1
|
Philipp LA, Bühler K, Ulber R, Gescher J. Beneficial applications of biofilms. Nat Rev Microbiol 2024; 22:276-290. [PMID: 37957398 DOI: 10.1038/s41579-023-00985-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/15/2023]
Abstract
Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.
Collapse
Affiliation(s)
- Laura-Alina Philipp
- Hamburg University of Technology, Institute of Technical Microbiology, Hamburg, Germany
| | - Katja Bühler
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Roland Ulber
- RPTU Kaiserslautern-Landau, Institute of Bioprocess Engineering, Kaiserslautern, Germany
| | - Johannes Gescher
- Hamburg University of Technology, Institute of Technical Microbiology, Hamburg, Germany.
| |
Collapse
|
2
|
Das A, Patro S, Simnani FZ, Singh D, Sinha A, Kumari K, Rao PV, Singh S, Kaushik NK, Panda PK, Suar M, Verma SK. Biofilm modifiers: The disparity in paradigm of oral biofilm ecosystem. Biomed Pharmacother 2023; 164:114966. [PMID: 37269809 DOI: 10.1016/j.biopha.2023.114966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023] Open
Abstract
A biofilm is a population of sessile microorganisms that has a distinct organized structure and characteristics like channels and projections. Good oral hygiene and reduction in the prevalence of periodontal diseases arise from minimal biofilm accumulation in the mouth, however, studies focusing on modifying the ecology of oral biofilms have not yet been consistently effective. The self-produced matrix of extracellular polymeric substances and greater antibiotic resistance make it difficult to target and eliminate biofilm infections, which lead to serious clinical consequences that are often lethal. Therefore, a better understanding is required to target and modify the ecology of biofilms in order to eradicate the infection, not only in instances of oral disorders but also in terms of nosocomial infections. The review focuses on several biofilm ecology modifiers to prevent biofilm infections, as well as the involvement of biofilm in antibiotic resistance, implants or in-dwelling device contamination, dental caries, and other periodontal disorders. It also discusses recent advances in nanotechnology that may lead to novel strategies for preventing and treating infections caused by biofilms as well as a novel outlook to infection control.
Collapse
Affiliation(s)
- Antarikshya Das
- KIIT School of Dental Sciences, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Swadheena Patro
- KIIT School of Dental Sciences, KIIT University, Bhubaneswar 751024, Odisha, India.
| | | | - Dibyangshee Singh
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Adrija Sinha
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Khushbu Kumari
- KIIT School of Dental Sciences, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Patnala Vedika Rao
- KIIT School of Medical Sciences, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Sarita Singh
- BVG Life Sciences Limited, Sagar Complex, Old Pune-Mumbai Road, Chinchwad, Pune 411034, India
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, Republic of Korea.
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Mrutyunjay Suar
- KIIT School of Dental Sciences, KIIT University, Bhubaneswar 751024, Odisha, India.
| | - Suresh K Verma
- KIIT School of Dental Sciences, KIIT University, Bhubaneswar 751024, Odisha, India.
| |
Collapse
|
3
|
Andreu C, Del Olmo ML. Biotechnological applications of biofilms formed by osmotolerant and halotolerant yeasts. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12589-y. [PMID: 37233754 DOI: 10.1007/s00253-023-12589-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Many microorganisms are capable of developing biofilms under adverse conditions usually related to nutrient limitation. They are complex structures in which cells (in many cases of different species) are embedded in the material that they secrete, the extracellular matrix (ECM), which is composed of proteins, carbohydrates, lipids, and nucleic acids. The ECM has several functions including adhesion, cellular communication, nutrient distribution, and increased community resistance, this being the main drawback when these microorganisms are pathogenic. However, these structures have also proven useful in many biotechnological applications. Until now, the most interest shown in these regards has focused on bacterial biofilms, and the literature describing yeast biofilms is scarce, except for pathological strains. Oceans and other saline reservoirs are full of microorganisms adapted to extreme conditions, and the discovery and knowledge of their properties can be very interesting to explore new uses. Halotolerant and osmotolerant biofilm-forming yeasts have been employed for many years in the food and wine industry, with very few applications in other areas. The experience gained in bioremediation, food production and biocatalysis with bacterial biofilms can be inspiring to find new uses for halotolerant yeast biofilms. In this review, we focus on the biofilms formed by halotolerant and osmotolerant yeasts such as those belonging to Candida, Saccharomyces flor yeasts, Schwannyomyces or Debaryomyces, and their actual or potential biotechnological applications. KEY POINTS: • Biofilm formation by halotolerant and osmotolerant yeasts is reviewed. • Yeasts biofilms have been widely used in food and wine production. • The use of bacterial biofilms in bioremediation can be expanded to halotolerant yeast counterparts.
Collapse
Affiliation(s)
- Cecilia Andreu
- Departament de Química Orgànica, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés S/N, 46100, València, Burjassot, Spain
| | - Marcel Lí Del Olmo
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de València, Dr. Moliner 50, 46100, València, Burjassot, Spain.
| |
Collapse
|
4
|
Portius M, Danneberg C, Pompe T. Biomaterial approaches for engineering and analyzing structure and metabolic states of microbial consortia within biofilms. Curr Opin Biotechnol 2023; 81:102916. [PMID: 36870250 DOI: 10.1016/j.copbio.2023.102916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 03/06/2023]
Abstract
Microbial consortia within biofilms are frequently found in structured organization in nature and are thought to bear great potential for productive biotechnological applications, such as the degradation of complex substrates, biosensing, or the production of chemical compounds. However, in-depth understanding of their organizational principles, as well as comprehensive design criteria of structured microbial consortia for industrial applications are still limited. It is hypothesized that biomaterial engineering of such consortia within scaffolds can advance the field by providing defined in vitro mimics of naturally occurring and industrially applicable biofilms. Such systems will allow for adjustment of important microenvironmental parameters and in-depth analysis with high temporal and spatial resolution. In this review, we provide the background of biomaterial engineering of structured biofilm consortia, show approaches for their design, and demonstrate tools to analyze their metabolic state.
Collapse
Affiliation(s)
- Matthias Portius
- Institute of Biochemistry, Leipzig University, Germany; Research and Transfer Center for Bioactive Matter, bioACTmatter, Leipzig University, Germany
| | | | - Tilo Pompe
- Institute of Biochemistry, Leipzig University, Germany; Research and Transfer Center for Bioactive Matter, bioACTmatter, Leipzig University, Germany.
| |
Collapse
|
5
|
Cardoso AF, da Silva RDSS, Prado IGDO, Bitencourt JAP, Gastauer M. Acquiring Iron-Reducing Enrichment Cultures: Environments, Methods and Quality Assessments. Microorganisms 2023; 11:microorganisms11020448. [PMID: 36838412 PMCID: PMC9959475 DOI: 10.3390/microorganisms11020448] [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: 11/14/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
Lateritic duricrusts cover iron ore deposits and form spatially restricted, unique canga ecosystems endangered by mining. Iron cycling, i.e., the dissolution and subsequent precipitation of iron, is able to restitute canga duricrusts, generating new habitats for endangered biota in post-mining landscapes. As iron-reducing bacteria can accelerate this iron cycling, we aim to retrieve microbial enrichment cultures suitable to mediate the large-scale restoration of cangas. For that, we collected water and sediment samples from the Carajás National Forest and cultivated the iron-reducing microorganisms therein using a specific medium. We measured the potential to reduce iron using ferrozine assays, growth rate and metabolic activity. Six out of seven enrichment cultures effectively reduced iron, showing that different environments harbor iron-reducing bacteria. The most promising enrichment cultures were obtained from environments with repeated flooding and drying cycles, i.e., periodically inundated grasslands and a plateau of an iron mining waste pile characterized by frequent soaking. Selected enrichment cultures contained iron-reducing and fermenting bacteria, such as Serratia and Enterobacter. We found higher iron-reducing potential in enrichment cultures with a higher cell density and microorganism diversity. The obtained enrichment cultures should be tested for canga restoration to generate benefits for biodiversity and contribute to more sustainable iron mining in the region.
Collapse
|
6
|
Tang Z, Zhang H, Xiong J, Li Y, Luo W. Enhanced iturin a production in a two-compartment biofilm reactor by Bacillus velezensis ND. Front Bioeng Biotechnol 2023; 11:1102786. [PMID: 36741766 PMCID: PMC9893019 DOI: 10.3389/fbioe.2023.1102786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
In this study, a two-compartment biofilm reactor was designed for iturin A production. The biofilm reactor consists of a stirred-tank fermentor containing exclusively suspended cells and a packing column where the biofilm is attached. Polyester fiber with sphere shape and rough surfaces was chosen as the carrier of biofilm in packing column. Batch, fed-batch, and repeated-batch fermentation using Bacillus velezensis ND in the biofilm reactor were studied. Compared to conventional suspended cell fermentations, the productivity of iturin A in batch and fed-batch biofilm fermentation were increased by 66.7% and 63.3%, respectively. Maximum itutin A concentration of 6.8 ± 0.1 g/L and productivity of 46.9 ± 0.2 mg/L/h were obtained in fed-batch biofilm fermentation. Repeated-batch fermentation showed high stability, with almost same profile as batch fermentation. After a step-wise temperature control strategy was introduced in the biofilm reactor, productivity of iturin A was increased by 131.9% compared to suspended cell reactor. This superior performance of biofilm reactor confirms that it has great potential in industrial production of iturin A.
Collapse
Affiliation(s)
- Zhongmin Tang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Huili Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China,*Correspondence: Huili Zhang,
| | - Jie Xiong
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Wei Luo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
7
|
Oda S, Tanikawa A. A new plate-hanging method for biofilm quantification and its application to evaluate the role of surface hydrophobicity. J Microbiol Methods 2022; 203:106608. [PMID: 36343771 DOI: 10.1016/j.mimet.2022.106608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
A novel procedure for the quantitative analysis of biofilm formation by bacteria and yeasts, the Plate-hanging method, was developed. In this system, various polymer disks were hung from the lid of a 6-well plate, immersed in a cell suspension, and moderately shaken (70 rpm). In order to verify the validity of the procedure, the effects of the solid surface hydrophobicity of the test disks and the cell surface hydrophobicities of microorganisms on biofilm formation were investigated. Biofilm formation of bacteria and yeasts on the solid surface strongly depended on hydrophobic interactions between the solid surface and the cell surface. A positive correlation between the hydrophobic properties of substratum and cell surfaces was observed. On the other hand, hydrophilic yeasts preferentially adsorbed onto relatively hydrophilic surfaces. Moreover, the plate-hanging method coupled with the periodic exchange of the liquid medium enabled the quantification of long-term biofilm growth.
Collapse
Affiliation(s)
- Shinobu Oda
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology, 3-1 Yatsukaho, Hakusan, Ishikawa 924-0838, Japan; Research Laboratory for Integrated Technological Systems, Kanazawa Institute of Technology, 3-1 Yatsukaho, Hakusan, Ishikawa 924-0838, Japan.
| | - Ayami Tanikawa
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology, 3-1 Yatsukaho, Hakusan, Ishikawa 924-0838, Japan
| |
Collapse
|
8
|
Gierl L, Horn H, Wagner M. Impact of Fe 2+ and Shear Stress on the Development and Mesoscopic Structure of Biofilms-A Bacillus subtilis Case Study. Microorganisms 2022; 10:2234. [PMID: 36422304 PMCID: PMC9699539 DOI: 10.3390/microorganisms10112234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/25/2023] Open
Abstract
Bivalent cations are known to affect the structural and mechanical properties of biofilms. In order to reveal the impact of Fe2+ ions within the cultivation medium on biofilm development, structure and stability, Bacillus subtilis biofilms were cultivated in mini-fluidic flow cells. Two different Fe2+ inflow concentrations (0.25 and 2.5 mg/L, respectively) and wall shear stress levels (0.05 and 0.27 Pa, respectively) were tested. Mesoscopic biofilm structure was determined daily in situ and non-invasively by means of optical coherence tomography. A set of ten structural parameters was used to quantify biofilm structure, its development and change. The study focused on characterizing biofilm structure and development at the mesoscale (mm-range). Therefore, biofilm replicates (n = 10) were cultivated and analyzed. Three hypotheses were defined in order to estimate the effect of Fe2+ inflow concentration and/or wall shear stress on biofilm development and structure, respectively. It was not the intention to investigate and describe the underlying mechanisms of iron incorporation as this would require a different set of tools applied at microscopic levels as well as the use of, i.e., omic approaches. Fe2+ addition influenced biofilm development (e.g., biofilm accumulation) and structure markedly. Experiments revealed the accumulation of FeO(OH) within the biofilm matrix and a positive correlation of Fe2+ inflow concentration and biofilm accumulation. In more detail, independent of the wall shear stress applied during cultivation, biofilms grew approximately four times thicker at 2.5 mg Fe2+/L (44.8 µmol/L; high inflow concentration) compared to the low Fe2+ inflow concentration of 0.25 mg Fe2+/L (4.48 µmol/L). This finding was statistically verified (Scheirer-Ray-Hare test, ANOVA) and hints at a higher stability of Bacillus subtilis biofilms (e.g., elevated cohesive and adhesive strength) when grown at elevated Fe2+ inflow concentrations.
Collapse
Affiliation(s)
- Luisa Gierl
- Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
| | - Harald Horn
- Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
- German Technical and Scientific Association for Gas and Water (DVGW) Research Site at Karlsruhe Institute of Technology, Water Chemistry and Water Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
| | - Michael Wagner
- Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
9
|
Kampouraki ZC, Petala M, Boumpakis A, Skordaris G, Michailidis N, Deliyanni E, Kostoglou M, Karapantsios TD. Wetting and Imbibition Characteristics of Pseudomonas fluorescens Biofilms Grown on Stainless Steel. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9810-9821. [PMID: 35786927 DOI: 10.1021/acs.langmuir.2c00828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study aims to provide insights into biofilm resistance associated with their structural properties acquired during formation and development. On this account, the wetting and imbibition behavior of dehydrated Pseudomonas fluorescens biofilms grown on stainless steel electropolished substrates is thoroughly examined at different biofilm ages. A polar liquid (water) and a non-polar liquid (diiodomethane) are employed as wetting agents in the form of sessile droplets. A mathematical model is applied to appraise the wetting and imbibition performance of biofilms incorporating the evaporation of sessile droplets. The present results show that the examined biofilms are hydrophilic. The progressive growth of biofilms leads to a gradual increase of substrate surface coverage─up to full coverage─accompanied by a gradual decrease of biofilm surface roughness. It is noteworthy that just after 24 h of biofilm growth, the surface roughness increases about 6.7 times the roughness of the clean stainless steel surface. It is further found that the imbibition of liquid in the biofilm matrix is restricted only to the biofilm region under the sessile droplet. The lack of further capillary imbibition into the biofilm structure, beyond the droplet deposition region, implies that the biofilm matrix is not in the form of an extended network of interconnected micro/nanopores. All in all, the present results indicate a resilient biofilm structure to biocide penetration despite its hydrophilic nature.
Collapse
Affiliation(s)
- Zoi Christina Kampouraki
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Maria Petala
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Apostolos Boumpakis
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Georgios Skordaris
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Nikolaos Michailidis
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Eleni Deliyanni
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Margaritis Kostoglou
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| | - Thodoris D Karapantsios
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124 Thessaloniki, Greece
| |
Collapse
|
10
|
Maksimova Y, Bykova Y, Maksimov A. Functionalization of Multi-Walled Carbon Nanotubes Changes Their Antibiofilm and Probiofilm Effects on Environmental Bacteria. Microorganisms 2022; 10:microorganisms10081627. [PMID: 36014045 PMCID: PMC9412586 DOI: 10.3390/microorganisms10081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Releasing multi-walled carbon nanotubes (MWCNTs) into ecosystems affects the biofilm formation and metabolic activity of bacteria in aquatic and soil environments. Pristine (pMWCNTs), oleophilic (oMWCNTs), hydrophilic (hMWCNTs), and carboxylated (cMWCNTs) carbon nanotubes were used to investigate their effects on bacterial biofilm. A pronounced probiofilm effect of modified MWCNTs was observed on the Gram-negative bacteria of Pseudomonas fluorescens C2, Acinetobacter guillouiae 11 h, and Alcaligenes faecalis 2. None of the studied nanomaterials resulted in the complete inhibition of biofilm formation. The complete eradication of biofilms exposed to MWCNTs was not observed. The functionalization of carbon nanotubes was shown to change their probiofilm and antibiofilm effects. Gram-negative bacteria were the most susceptible to destruction, and among the modified MWCNTs, oMWCNTs had the greatest effect on biofilm destruction. The number of living cells in the biofilms was assessed by the reduction of XTT, and metabolic activity was assessed by the reduction of resazurin to fluorescent resorufin. The biofilms formed in the presence of MWCNTs reduced tetrozolium to formazan more actively than the control biofilms. When mature biofilms were exposed to MWCNTs, dehydrogenase activity decreased in Rhodococcus erythropolis 4-1, A. guillouiae 11 h, and A. faecalis 2 in the presence of pMWCNTs and hMWCNTs, as well as in A. guillouiae 11 h exposed to cMWCNTs. When mature biofilms were exposed to pMWCNTs, hMWCNTs, and cMWCNTs, the metabolism of cells decreased in most strains, and oMWCNTs did not have a pronounced inhibitory effect. The antibiofilm and probiofilm effects of MWCNTs were strain-dependent.
Collapse
Affiliation(s)
- Yuliya Maksimova
- Laboratory of Molecular Biotechnology, Institute of Ecology and Genetics of Microorganisms UB RAS, Perm 614081, Russia
- Department of Microbiology and Immunology, Perm State University, Perm 614990, Russia
- Correspondence:
| | - Yana Bykova
- Laboratory of Molecular Biotechnology, Institute of Ecology and Genetics of Microorganisms UB RAS, Perm 614081, Russia
| | - Aleksandr Maksimov
- Laboratory of Molecular Biotechnology, Institute of Ecology and Genetics of Microorganisms UB RAS, Perm 614081, Russia
- Department of Microbiology and Immunology, Perm State University, Perm 614990, Russia
| |
Collapse
|
11
|
Carvalho FM, Azevedo A, Ferreira MM, Mergulhão FJM, Gomes LC. Advances on Bacterial and Fungal Biofilms for the Production of Added-Value Compounds. BIOLOGY 2022; 11:biology11081126. [PMID: 36009752 PMCID: PMC9405441 DOI: 10.3390/biology11081126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022]
Abstract
Simple Summary The production of bio-based materials, including organic acids, antibiotics, enzymes, ethanol, and hydrogen, is generally done by the cultivation of suspended cells rather than using immobilized cells. However, several studies suggest the application of productive biofilms as a reliable alternative for biocatalysis, with many advantages over suspended-growth systems. This review gives an overview of the breakthrough in the application of biofilm platforms for the sustainable production of valuable compounds, with particular insight into the latest advances in the production of recombinant proteins. Productive biofilms are shown to improve production rates and product yields, demonstrating great potential for industrial applications. Abstract In recent years, abundant research has been performed on biofilms for the production of compounds with biotechnological and industrial relevance. The use of biofilm platforms has been seen as a compelling approach to producing fine and bulk chemicals such as organic acids, alcohols, and solvents. However, the production of recombinant proteins using this system is still scarce. Biofilm reactors are known to have higher biomass density, operational stability, and potential for long-term operation than suspended cell reactors. In addition, there is an increasing demand to harness industrial and agricultural wastes and biorefinery residues to improve process sustainability and reduce production costs. The synthesis of recombinant proteins and other high-value compounds is mainly achieved using suspended cultures of bacteria, yeasts, and fungi. This review discusses the use of biofilm reactors for the production of recombinant proteins and other added-value compounds using bacteria and fungi.
Collapse
Affiliation(s)
- Fábio M. Carvalho
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (F.M.C.); (A.A.); (M.M.F.); (F.J.M.M.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (F.M.C.); (A.A.); (M.M.F.); (F.J.M.M.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Marta M. Ferreira
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (F.M.C.); (A.A.); (M.M.F.); (F.J.M.M.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Filipe J. M. Mergulhão
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (F.M.C.); (A.A.); (M.M.F.); (F.J.M.M.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Luciana C. Gomes
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (F.M.C.); (A.A.); (M.M.F.); (F.J.M.M.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- Correspondence:
| |
Collapse
|
12
|
Boron Derivatives Accelerate Biofilm Formation of Recombinant Escherichia coli via Increasing Quorum Sensing System Autoinducer-2 Activity. Int J Mol Sci 2022; 23:ijms23158059. [PMID: 35897636 PMCID: PMC9332218 DOI: 10.3390/ijms23158059] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Boron is an essential element for autoinducer-2 (AI-2) synthesis of quorum sensing (QS) system, which affects bacterial collective behavior. As a living biocatalyst, biofilms can stably catalyze the activity of intracellular enzymes. However, it is unclear how boron affects biofilm formation in E. coli, particularly recombinant E. coli with intracellular enzymes. This study screened different boron derivatives to explore their effect on biofilm formation. The stress response of biofilm formation to boron was illuminated by analyzing AI-2 activity, extracellular polymeric substances (EPS) composition, gene expression levels, etc. Results showed that boron derivatives promote AI-2 activity in QS system. After treatment with H3BO3 (0.6 mM), the AI-2 activity increased by 65.99%, while boron derivatives increased the biomass biofilms in the order H3BO3 > NaBO2 > Na2B4O7 > NaBO3. Moreover, treatment with H3BO3 (0.6 mM) increased biomass by 88.54%. Meanwhile, AI-2 activity had a linear correlation with polysaccharides and protein of EPS at 0−0.6 mM H3BO3 and NaBO2 (R2 > 0.8). Furthermore, H3BO3 upregulated the expression levels of biofilm formation genes, quorum sensing genes, and flagellar movement genes. These findings demonstrated that boron promoted biofilm formation by upregulating the expression levels of biofilm-related genes, improving the QS system AI-2 activity, and increasing EPS secretion in E. coli.
Collapse
|
13
|
Shen H, Rösch P, Pletz MW, Popp J. In Vitro Fiber-Probe-Based Identification of Pathogens in Biofilms by Raman Spectroscopy. Anal Chem 2022; 94:5375-5381. [PMID: 35319199 DOI: 10.1021/acs.analchem.2c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biofilms are the preferred habitat of microorganisms on living and artificial surfaces. Biofilm-related infections, such as infections of medical implants, are difficult to treat, and due to a reduced cultivability of the included bacteria, difficult to diagnose. Therefore, it is highly important to rapidly identify and investigate biofilms on implant surfaces, e.g., during surgery. In this study, we present fiber-probe-based Raman spectroscopy with an excitation wavelength of 785 nm, which was applied to investigate six different pathogen species involved in biofilm-related infections. Biofilms were cultivated in a drip flow reactor, which can model a biofilm growth environment. The signals collected from a fiber probe allowed us to collect Raman spectra not only from the embedded bacterial and yeast cells but also the surrounding extracellular polymeric substance matrix. This information was used in a classification model. The model consists of a principal component analysis in combination with linear discriminant analysis and was examined by applying a leave-one-batch-out cross-validation. This model achieved a classification accuracy of 93.8%. In addition, the identification accuracy increased up to 97.5% when clinical strains were used for identification. A fiber-probe-based Raman spectroscopy method combined with a chemometric analysis might therefore serve as a fast, accurate, and portable strategy for the species identification of biofilm-related infections, e.g., during surgical procedures.
Collapse
Affiliation(s)
- Haodong Shen
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
| |
Collapse
|
14
|
Potential spoilage of extended shelf-life (ESL) milk by Bacillus subtilis and Bacillus velezensis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
15
|
Fraile S, Briones M, Revenga-Parra M, de Lorenzo V, Lorenzo E, Martínez-García E. Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies. ACS Synth Biol 2021; 10:2049-2059. [PMID: 34337948 PMCID: PMC8397431 DOI: 10.1021/acssynbio.1c00227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Indexed: 12/15/2022]
Abstract
Gram-negative bacteria are endowed with complex outer membrane (OM) structures that allow them to both interact with other organisms and attach to different physical structures. However, the design of reliable bacterial coatings of solid surfaces is still a considerable challenge. In this work, we report that ectopic expression of a fibrinogen-specific nanobody on the envelope of Pseudomonas putida cells enables controllable formation of a bacterial monolayer strongly bound to an antigen-coated support. To this end, either the wild type or a surface-naked derivative of P. putida was engineered to express a hybrid between the β-barrel of an intimin-type autotransporter inserted in the outer membrane and a nanobody (VHH) moiety that targets fibrinogen as its cognate interaction partner. The functionality of the thereby presented VHH and the strength of the resulting cell attachment to a solid surface covered with the cognate antigen were tested and parametrized with Quartz Crystal Microbalance technology. The results not only demonstrated the value of using bacteria with reduced OM complexity for efficient display of artificial adhesins, but also the potential of this approach to engineer specific bacterial coverings of predetermined target surfaces.
Collapse
Affiliation(s)
- Sofía Fraile
- Systems Biology Department, Centro Nacional
de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - María Briones
- Departamento de Química Analítica y Análisis
Instrumental, Universidad Autónoma
de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mónica Revenga-Parra
- Departamento de Química Analítica y Análisis
Instrumental, Universidad Autónoma
de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional
de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Encarnación Lorenzo
- Departamento de Química Analítica y Análisis
Instrumental, Universidad Autónoma
de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Esteban Martínez-García
- Systems Biology Department, Centro Nacional
de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
16
|
Patel A, Carlson RP, Henson MA. In silico analysis of synthetic multispecies biofilms for cellobiose-to-isobutanol conversion reveals design principles for stable and productive communities. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
17
|
Ng CK, Putra SL, Kennerley J, Habgood R, Roy RA, Raymond JL, Thompson IP, Huang WE. Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery. Microb Biotechnol 2021; 14:1580-1593. [PMID: 33993638 PMCID: PMC8313276 DOI: 10.1111/1751-7915.13823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 11/27/2022] Open
Abstract
The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10-7 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm-2 ) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm-2 ). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm3 and 300 cm3 , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.
Collapse
Affiliation(s)
- Chun Kiat Ng
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Samuel L. Putra
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Joseph Kennerley
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Robert Habgood
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Ronald A. Roy
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Jason L. Raymond
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Ian P. Thompson
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Wei E. Huang
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| |
Collapse
|
18
|
Leonov PS, Flores-Alsina X, Gernaey KV, Sternberg C. Microbial biofilms in biorefinery - Towards a sustainable production of low-value bulk chemicals and fuels. Biotechnol Adv 2021; 50:107766. [PMID: 33965529 DOI: 10.1016/j.biotechadv.2021.107766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/11/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022]
Abstract
Harnessing the potential of biocatalytic conversion of renewable biomass into value-added products is still hampered by unfavorable process economics. This has promoted the use of biofilms as an alternative to overcome the limitations of traditional planktonic systems. In this paper, the benefits and challenges of biofilm fermentations are reviewed with a focus on the production of low-value bulk chemicals and fuels from waste biomass. Our study demonstrates that biofilm fermentations can potentially improve productivities and product yields by increasing biomass retention and allowing for continuous operation at high dilution rates. Furthermore, we show that biofilms can tolerate hazardous environments, which improve the conversion of crude biomass under substrate and product inhibitory conditions. Additionally, we present examples for the improved conversion of pure and crude substrates into bulk chemicals by mixed microbial biofilms, which can benefit from microenvironments in biofilms for synergistic multi-species reactions, and improved resistance to contaminants. Finally, we suggest the use of mathematical models as useful tools to supplement experimental insights related to the effects of physico-chemical and biological phenomena on the process. Major challenges for biofilm fermentations arise from inconsistent fermentation performance, slow reactor start-up, biofilm carrier costs and carrier clogging, insufficient biofilm monitoring and process control, challenges in reactor sterilization and scale-up, and issues in recovering dilute products. The key to a successful commercialization of the technology is likely going to be an interdisciplinary approach. Crucial research areas might include genetic engineering combined with the development of specialized biofilm reactors, biofilm carrier development, in-situ biofilm monitoring, model-based process control, mixed microbial biofilm technology, development of suitable biofilm reactor scale-up criteria, and in-situ product recovery.
Collapse
Affiliation(s)
- Pascal S Leonov
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark
| | - Xavier Flores-Alsina
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark
| | - Claus Sternberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
19
|
Dorado‐Morales P, Martínez I, Rivero‐Buceta V, Díaz E, Bähre H, Lasa I, Solano C. Elevated c-di-GMP levels promote biofilm formation and biodesulfurization capacity of Rhodococcus erythropolis. Microb Biotechnol 2021; 14:923-937. [PMID: 33128507 PMCID: PMC8085952 DOI: 10.1111/1751-7915.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022] Open
Abstract
Bacterial biofilms provide high cell density and a superior adaptation and protection from stress conditions compared to planktonic cultures, making them a very promising approach for bioremediation. Several Rhodococcus strains can desulfurize dibenzothiophene (DBT), a major sulphur pollutant in fuels, reducing air pollution from fuel combustion. Despite multiple efforts to increase Rhodococcus biodesulfurization activity, there is still an urgent need to develop better biocatalysts. Here, we implemented a new approach that consisted in promoting Rhodococcus erythropolis biofilm formation through the heterologous expression of a diguanylate cyclase that led to the synthesis of the biofilm trigger molecule cyclic di-GMP (c-di-GMP). R. erythropolis biofilm cells displayed a significantly increased DBT desulfurization activity when compared to their planktonic counterparts. The improved biocatalyst formed a biofilm both under batch and continuous flow conditions which turns it into a promising candidate for the development of an efficient bioreactor for the removal of sulphur heterocycles present in fossil fuels.
Collapse
Affiliation(s)
- Pedro Dorado‐Morales
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| | - Igor Martínez
- Department of Systems BiologyCentro Nacional de BiotecnologíaAgencia Estatal Consejo Superior de Investigaciones CientíficasDarwin 3Madrid28049Spain
| | - Virginia Rivero‐Buceta
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones CientíficasRamiro de Maeztu 9Madrid28040Spain
| | - Eduardo Díaz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones CientíficasRamiro de Maeztu 9Madrid28040Spain
| | - Heike Bähre
- Research Core Unit MetabolomicsHannover Medical SchoolCarl‐Neuberg‐Straße 1Hannover30625Germany
| | - Iñigo Lasa
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| | - Cristina Solano
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| |
Collapse
|
20
|
Heuschkel I, Hanisch S, Volke DC, Löfgren E, Hoschek A, Nikel PI, Karande R, Bühler K. Pseudomonas taiwanensis biofilms for continuous conversion of cyclohexanone in drip flow and rotating bed reactors. Eng Life Sci 2021; 21:258-269. [PMID: 33716623 PMCID: PMC7923564 DOI: 10.1002/elsc.202000072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/25/2022] Open
Abstract
In this study, the biocatalytic performance of a Baeyer-Villiger monooxygenase (BVMO) catalyzing the reaction of cyclohexanone to ε-caprolactone was investigated in Pseudomonas biofilms. Biofilm growth and development of two Pseudomonas taiwanensis VLB120 variants, Ps_BVMO and Ps_BVMO_DGC, were evaluated in drip flow reactors (DFRs) and rotating bed reactors (RBRs). Engineering a hyperactive diguanylate cyclase (DGC) from Caulobacter crescentus into Ps_BVMO resulted in faster biofilm growth compared to the control Ps_BVMO strain in the DFRs. The maximum product formation rates of 92 and 87 g m-2 d-1 were observed for mature Ps_BVMO and Ps_ BVMO_DGC biofilms, respectively. The application of the engineered variants in the RBR was challenged by low biofilm surface coverage (50-60%) of rotating bed cassettes, side-products formation, oxygen limitation, and a severe drop in production rates with time. By implementing an active oxygen supply mode and a twin capillary spray feed, the biofilm surface coverage was maximized to 70-80%. BVMO activity was severely inhibited by cyclohexanol formation, resulting in a decrease in product formation rates. By controlling the cyclohexanone feed concentration at 4 mM, a stable product formation rate of 14 g m-2 d-1 and a substrate conversion of 60% was achieved in the RBR.
Collapse
Affiliation(s)
- Ingeborg Heuschkel
- Department of Solar MaterialsHelmholtz‐Centre for Environmental ResearchLeipzigGermany
| | - Selina Hanisch
- Department of Solar MaterialsHelmholtz‐Centre for Environmental ResearchLeipzigGermany
- ZINT ‐ Zentrum für integrierte NaturstofftechnikTU DresdenDresdenGermany
| | - Daniel C. Volke
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | | | - Anna Hoschek
- Department of Solar MaterialsHelmholtz‐Centre for Environmental ResearchLeipzigGermany
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Rohan Karande
- Department of Solar MaterialsHelmholtz‐Centre for Environmental ResearchLeipzigGermany
| | - Katja Bühler
- Department of Solar MaterialsHelmholtz‐Centre for Environmental ResearchLeipzigGermany
- ZINT ‐ Zentrum für integrierte NaturstofftechnikTU DresdenDresdenGermany
| |
Collapse
|
21
|
Jiang Y, Liu Y, Zhang X, Gao H, Mou L, Wu M, Zhang W, Xin F, Jiang M. Biofilm application in the microbial biochemicals production process. Biotechnol Adv 2021; 48:107724. [PMID: 33640404 DOI: 10.1016/j.biotechadv.2021.107724] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022]
Abstract
Biofilms can be naturally formed through the attachment of microorganisms on the supporting materials. However, natural biofilms formed in the environment may cause some detrimental effects, such as the equipment contamination and food safety issues et al. On the contrary, biofilms mediated microbial fermentation provides a promising approach for the efficient biochemicals production owing to the properties of self-immobilization, high resistance to toxic reactants and maintenance of long-term cells activity. While few reviews have specifically addressed the biological application of biofilms in the microbial fermentation process. Accordingly, this review will comprehensively summarize the biofilms formation mechanism and potential functions in the microbial fermentation process. Furthermore, the construction strategies for the formation of stable biofilms through synthetic biology technology or the modification of suitable supporting materials will be also discussed. The application of biofilms mediated fermentation will provide an outlook for the biorefinery platform in the future.
Collapse
Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Yansong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Xiaoyu Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Hao Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Lu Mou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Mengdi Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| |
Collapse
|
22
|
Formation and characterization of biofilms formed by salt-tolerant yeast strains in seawater-based growth medium. Appl Microbiol Biotechnol 2021; 105:2411-2426. [PMID: 33630153 DOI: 10.1007/s00253-021-11132-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/30/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Yeast whole cells have been widely used in modern biotechnology as biocatalysts to generate numerous compounds of industrial, chemical, and pharmaceutical importance. Since many of the biocatalysis-utilizing manufactures have become more concerned about environmental issues, seawater is now considered a sustainable alternative to freshwater for biocatalytic processes. This approach plausibly commenced new research initiatives into exploration of salt-tolerant yeast strains. Recently, there has also been a growing interest in possible applications of microbial biofilms in the field of biocatalysis. In these complex communities, cells demonstrate higher resistance to adverse environmental conditions due to their embedment in an extracellular matrix, in which physical, chemical, and physiological gradients exist. Considering these two topics, seawater and biofilms, in this work, we characterized biofilm formation in seawater-based growth media by several salt-tolerant yeast strains with previously demonstrated biocatalytic capacities. The tested strains formed both air-liquid-like biofilms and biofilms on silicone surfaces, with Debaryomyces fabryi, Schwanniomyces etchellsii, Schwanniomyces polymorphus, and Kluyveromyces marxianus showing the highest biofilm formation. The extracted biofilm extracellular matrices mostly consisted of carbohydrates and proteins. The latter group was primarily represented by enzymes involved in metabolic processes, particularly the biosynthetic ones, and in the response to stimuli. Specific features were also found in the carbohydrate composition of the extracellular matrix, which were dependent both on the yeast isolate and the nature of formed biofilms. Overall, our findings presented herein provide a unique data resource for further development and optimization of biocatalytic processes and applications employing seawater and halotolerant yeast biofilms.Key points• Ability for biofilm formation of some yeast-halotolerant strains in seawater medium• ECM composition dependent on strain and biofilm-forming surface• Metabolic enzymes in the ECM with potential applications for biocatalysis.
Collapse
|
23
|
Adebar N, Nastke A, Gröger H. Concepts for flow chemistry with whole-cell biocatalysts. REACT CHEM ENG 2021. [DOI: 10.1039/d0re00331j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
By combining continuous flow processing and biocatalysis, efficient, stable and cost-effective processes can be realised. In this review, an overview about different concepts for continuous flow processes based on the use of whole-cells as catalysts is given.
Collapse
Affiliation(s)
- Niklas Adebar
- Chair of Industrial Organic Chemistry and Biotechnology
- Faculty of Chemistry
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Alina Nastke
- Chair of Industrial Organic Chemistry and Biotechnology
- Faculty of Chemistry
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology
- Faculty of Chemistry
- Bielefeld University
- 33615 Bielefeld
- Germany
| |
Collapse
|
24
|
Fasim A, More VS, More SS. Large-scale production of enzymes for biotechnology uses. Curr Opin Biotechnol 2020; 69:68-76. [PMID: 33388493 DOI: 10.1016/j.copbio.2020.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023]
Abstract
Enzymes are biocatalysts that speed up the chemical reaction to obtain the final valuable product/s. Biotechnology has revolutionized the use of traditional enzymes to be applicable in industries such as food, beverage, personal and household care, agriculture, bioenergy, pharmaceutical, and various other segments. With respect to the exponential growth of enzymes in biotech industries, it becomes important to highlight the advancements and impact of enzyme technology over recent years. In this review article, we discuss the existing and emerging production approaches, applications, developments, and global need for enzymes. Special emphasis is given to the predominantly utilized hydrolytic microbial enzymes in industrial bioprocesses.
Collapse
Affiliation(s)
- Aneesa Fasim
- School of Basic and Applied Sciences, Dayananda Sagar University, Bengaluru 560 111, Karnataka, India
| | - Veena S More
- Department of Biotechnology, Sapthagiri College of Engineering, Bengaluru 560 057 Karnataka, India
| | - Sunil S More
- School of Basic and Applied Sciences, Dayananda Sagar University, Bengaluru 560 111, Karnataka, India.
| |
Collapse
|
25
|
Grobas I, Bazzoli DG, Asally M. Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools. Biochem Soc Trans 2020; 48:2903-2913. [PMID: 33300966 PMCID: PMC7752047 DOI: 10.1042/bst20200972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell-cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.
Collapse
Affiliation(s)
- Iago Grobas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Dario G. Bazzoli
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, U.K
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
26
|
Park H, Patel A, Hunt KA, Henson MA, Carlson RP. Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis. NPJ Biofilms Microbiomes 2020; 6:59. [PMID: 33268782 PMCID: PMC7710750 DOI: 10.1038/s41522-020-00170-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/23/2020] [Indexed: 01/03/2023] Open
Abstract
Planktonic cultures, of a rationally designed consortium, demonstrated emergent properties that exceeded the sums of monoculture properties, including a >200% increase in cellobiose catabolism, a >100% increase in glycerol catabolism, a >800% increase in ethanol production, and a >120% increase in biomass productivity. The consortium was designed to have a primary and secondary-resource specialist that used crossfeeding with a positive feedback mechanism, division of labor, and nutrient and energy transfer via necromass catabolism. The primary resource specialist was Clostridium phytofermentans (a.k.a. Lachnoclostridium phytofermentans), a cellulolytic, obligate anaerobe. The secondary-resource specialist was Escherichia coli, a versatile, facultative anaerobe, which can ferment glycerol and byproducts of cellobiose catabolism. The consortium also demonstrated emergent properties of enhanced biomass accumulation when grown as biofilms, which created high cell density communities with gradients of species along the vertical axis. Consortium biofilms were robust to oxic perturbations with E. coli consuming O2, creating an anoxic environment for C. phytofermentans. Anoxic/oxic cycling further enhanced biomass productivity of the biofilm consortium, increasing biomass accumulation ~250% over the sum of the monoculture biofilms. Consortium emergent properties were credited to several synergistic mechanisms. E. coli consumed inhibitory byproducts from cellobiose catabolism, driving higher C. phytofermentans growth and higher cellulolytic enzyme production, which in turn provided more substrate for E. coli. E. coli necromass enhanced C. phytofermentans growth while C. phytofermentans necromass aided E. coli growth via the release of peptides and amino acids, respectively. In aggregate, temporal cycling of necromass constituents increased flux of cellulose-derived resources through the consortium. The study establishes a consortia-based, bioprocessing strategy built on naturally occurring interactions for improved conversion of cellulose-derived sugars into bioproducts.
Collapse
Affiliation(s)
- Heejoon Park
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Engineering and Technology, University of North Alabama, Florence, AL, USA
| | - Ayushi Patel
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kristopher A Hunt
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA. .,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
27
|
Ng CK, Xu J, Cai Z, Yang L, Thompson IP, Huang WE, Cao B. Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes. Microb Biotechnol 2020; 13:1904-1916. [PMID: 32729223 PMCID: PMC7533324 DOI: 10.1111/1751-7915.13636] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/03/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Electrochemically active biofilms are capable of exchanging electrons with solid electron acceptors and have many energy and environmental applications such as bioelectricity generation and environmental remediation. The performance of electrochemically active biofilms is usually dependent on c-type cytochromes, while biofilm development is controlled by a signal cascade mediated by the intracellular secondary messenger bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP). However, it is unclear whether there are any links between the c-di-GMP regulatory system and the expression of c-type cytochromes. In this study, we constructed a S. oneidensis MR-1 strain with a higher cytoplasmic c-di-GMP level by constitutively expressing a c-di-GMP synthase and it exhibited expected c-di-GMP-influenced traits, such as lowered motility and increased biofilm formation. Compared to MR-1 wild-type strain, the high c-di-GMP strain had a higher Fe(III) reduction rate (21.58 vs 11.88 pM of Fe(III)/h cell) and greater expression of genes that code for the proteins involved in the Mtr pathway, including CymA, MtrA, MtrB, MtrC and OmcA. Furthermore, single-cell Raman microspectroscopy (SCRM) revealed a great increase of c-type cytochromes in the high c-di-GMP strain as compared to MR-1 wild-type strain. Our results reveal for the first time that the c-di-GMP regulation system indirectly or directly positively regulates the expression of cytochromes involved in the extracellular electron transport (EET) in S. oneidensis, which would help to understand the regulatory mechanism of c-di-GMP on electricity production in bacteria.
Collapse
Affiliation(s)
- Chun Kiat Ng
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore City, Singapore
| |
Collapse
|
28
|
Heuschkel I, Dagini R, Karande R, Bühler K. The Impact of Glass Material on Growth and Biocatalytic Performance of Mixed-Species Biofilms in Capillary Reactors for Continuous Cyclohexanol Production. Front Bioeng Biotechnol 2020; 8:588729. [PMID: 33042983 PMCID: PMC7522790 DOI: 10.3389/fbioe.2020.588729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022] Open
Abstract
In this study, the growth and catalytic performance of mixed-species biofilms consisting of photoautotrophic Synechocystis sp. PCC 6803 and chemoheterotrophic Pseudomonas sp. VLB120 was investigated. Both strains contained a cytochrome P450 monooxygenase enzyme system catalyzing the oxyfunctionalization of cyclohexane to cyclohexanol. Biofilm cultivation was performed in capillary glass reactors made of either, borosilicate glass (Duran) or quartz glass, in different flow regimes. Consequently, four phases could be distinguished for mixed-species biofilm growth and development in the glass-capillaries. The first phase represents the limited growth of mixed-species biofilm in the single-phase flow condition. The second phase includes a rapid increase in biofilm spatial coverage after the start of air-segments. The third phase starts with the sloughing of large biofilm patches from well-grown biofilms, and the final stage consists of biofilm regrowth and the expansion of the spatial coverage. The catalytic performance of the mixed-species biofilm after the detachment process was compared to a well-grown biofilm. With an increase in the biofilm surface coverage, the cyclohexanol production rate improved from 1.75 to 6.4 g m–2 d–1, resulting in comparable production rates to the well-grown biofilms. In summary, high productivities can be reached for biofilms cultivated in glass capillaries, but stable product formation was disturbed by sloughing events.
Collapse
Affiliation(s)
- Ingeborg Heuschkel
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Rakesh Dagini
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| |
Collapse
|
29
|
Biofilm reactors for value-added products production: An in-depth review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101662] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
30
|
Muhammad MH, Idris AL, Fan X, Guo Y, Yu Y, Jin X, Qiu J, Guan X, Huang T. Beyond Risk: Bacterial Biofilms and Their Regulating Approaches. Front Microbiol 2020; 11:928. [PMID: 32508772 PMCID: PMC7253578 DOI: 10.3389/fmicb.2020.00928] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Bacterial biofilms are complex surface attached communities of bacteria held together by self-produced polymer matrixs mainly composed of polysaccharides, secreted proteins, and extracellular DNAs. Bacterial biofilm formation is a complex process and can be described in five main phases: (i) reversible attachment phase, where bacteria non-specifically attach to surfaces; (ii) irreversible attachment phase, which involves interaction between bacterial cells and a surface using bacterial adhesins such as fimbriae and lipopolysaccharide (LPS); (iii) production of extracellular polymeric substances (EPS) by the resident bacterial cells; (iv) biofilm maturation phase, in which bacterial cells synthesize and release signaling molecules to sense the presence of each other, conducing to the formation of microcolony and maturation of biofilms; and (v) dispersal/detachment phase, where the bacterial cells depart biofilms and comeback to independent planktonic lifestyle. Biofilm formation is detrimental in healthcare, drinking water distribution systems, food, and marine industries, etc. As a result, current studies have been focused toward control and prevention of biofilms. In an effort to get rid of harmful biofilms, various techniques and approaches have been employed that interfere with bacterial attachment, bacterial communication systems (quorum sensing, QS), and biofilm matrixs. Biofilms, however, also offer beneficial roles in a variety of fields including applications in plant protection, bioremediation, wastewater treatment, and corrosion inhibition amongst others. Development of beneficial biofilms can be promoted through manipulation of adhesion surfaces, QS and environmental conditions. This review describes the events involved in bacterial biofilm formation, lists the negative and positive aspects associated with bacterial biofilms, elaborates the main strategies currently used to regulate establishment of harmful bacterial biofilms as well as certain strategies employed to encourage formation of beneficial bacterial biofilms, and highlights the future perspectives of bacterial biofilms.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Tianpei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences & College of Plant Protection & International College, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
31
|
Brück HL, Coutte F, Dhulster P, Gofflot S, Jacques P, Delvigne F. Growth Dynamics of Bacterial Populations in a Two-Compartment Biofilm Bioreactor Designed for Continuous Surfactin Biosynthesis. Microorganisms 2020; 8:microorganisms8050679. [PMID: 32392736 PMCID: PMC7285194 DOI: 10.3390/microorganisms8050679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/28/2020] [Accepted: 05/01/2020] [Indexed: 11/16/2022] Open
Abstract
Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment biofilm bioreactor was designed consisting of a stirred tank reactor and a trickle-bed reactor containing a structured metal packing for biofilm formation. A strong and poor biofilm forming B. subtilis 168 strain due to restored exopolysaccharides (EPS) production or not were cultivated in the system to study the growth behavior of the planktonic and biofilm population for the establishment of a growth model. A high dilution rate was used in order to promote biofilm formation on the packing and wash out unwanted planktonic cells. Biofilm development kinetics on the packing were assessed through a total organic carbon mass balance. The EPS+ strain showed a significantly improved performance in terms of adhesion capacity and surfactin production. The mean surfactin productivity of the EPS+ strain was about 37% higher during the continuous cultivation compared to the EPS- strain. The substrate consumption together with the planktonic cell and biofilm development were properly predicted by the model (α = 0.05). The results show the efficiency of the biofilm bioreactor for continuous surfactin production using an EPS producing strain.
Collapse
Affiliation(s)
- Hannah Luise Brück
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro N° 1158, Gembloux Agro-Bio Tech, University Liège, University Lille, INRAE, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, B-5030 Gembloux, Belgium; (H.L.B.); (P.J.)
- ICV—Institut Charles Viollette, Joint Research Unit BioEcoAgro N° 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, F-59000 Lille, France; (F.C.); (P.D.)
| | - François Coutte
- ICV—Institut Charles Viollette, Joint Research Unit BioEcoAgro N° 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, F-59000 Lille, France; (F.C.); (P.D.)
| | - Pascal Dhulster
- ICV—Institut Charles Viollette, Joint Research Unit BioEcoAgro N° 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, F-59000 Lille, France; (F.C.); (P.D.)
| | - Sébastien Gofflot
- Walloon Agricultural Research Center (CRA-W), Agricultural Product Technology Unit, Chaussée de Namur, 24, B-5030 Gembloux, Belgium;
| | - Philippe Jacques
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro N° 1158, Gembloux Agro-Bio Tech, University Liège, University Lille, INRAE, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, B-5030 Gembloux, Belgium; (H.L.B.); (P.J.)
| | - Frank Delvigne
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro N° 1158, Gembloux Agro-Bio Tech, University Liège, University Lille, INRAE, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, B-5030 Gembloux, Belgium; (H.L.B.); (P.J.)
- Correspondence:
| |
Collapse
|
32
|
Di Meglio LG, Busalmen JP, Pegoraro CN, Nercessian D. Biofilms of Halobacterium salinarum as a tool for phenanthrene bioremediation. BIOFOULING 2020; 36:564-575. [PMID: 32580583 DOI: 10.1080/08927014.2020.1779709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
The use of hyperhalophilic microorganisms is emerging as a sustainable alternative to clean hydrocarbon-polluted hypersaline water bodies. In line with this practice, this work reports on the ability of the archaeon Halobacterium salinarum to develop biofilms on a solid surface conditioned by the presence of phenanthrene crystals, which results in the removal of the contaminating compound. The cell surface hydrophobicity does not change during the removal process and this organism is shown to constitutively produce a surfactant molecule with specific action on aromatic hydrocarbons, both indicating that phenanthrene removal might proceed through a non-contact mechanism. A new approach is presented to follow the process in situ through epifluorescence microscopy by monitoring phenanthrene auto-fluorescence.
Collapse
Affiliation(s)
- Leonardo Gabriel Di Meglio
- Instituto de Investigaciones Biológicas (CONICET-UNMdP), Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina
- Laboratorio de Bioelectroquímica, INTEMA (CONICET-UNMdP), Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA (CONICET-UNMdP), Mar del Plata, Argentina
| | - César Nicolas Pegoraro
- Instituto de Investigaciones Biológicas (CONICET-UNMdP), Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas (CONICET-UNMdP), Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina
| |
Collapse
|
33
|
Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
|
34
|
Fang K, Park OJ, Hong SH. Controlling biofilms using synthetic biology approaches. Biotechnol Adv 2020; 40:107518. [PMID: 31953206 PMCID: PMC7125041 DOI: 10.1016/j.biotechadv.2020.107518] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/22/2022]
Abstract
Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.
Collapse
Affiliation(s)
- Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA; Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA.
| |
Collapse
|
35
|
Leech J, Golub S, Allan W, Simmons MJH, Overton TW. Non-pathogenic Escherichia coli biofilms: effects of growth conditions and surface properties on structure and curli gene expression. Arch Microbiol 2020; 202:1517-1527. [PMID: 32222779 PMCID: PMC7355273 DOI: 10.1007/s00203-020-01864-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/21/2020] [Accepted: 03/12/2020] [Indexed: 11/28/2022]
Abstract
Biofilm formation is a harmful phenomenon in many areas, such as in industry and clinically, but offers advantages in the field of biocatalysis for the generation of robust biocatalytic platforms. In this work, we optimised growth conditions for the production of Escherichia coli biofilms by three strains (PHL644, a K-12 derivative with enhanced expression of the adhesin curli; the commercially-used strain BL21; and the probiotic Nissle 1917) on a variety of surfaces (plastics, stainless steel and PTFE). E. coli PHL644 and PTFE were chosen as optimal strain and substratum, respectively, and conditions (including medium, temperature, and glucose concentration) for biofilm growth were determined. Finally, the impact of these growth conditions on expression of the curli genes was determined using flow cytometry for planktonic and sedimented cells. We reveal new insights into the formation of biofilms and expression of curli in E. coli K-12 in response to environmental conditions.
Collapse
Affiliation(s)
- James Leech
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Stacey Golub
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Wendy Allan
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark J H Simmons
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. .,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
36
|
Furuichi Y, Yoshimoto S, Inaba T, Nomura N, Hori K. Process Description of an Unconventional Biofilm Formation by Bacterial Cells Autoagglutinating through Sticky, Long, and Peritrichate Nanofibers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2520-2529. [PMID: 31972092 DOI: 10.1021/acs.est.9b06577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this study, we elucidated the formation process of an unconventional biofilm formed by a bacterium autoagglutinating through sticky, long, and peritrichate nanofibers. Understanding the mechanisms of biofilm formation is essential to control microbial behavior and improve environmental biotechnologies. Acinetobacter sp. Tol 5 autoagglutinate through the interaction of the long, peritrichate nanofiber protein AtaA, a trimeric autotransporter adhesin. Using AtaA, without cell growth or extracellular polymeric substances production, Tol 5 cells quickly form an unconventional biofilm. The process forming this unconventional biofilm started with cell-cell interactions, proceeded to cell clumping, and led to the formation of large cell aggregates. The cell-cell interaction was described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory based on a new concept, which considers two independent interactions between two cell bodies and between two AtaA fiber tips forming a discontinuous surface. If cell bodies cannot collide owing to an energy barrier at low ionic strengths but approach within the interactive distance of AtaA fibers, cells can agglutinate through their contact. Cell clumping proceeds following the cluster-cluster aggregation model, and an unconventional biofilm containing void spaces and a fractal nature develops. Understanding its formation process would extend the utilization of various types of biofilms, enhancing environmental biotechnologies.
Collapse
Affiliation(s)
- Yoshihide Furuichi
- Department of Biotechnology, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , Aichi 464-8603 , Japan
| | - Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , Aichi 464-8603 , Japan
| | - Tomohiro Inaba
- Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Ibaraki 305-0006 , Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Ibaraki 305-0006 , Japan
- Microbiology Research Center for Sustainability , University of Tsukuba , Tsukuba , Ibaraki 305-8572 , Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , Aichi 464-8603 , Japan
| |
Collapse
|
37
|
Morinaga K, Yoshida K, Takahashi K, Nomura N, Toyofuku M. Peculiarities of biofilm formation by Paracoccus denitrificans. Appl Microbiol Biotechnol 2020; 104:2427-2433. [PMID: 32002601 PMCID: PMC7223048 DOI: 10.1007/s00253-020-10400-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 01/24/2023]
Abstract
Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.
Collapse
Affiliation(s)
- Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Keitaro Yoshida
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2-17-2-1, Tsukisamu-higashi, Toyohira-ku, Sapporo, Japan
| | - Kohei Takahashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
| |
Collapse
|
38
|
Hu Y, Liu X, Ren ATM, Gu JD, Cao B. Optogenetic Modulation of a Catalytic Biofilm for the Biotransformation of Indole into Tryptophan. CHEMSUSCHEM 2019; 12:5142-5148. [PMID: 31621183 DOI: 10.1002/cssc.201902413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
In green chemical synthesis, biofilms as biocatalysts have shown great promise. Efficient biofilm-mediated biocatalysis requires the modulation of biofilm formation. Optogenetic tools are ideal to control biofilms because light is noninvasive, easily controllable, and cost-efficient. In this study, a gene circuit responsive to near-infrared (NIR) light was used to modulate the cellular level of bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP), a central regulator of the prokaryote biofilm lifestyle, which allowed the regulation of biofilm formation by using NIR light. The engineered biofilm was applied to catalyze the biotransformation of indole into tryptophan in submerged biofilm reactors and NIR-light-enhanced biofilm formation resulted in an approximately 30 % increase in tryptophan yield, which demonstrates the feasibility of the application of light to modulate the formation and performance of catalytic biofilms for chemical production. The c-di-GMP-targeted optogenetic approach to modulate catalytic biofilms showcases applications for biofilm-mediated biocatalysis.
Collapse
Affiliation(s)
- Yidan Hu
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Xiaobo Liu
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, P.R. China
| | - Aloysius Teng Min Ren
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, P.R. China
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore, 639798, Singapore
| |
Collapse
|
39
|
Wynands B, Otto M, Runge N, Preckel S, Polen T, Blank LM, Wierckx N. Streamlined Pseudomonas taiwanensis VLB120 Chassis Strains with Improved Bioprocess Features. ACS Synth Biol 2019; 8:2036-2050. [PMID: 31465206 DOI: 10.1021/acssynbio.9b00108] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Microbes harbor many traits that are dispensable or even unfavorable under industrial and laboratory settings. The elimination of such traits could improve the host's efficiency, genetic stability, and robustness, thereby increasing the predictability and boosting its performance as a microbial cell factory. We engineered solvent-tolerant Pseudomonas taiwanensis VLB120 to yield streamlined chassis strains with higher growth rates and biomass yields, enhanced solvent tolerance, and improved process performance. In total, the genome was reduced by up to 10%. This was achieved by the elimination of genes that enable the cell to swim and form biofilms and by the deletion of the megaplasmid pSTY and large proviral segments. The resulting strain GRC1 had a 15% higher growth rate and biomass yield than the wildtype. However, this strain lacks the pSTY-encoded efflux pump TtgGHI, rendering it solvent-sensitive. Through reintegration of ttgGHI by chromosomal insertion without (GRC2) and with (GRC3) the corresponding regulator genes, the solvent-tolerant phenotype was enhanced. The generated P. taiwanensis GRC strains enlarge the repertoire of streamlined chassis with enhanced key performance indicators, making them attractive hosts for biotechnological applications. The different solvent tolerance levels of GRC1, GRC2, and GRC3 enable the selection of a fitting host platform in relation to the desired process requirements in a chassis à la carte principle. This was demonstrated in a metabolic engineering approach for the production of phenol from glycerol. The streamlined producer GRC1Δ5-TPL38 outperformed the equivalent nonstreamlined producer VLB120Δ5-TPL38 concerning phenol titer, rate, and yield, thereby highlighting the added value of the streamlined chassis.
Collapse
Affiliation(s)
- Benedikt Wynands
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Maike Otto
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nadine Runge
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Sarah Preckel
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
40
|
Modulation of fungal biofilm physiology and secondary product formation based on physico-chemical surface properties. Bioprocess Biosyst Eng 2019; 42:1935-1946. [DOI: 10.1007/s00449-019-02187-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/24/2019] [Accepted: 08/01/2019] [Indexed: 11/29/2022]
|
41
|
Abstract
The biocatalytic application of photoautotrophic organisms is a promising alternative for the production of biofuels and value-added compounds as they do not rely on carbohydrates as a source of carbon, electrons, and energy. Although the photoautotrophic organisms hold potential for the development of sustainable processes, suitable reactor concepts that allow high cell density (HCD) cultivation of photoautotrophic microorganisms are limited. Such reactors need a high surface to volume ratio to enhance light availability. Furthermore, the accumulation of high oxygen concentrations as a consequence of oxygenic photosynthesis, and its inhibitory effect on cell growth needs to be prevented. Here, we present a method for HCD cultivation of oxygenic phototrophs based on the co-cultivation of different trophies in a biofilm format to avoid high oxygen partial-pressure and attain HCDs of up to 51.8 gBDW L−1 on a lab scale. In this article, we show: A robust method for mixed trophies biofilm cultivation in capillary reactors Set-up and operation of a biofilm capillary reactor A method to quantify oxygen in the continuous biofilm capillary reactor
Collapse
|
42
|
Cuny L, Pfaff D, Luther J, Ranzinger F, Ödman P, Gescher J, Guthausen G, Horn H, Hille‐Reichel A. Evaluation of productive biofilms for continuous lactic acid production. Biotechnol Bioeng 2019; 116:2687-2697. [DOI: 10.1002/bit.27080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/11/2019] [Accepted: 05/25/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Laure Cuny
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
| | - Daniel Pfaff
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
| | - Jonas Luther
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
| | - Florian Ranzinger
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
| | | | - Johannes Gescher
- Department of Applied Biology, Institute for Applied BiologyKarlsruhe Institute of Technology Karlsruhe Germany
| | - Gisela Guthausen
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
- Karlsruhe Institute of TechnologyMechanical Process Engineering and Mechanics Karlsruhe Germany
| | - Harald Horn
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
- DVGW Research Laboratories for Water Chemistry and Water Technology Karlsruhe Germany
| | - Andrea Hille‐Reichel
- Karlsruhe Institute of Technology, Engler‐Bunte‐InstitutWater Chemistry and Water Technology Karlsruhe Germany
| |
Collapse
|
43
|
Patel A, Carlson RP, Henson MA. In Silico Metabolic Design of Two-Strain Biofilm Systems Predicts Enhanced Biomass Production and Biochemical Synthesis. Biotechnol J 2019; 14:e1800511. [PMID: 30927492 DOI: 10.1002/biot.201800511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/20/2019] [Indexed: 11/09/2022]
Abstract
Engineered biofilm consortia have the potential to solve important biotechnological problems that have proved difficult for monoculture biofilms and planktonic consortia, such as conversion of lignocellulosic material to useful biochemicals. While considerable experimental progress has been reported for engineering and characterizing biofilm consortia, the field still lacks in silico tools for simulation, design, and optimization of stable, robust, and productive designed consortia. We developed biofilm consortia metabolic models for two coculture systems centered around the ecological design motif of a primary cell type that utilizes a supplied electron donor and secretes acetate as a byproduct and a secondary cell type that consumes the acetate, relieving byproduct inhibition on the primary cell type and enhancing overall system biomass. The models presented in this paper predict that distinct metabolic niches for the two cell types could be established by supplying electron donors and acceptors at opposite ends of the biofilm and that acetate consumption by the secondary cell type could increase total biomass accumulation and the synthesis of valuable biochemicals, such as isobutanol, by the primary cell type. System tunability is enhanced when each cell type is supplied with a unique terminal electron acceptor at opposite ends of the biofilm rather than competing for a common electron acceptor. Our model provides good qualitative agreement with data for a synthetic Escherichia coli coculture system, suggesting that the proposed design rules may have wide applicability to engineered biofilm consortia.
Collapse
Affiliation(s)
- Ayushi Patel
- Department of Chemical Engineering, Institute for Applied Life Sciences University of Massachusetts, 240 Thatcher Way, Amherst, MA, 01003, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering Montana State University, Bozeman, MT, 59717, USA
| | - Michael A Henson
- Department of Chemical Engineering, Institute for Applied Life Sciences University of Massachusetts, 240 Thatcher Way, Amherst, MA, 01003, USA
| |
Collapse
|
44
|
Zarabadi MP, Couture M, Charette SJ, Greener J. A Generalized Kinetic Framework Applied to Whole‐Cell Bioelectrocatalysis in Bioflow Reactors Clarifies Performance Enhancements for
Geobacter Sulfurreducens
Biofilms. ChemElectroChem 2019. [DOI: 10.1002/celc.201900732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mir Pouyan Zarabadi
- Département de Chimie, Faculté des sciences et de génieUniversité Laval, Québec City, QC Canada
| | - Manon Couture
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génieUniversité Laval Québec City, QC Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génieUniversité Laval Québec City, QC Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec Québec City, QC Canada
| | - Jesse Greener
- Département de Chimie, Faculté des sciences et de génieUniversité Laval, Québec City, QC Canada
- CHU de Québec, centre de rechercheUniversité Laval, 10 rue de l'Espinay Québec, QC Canada
| |
Collapse
|
45
|
Biofilm systems as tools in biotechnological production. Appl Microbiol Biotechnol 2019; 103:5095-5103. [PMID: 31079168 DOI: 10.1007/s00253-019-09869-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 01/08/2023]
Abstract
The literature provides more and more examples of research projects that develop novel production processes based on microorganisms organized in the form of biofilms. Biofilms are aggregates of microorganisms that are attached to interfaces. These viscoelastic aggregates of cells are held together and are embedded in a matrix consisting of multiple carbohydrate polymers as well as proteins. Biofilms are characterized by a very high cell density and by a natural retentostat behavior. Both factors can contribute to high productivities and a facilitated separation of the desired end-product from the catalytic biomass. Within the biofilm matrix, stable gradients of substrates and products form, which can lead to a differentiation and adaptation of the microorganisms' physiology to the specific process conditions. Moreover, growth in a biofilm state is often accompanied by a higher resistance and resilience towards toxic or growth inhibiting substances and factors. In this short review, we summarize how biofilms can be studied and what most promising niches for their application can be. Moreover, we highlight future research directions that will accelerate the advent of productive biofilms in biology-based production processes.
Collapse
|
46
|
Hu MX, Li JN, Guo Q, Zhu YQ, Niu HM. Probiotics Biofilm-Integrated Electrospun Nanofiber Membranes: A New Starter Culture for Fermented Milk Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3198-3208. [PMID: 30838858 DOI: 10.1021/acs.jafc.8b05024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Electrospun nanofiber membranes are widely investigated in the past few decades as candidates for tissue engineering, which can mimic natural extracellular matrix (ECM) and improve cell adhesion, proliferation, and expression on nanofiber membranes. However, the formation of bacterial biofilms on nanofiber membranes and application of the biofilm-integrated nanofiber membranes remain largely unknown. Here, electrospun cellulose acetate nanofiber membranes are first utilized as scaffold materials for Lactobacillus plantarum ( L. plantarum) biofilm formation. Nanofiber membranes proved to be an excellent scaffold for bacteria biofilm with high stability, where biofilms were interlocked with nanofibers forming a cohesive structure. In comparison with planktonic bacteria, L. plantarum biofilms on nanofiber membranes show excellent gastrointestinal resistance. Instead of decreasing, the number of viable cells increased after 3 h digestion in vitro. The L. plantarum biofilm-integrated nanofiber membranes were used as reusable starter cultures for fermented milk production showing excellent fermentative ability and higher survival of L. plantarum during shelf life. The viable cells in fermented milk remained at 11 log CFU/g throughout the reusable batches, which is far above the required value of 7 log CFU/g in commercial products. In addition, the produced fermented milk possesses shorter fermentation time and higher survival of probiotics during shelf life. The results suggest electrospun nanofiber membranes are ideal scaffold materials for bacteria biofilms immobilization in biotechnology and fermentation engineering, which broaden the potential use of electrospun nanofiber membranes in microbiology and strengthen the application of biofilms in fermentation engineering.
Collapse
Affiliation(s)
- Meng-Xin Hu
- School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310018 , P. R. China
| | - Ji-Nian Li
- School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310018 , P. R. China
| | - Qian Guo
- School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310018 , P. R. China
| | - Ya-Qian Zhu
- School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310018 , P. R. China
| | - Hong-Mei Niu
- School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310018 , P. R. China
| |
Collapse
|
47
|
Pousti M, Joly M, Roberge P, Amirdehi MA, Bégin-Drolet A, Greener J. Linear Scanning ATR-FTIR for Chemical Mapping and High-Throughput Studies of Pseudomonas sp. Biofilms in Microfluidic Channels. Anal Chem 2018; 90:14475-14483. [DOI: 10.1021/acs.analchem.8b04279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Mohammad Pousti
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Maxime Joly
- Département de génie mécanique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Patrice Roberge
- Département de génie mécanique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
| | | | - Andre Bégin-Drolet
- Département de génie mécanique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Jesse Greener
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- CHU de Quebec Research Centre, Laval University, 10 rue de l’Espinay, Québec, QC G1L 3L5, Canada
| |
Collapse
|
48
|
Paracoccus seriniphilus adhered on surfaces: Resistance of a seawater bacterium against shear forces under the influence of roughness, surface energy, and zeta potential of the surfaces. Biointerphases 2018; 13:051003. [PMID: 30336679 DOI: 10.1116/1.5049226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Bacteria in flowing media are exposed to shear forces exerted by the fluid. Before a biofilm can be formed, the bacteria have to attach to a solid surface and have to resist these shear forces. Here, the authors determined dislodgement forces of single Paracoccus seriniphilus bacteria by means of lateral force microscopy. The first measurement set was performed on very flat glass and titanium (both as very hydrophilic samples with water contact angles below 20°) as well as highly oriented pyrolytic graphite (HOPG) and steel surfaces (both as more hydrophobic surfaces in the context of biological interaction with water contact angles above 50°). The different surfaces also show different zeta potentials in the range between -18 and -108 mV at the measurement pH of 7. The second set comprised titanium with different RMS (root mean square) roughness values from a few nanometers up to 22 nm. Lateral forces between 0.5 and 3 nN were applied. For Paracoccus seriniphilus, the authors found as a general trend that the surface energy of the substrate at comparable roughness determines the detachment process. The surface energy is inversely proportional to the initial adhesion forces of the bacterium with the surface. The higher the surface energy (and the lower the initial adhesion force) is, the easier the dislodgement of the bacteria happens. In contrast, electrostatics play only a secondary role in the lateral dislodgement of the bacteria and may come only into play if surface energies are the same. Furthermore, the surface chemistry (glass, titanium, and steel as oxidic surfaces and HOPG as a nonoxidic surface) seems to play an important role because HOPG does not completely follow the above mentioned general trend found for the oxide covered surfaces. In addition, the roughness of the substrates (made of the same material) is limiting the lateral dislodgement of the bacteria. All examined structures with RMS roughness of about 8-22 nm on titanium prevent the bacteria from the lateral dislodgement compared to polished titanium with an RMS roughness of about 3 nm.
Collapse
|
49
|
Yin B, Zhu L, Zhang Y, Dong P, Mao Y, Liang R, Niu L, Luo X. The Characterization of Biofilm Formation and Detection of Biofilm-Related Genes in Salmonella Isolated from Beef Processing Plants. Foodborne Pathog Dis 2018; 15:660-667. [DOI: 10.1089/fpd.2018.2466] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Binru Yin
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Lixian Zhu
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yimin Zhang
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Pengcheng Dong
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yanwei Mao
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Rongrong Liang
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Lebao Niu
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xin Luo
- Department of Food Science, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| |
Collapse
|
50
|
Zhang J, Poh CL. Regulating exopolysaccharide gene wcaF allows control of Escherichia coli biofilm formation. Sci Rep 2018; 8:13127. [PMID: 30177768 PMCID: PMC6120894 DOI: 10.1038/s41598-018-31161-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022] Open
Abstract
While biofilms are known to cause problems in many areas of human health and the industry, biofilms are important in a number of engineering applications including wastewater management, bioremediation, and bioproduction of valuable chemicals. However, excessive biofilm growth remains a key challenge in the use of biofilms in these applications. As certain amount of biofilm growth is required for efficient use of biofilms, the ability to control and maintain biofilms at desired thickness is vital. To this end, we developed synthetic gene circuits to control E. coli MG1655 biofilm formation by using CRISPRi/dCas9 to regulate a gene (wcaF) involved in the synthesis of colanic acid (CA), a key polysaccharide in E. coli biofilm extracellular polymeric substance (EPS). We showed that the biofilm formation was inhibited when wcaF was repressed and the biofilms could be maintained at a different thickness over a period of time. We also demonstrated that it is also possible to control the biofilm thickness spatially by inhibiting wcaF gene using a genetic light switch. The results demonstrate that the approach has great potential as a new means to control and maintain biofilm thickness in biofilm related applications.
Collapse
Affiliation(s)
- Jingyun Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 117583, 4 Engineering Drive 3, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 117456, 28 Medical Drive, Singapore, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 117583, 4 Engineering Drive 3, Singapore, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 117456, 28 Medical Drive, Singapore, Singapore.
| |
Collapse
|