fickers P, Grünberger A, Dusny C. Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses. Biotechnol J 2017; 12. [PMID: 28544731 DOI: 10.1002/biot.201600549] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 01/19/2023]
Abstract
Phenotypic plasticity of microbial cells has attracted much attention and several research efforts have been dedicated to the description of methods aiming at characterizing phenotypic heterogeneity and its impact on microbial populations. However, different approaches have also been suggested in order to take benefit from noise in a bioprocess perspective, e.g. by increasing the robustness or productivity of a microbial population. This review is dedicated to outline these controlling methods. A common issue, that has still to be addressed, is the experimental identification and the mathematical expression of noise. Indeed, the effective interfacing of microbial physiology with external parameters that can be used for controlling physiology depends on the acquisition of reliable signals. Latest technologies, like single cell microfluidics and advanced flow cytometric approaches, enable linking physiology, noise, heterogeneity in productive microbes with environmental cues and hence allow correctly mapping and predicting biological behavior via mathematical representations. However, like in the field of electronics, signals are perpetually subjected to noise. If appropriately interpreted, this noise can give an additional insight into the behavior of the individual cells within a microbial population of interest. This review focuses on recent progress made at describing, treating and exploiting biological noise in the context of microbial populations used in various bioprocess applications.
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Affiliation(s)
- Frank Delvigne
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Jonathan Baert
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Hosni Sassi
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Patrick Fickers
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Alexander Grünberger
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Christian Dusny
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
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