101
|
Ecological roles and biotechnological applications of marine and intertidal microbial biofilms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 146:163-205. [PMID: 24817086 DOI: 10.1007/10_2014_271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This review is a retrospective of ecological effects of bioactivities produced by biofilms of surface-dwelling marine/intertidal microbes as well as of the industrial and environmental biotechnologies developed exploiting the knowledge of biofilm formation. Some examples of significant interest pertaining to the ecological aspects of biofilm-forming species belonging to the Roseobacter clade include autochthonous bacteria from turbot larvae-rearing units with potential application as a probiotic as well as production of tropodithietic acid and indigoidine. Species of the Pseudoalteromonas genus are important examples of successful surface colonizers through elaboration of the AlpP protein and antimicrobial agents possessing broad-spectrum antagonistic activity against medical and environmental isolates. Further examples of significance comprise antiprotozoan activity of Pseudoalteromonas tunicata elicited by violacein, inhibition of fungal colonization, antifouling activities, inhibition of algal spore germination, and 2-n-pentyl-4-quinolinol production. Nitrous oxide, an important greenhouse gas, emanates from surface-attached microbial activity of marine animals. Marine and intertidal biofilms have been applied in the biotechnological production of violacein, phenylnannolones, and exopolysaccharides from marine and tropical intertidal environments. More examples of importance encompass production of protease, cellulase, and xylanase, melanin, and riboflavin. Antifouling activity of Bacillus sp. and application of anammox bacterial biofilms in bioremediation are described. Marine biofilms have been used as anodes and cathodes in microbial fuel cells. Some of the reaction vessels for biofilm cultivation reviewed are roller bottle, rotating disc bioreactor, polymethylmethacrylate conico-cylindrical flask, fixed bed reactor, artificial microbial mats, packed-bed bioreactors, and the Tanaka photobioreactor.
Collapse
|
102
|
|
103
|
Disruption of putrescine biosynthesis in Shewanella oneidensis enhances biofilm cohesiveness and performance in Cr(VI) immobilization. Appl Environ Microbiol 2013; 80:1498-506. [PMID: 24362428 DOI: 10.1128/aem.03461-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although biofilm-based bioprocesses have been increasingly used in various applications, the long-term robust and efficient biofilm performance remains one of the main bottlenecks. In this study, we demonstrated that biofilm cohesiveness and performance of Shewanella oneidensis can be enhanced through disrupting putrescine biosynthesis. Through random transposon mutagenesis library screening, one hyperadherent mutant strain, CP2-1-S1, exhibiting an enhanced capability in biofilm formation, was obtained. Comparative analysis of the performance of biofilms formed by S. oneidensis MR-1 wild type (WT) and CP2-1-S1 in removing dichromate (Cr2O7(2-)), i.e., Cr(VI), from the aqueous phase showed that, compared with the WT biofilms, CP2-1-S1 biofilms displayed a substantially lower rate of cell detachment upon exposure to Cr(VI), suggesting a higher cohesiveness of the mutant biofilms. In addition, the amount of Cr(III) immobilized by CP2-1-S1 biofilms was much larger, indicating an enhanced performance in Cr(VI) bioremediation. We further showed that speF, a putrescine biosynthesis gene, was disrupted in CP2-1-S1 and that the biofilm phenotypes could be restored by both genetic and chemical complementations. Our results also demonstrated an important role of putrescine in mediating matrix disassembly in S. oneidensis biofilms.
Collapse
|
104
|
Zhao N, Bai Y, Liu CG, Zhao XQ, Xu JF, Bai FW. FlocculatingZymomonas mobilisis a promising host to be engineered for fuel ethanol production from lignocellulosic biomass. Biotechnol J 2013; 9:362-71. [DOI: 10.1002/biot.201300367] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/31/2013] [Indexed: 11/07/2022]
|
105
|
|
106
|
Immobilization of pectinase on oxidized pulp fiber and its application in whitewater treatment. Carbohydr Polym 2013; 97:523-9. [DOI: 10.1016/j.carbpol.2013.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/17/2013] [Accepted: 05/11/2013] [Indexed: 11/21/2022]
|
107
|
Ishikawa M, Shigemori K, Hori K. Application of the adhesive bacterionanofiber AtaA to a novel microbial immobilization method for the production of indigo as a model chemical. Biotechnol Bioeng 2013; 111:16-24. [PMID: 23893702 DOI: 10.1002/bit.25012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 07/06/2013] [Accepted: 07/15/2013] [Indexed: 11/09/2022]
Abstract
The toluene-degrading bacterium Acinetobacter sp. Tol 5 shows high adhesiveness mediated by the bacterionanofiber protein AtaA, which is a new member of the trimeric autotransporter adhesin (TAA) family. In contrast to other reported TAAs, AtaA mediates the adhesion of Tol 5 to various abiotic surfaces ranging from hydrophobic plastics to hydrophilic glass and stainless steel. The expression of ataA in industrially relevant bacteria improves their adhesiveness and enables immobilization directly onto support materials. This represents a new method that can be alternated with conventional immobilization via gel entrapment and chemical bonding. In this study, we demonstrate the feasibility of this immobilizing method by utilizing AtaA. As a model case for this method, the indigo producer Acinetobacter sp. ST-550 was transformed with ataA and immobilized on a polyurethane support. The immobilized ST-550 cells were transferred directly to a reaction solution containing indole as the substrate. The immobilized ST-550 cells showed a faster indigo production rate at high concentrations of indole compared with planktonic ST-550 not expressing the ataA gene, implying that immobilization enhanced the tolerance of ST-550 to the substrate indole. As a result, the immobilized ST-550 produced fivefold higher levels of indigo than planktonic ST-550. These results proved that AtaA is useful for bacterial immobilization.
Collapse
Affiliation(s)
- Masahito Ishikawa
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | | | | |
Collapse
|
108
|
Zi LH, Liu CG, Xin CB, Bai FW. Stillage backset and its impact on ethanol fermentation by the flocculating yeast. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
109
|
|
110
|
Bolivar JM, Consolati T, Mayr T, Nidetzky B. Shine a light on immobilized enzymes: real-time sensing in solid supported biocatalysts. Trends Biotechnol 2013; 31:194-203. [PMID: 23384504 DOI: 10.1016/j.tibtech.2013.01.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/06/2013] [Accepted: 01/07/2013] [Indexed: 01/01/2023]
Abstract
Enzyme immobilization on solid supports has been key to biotransformation development. Although technologies for immobilization have largely reached maturity, the resulting biocatalysts are not well understood mechanistically. One limitation is that their internal environment is usually inferred from external data. Therefore, biological consequences of the immobilization remain masked by physical effects of mass transfer, obstructing further development. Work reviewed herein shows that opto-chemical sensing performed directly within the solid support enables the biocatalyst's internal environment to be uncovered quantitatively and in real time. Non-invasive methods of intraparticle pH and O2 determination are presented, and their use as process analytical tools for development of heterogeneous biocatalysts is described. Method diversification to other analytes remains a challenging task for the future.
Collapse
Affiliation(s)
- Juan M Bolivar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | | | | | | |
Collapse
|
111
|
|
112
|
|
113
|
Gross R, Buehler K, Schmid A. Engineered catalytic biofilms for continuous large scale production of n-octanol and (S)-styrene oxide. Biotechnol Bioeng 2012; 110:424-36. [PMID: 22886684 DOI: 10.1002/bit.24629] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 07/11/2012] [Accepted: 07/26/2012] [Indexed: 11/08/2022]
Abstract
This study evaluates the technical feasibility of biofilm-based biotransformations at an industrial scale by theoretically designing a process employing membrane fiber modules as being used in the chemical industry and compares the respective process parameters to classical stirred-tank studies. To our knowledge, catalytic biofilm processes for fine chemicals production have so far not been reported on a technical scale. As model reactions, we applied the previously studied asymmetric styrene epoxidation employing Pseudomonas sp. strain VLB120ΔC biofilms and the here-described selective alkane hydroxylation. Using the non-heme iron containing alkane hydroxylase system (AlkBGT) from P. putida Gpo1 in the recombinant P. putida PpS81 pBT10 biofilm, we were able to continuously produce 1-octanol from octane with a maximal productivity of 1.3 g L ⁻¹(aq) day⁻¹ in a single tube micro reactor. For a possible industrial application, a cylindrical membrane fiber module packed with 84,000 polypropylene fibers is proposed. Based on the here presented calculations, 59 membrane fiber modules (of 0.9 m diameter and 2 m length) would be feasible to realize a production process of 1,000 tons/year for styrene oxide. Moreover, the product yield on carbon can at least be doubled and over 400-fold less biomass waste would be generated compared to classical stirred-tank reactor processes. For the octanol process, instead, further intensification in biological activity and/or surface membrane enlargement is required to reach production scale. By taking into consideration challenges such as biomass growth control and maintaining a constant biological activity, this study shows that a biofilm process at an industrial scale for the production of fine chemicals is a sustainable alternative in terms of product yield and biomass waste production.
Collapse
Affiliation(s)
- Rainer Gross
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Str. 66, Dortmund 44221, Germany
| | | | | |
Collapse
|
114
|
Bernstein HC, Carlson RP. Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems. Comput Struct Biotechnol J 2012; 3:e201210017. [PMID: 24688677 PMCID: PMC3962199 DOI: 10.5936/csbj.201210017] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/24/2012] [Accepted: 11/28/2012] [Indexed: 01/29/2023] Open
Abstract
This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery.
Collapse
Affiliation(s)
- Hans C Bernstein
- Department of Chemical and Biological Engineering & Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
| | - Ross P Carlson
- Department of Chemical and Biological Engineering & Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
| |
Collapse
|
115
|
Gosse JL, Chinn MS, Grunden AM, Bernal OI, Jenkins JS, Yeager C, Kosourov S, Seibert M, Flickinger MC. A versatile method for preparation of hydrated microbial–latex biocatalytic coatings for gas absorption and gas evolution. ACTA ACUST UNITED AC 2012; 39:1269-78. [DOI: 10.1007/s10295-012-1135-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/18/2012] [Indexed: 10/28/2022]
Abstract
Abstract
We describe a latex wet coalescence method for gas-phase immobilization of microorganisms on paper which does not require drying for adhesion. This method reduces drying stresses to the microbes. It is applicable for microorganisms that do not tolerate desiccation stress during latex drying even in the presence of carbohydrates. Small surface area, 10–65 μm thick coatings were generated on chromatography paper strips and placed in the head-space of vertical sealed tubes containing liquid to hydrate the paper. These gas-phase microbial coatings hydrated by liquid in the paper pore space demonstrated absorption or evolution of H2, CO, CO2 or O2. The microbial products produced, ethanol and acetate, diffuse into the hydrated paper pores and accumulate in the liquid at the bottom of the tube. The paper provides hydration to the back side of the coating and also separates the biocatalyst from the products. Coating reactivity was demonstrated for Chlamydomonas reinhardtii CC124, which consumed CO2 and produced 10.2 ± 0.2 mmol O2 m−2 h−1, Rhodopseudomonas palustris CGA009, which consumed acetate and produced 0.47 ± 0.04 mmol H2 m−2 h−1, Clostridium ljungdahlii OTA1, which consumed 6 mmol CO m−2 h−1, and Synechococcus sp. PCC7002, which consumed CO2 and produced 5.00 ± 0.25 mmol O2 m−2 h−1. Coating thickness and microstructure were related to microbe size as determined by digital micrometry, profilometry, and confocal microscopy. The immobilization of different microorganisms in thin adhesive films in the gas phase demonstrates the utility of this method for evaluating genetically optimized microorganisms for gas absorption and gas evolution.
Collapse
Affiliation(s)
- Jimmy L Gosse
- grid.40803.3f 0000000121736074 Department of Biological and Agricultural Engineering North Carolina State University 277D.S. Weaver Labs 27695 Raleigh NC USA
- BioCee, Inc. 1479 Gortner Ave Suite 322 55108 St. Paul MN USA
| | - Mari S Chinn
- grid.40803.3f 0000000121736074 Department of Biological and Agricultural Engineering North Carolina State University 277D.S. Weaver Labs 27695 Raleigh NC USA
| | - Amy M Grunden
- grid.40803.3f 0000000121736074 Department of Microbiology North Carolina State University 4550 Thomas Hall 27695 Raleigh NC USA
| | - Oscar I Bernal
- grid.40803.3f 0000000121736074 Department of Chemical and Biomolecular Engineering North Carolina State University 911 Partners Way 27695 Raleigh NC USA
| | - Jessica S Jenkins
- grid.40803.3f 0000000121736074 Department of Chemical and Biomolecular Engineering North Carolina State University 911 Partners Way 27695 Raleigh NC USA
| | - Chris Yeager
- grid.451247.1 0000000403674086 Environmental Sciences and Biotechnology Savannah River National Laboratory Building 999-W 29808 Aiken SC USA
| | - Sergey Kosourov
- grid.419357.d 0000000121993636 Energy Sciences Directorate, National Renewable Energy Laboratory 1617 Cole Blvd. 80401 Golden CO USA
| | - Michael Seibert
- grid.419357.d 0000000121993636 Energy Sciences Directorate, National Renewable Energy Laboratory 1617 Cole Blvd. 80401 Golden CO USA
| | - Michael C Flickinger
- grid.40803.3f 0000000121736074 Department of Chemical and Biomolecular Engineering, Golden-LEAF Biomanufacturing Training and Education Center North Carolina State University Campus Box 7928 27695 Raleigh NC USA
| |
Collapse
|
116
|
Halan B, Buehler K, Schmid A. Biofilms as living catalysts in continuous chemical syntheses. Trends Biotechnol 2012; 30:453-65. [PMID: 22704028 DOI: 10.1016/j.tibtech.2012.05.003] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 04/04/2012] [Accepted: 05/08/2012] [Indexed: 12/11/2022]
Abstract
Biofilms are resilient to a wide variety of environmental stresses. This inherited robustness has been exploited mainly for bioremediation. With a better understanding of their physiology, the application of these living catalysts has been extended to the production of bulk and fine chemicals as well as towards biofuels, biohydrogen, and electricity production in microbial fuel cells. Numerous challenges call for novel solutions and concepts of analytics, biofilm reactor design, product recovery, and scale-up strategies. In this review, we highlight recent advancements in spatiotemporal biofilm characterization and new biofilm reactor developments for the production of value-added fine chemicals as well as current challenges and future scenarios.
Collapse
Affiliation(s)
- Babu Halan
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse 66, Dortmund 44227, Germany
| | | | | |
Collapse
|
117
|
Gutiérrez-Correa M, Ludeña Y, Ramage G, Villena GK. Recent Advances on Filamentous Fungal Biofilms for Industrial Uses. Appl Biochem Biotechnol 2012; 167:1235-53. [DOI: 10.1007/s12010-012-9555-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/06/2012] [Indexed: 11/28/2022]
|
118
|
Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 2012; 93:2279-90. [DOI: 10.1007/s00253-012-3928-0] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/29/2022]
|
119
|
|
120
|
Developing symbiotic consortia for lignocellulosic biofuel production. Appl Microbiol Biotechnol 2012; 93:1423-35. [PMID: 22278256 DOI: 10.1007/s00253-011-3762-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 11/12/2011] [Accepted: 11/14/2011] [Indexed: 10/14/2022]
Abstract
The search for petroleum alternatives has motivated intense research into biological breakdown of lignocellulose to produce liquid fuels such as ethanol. Degradation of lignocellulose for biofuel production is a difficult process which is limited by, among other factors, the recalcitrance of lignocellulose and biological toxicity of the products. Consolidated bioprocessing has been suggested as an efficient and economical method of producing low value products from lignocellulose; however, it is not clear whether this would be accomplished more efficiently with a single organism or community of organisms. This review highlights examples of mixtures of microbes in the context of conceptual models for developing symbiotic consortia for biofuel production from lignocellulose. Engineering a symbiosis within consortia is a putative means of improving both process efficiency and stability relative to monoculture. Because microbes often interact and exist attached to surfaces, quorum sensing and biofilm formation are also discussed in terms of consortia development and stability. An engineered, symbiotic culture of multiple organisms may be a means of assembling a novel combination of metabolic capabilities that can efficiently produce biofuel from lignocellulose.
Collapse
|
121
|
Winn M, Foulkes JM, Perni S, Simmons MJH, Overton TW, Goss RJM. Biofilms and their engineered counterparts: A new generation of immobilised biocatalysts. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20085f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
122
|
Ma Q, Zhang G, Wood TK. Escherichia coli BdcA controls biofilm dispersal in Pseudomonas aeruginosa and Rhizobium meliloti. BMC Res Notes 2011; 4:447. [PMID: 22029875 PMCID: PMC3214192 DOI: 10.1186/1756-0500-4-447] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background Previously we showed that BdcA controls Escherichia coli biofilm dispersal by binding the ubiquitous bacterial signal cyclic diguanylate (c-di-GMP); upon reducing the concentration of c-di-GMP, the cell shifts to the planktonic state by increasing motility, decreasing aggregation, and decreasing production of biofilm adhesins. Findings Here we report that BdcA also increases biofilm dispersal in other Gram-negative bacteria including Pseudomonas aeruginosa, Pseudomonas fluorescens, and Rhizobium meliloti. BdcA binds c-di-GMP in these strains and thereby reduces the effective c-di-GMP concentrations as demonstrated by increases in swimming motility and swarming motility as well as by a reduction in extracellular polysaccharide production. We also develop a method to displace existing biofilms by adding BdcA via conjugation from E. coli in mixed-species biofilms. Conclusion Since BdcA shows the ability to control biofilm dispersal in diverse bacteria, BdcA has the potential to be used as a tool to disperse biofilms for engineering and medical applications.
Collapse
Affiliation(s)
- Qun Ma
- Department of Chemical Engineering, Texas A & M University, College Station, TX 77843-3122, USA.
| | | | | |
Collapse
|
123
|
Bernstein HC, Paulson SD, Carlson RP. Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. J Biotechnol 2011; 157:159-66. [PMID: 22015987 DOI: 10.1016/j.jbiotec.2011.10.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/29/2011] [Accepted: 10/05/2011] [Indexed: 11/16/2022]
Abstract
Synthetic Escherichia coli consortia engineered for syntrophy demonstrated enhanced biomass productivity relative to monocultures. Binary consortia were designed to mimic a ubiquitous, naturally occurring ecological template of primary productivity supported by secondary consumption. The synthetic consortia replicated this evolution-proven strategy by combining a glucose positive E. coli strain, which served as the system's primary producer, with a glucose negative E. coli strain which consumed metabolic byproducts from the primary producer. The engineered consortia utilized strategic division of labor to simultaneously optimize multiple tasks enhancing overall culture performance. Consortial interactions resulted in the emergent property of enhanced system biomass productivity which was demonstrated with three distinct culturing systems: batch, chemostat and biofilm growth. Glucose-based biomass productivity increased by ∼15, 20 and 50% compared to appropriate monoculture controls for these three culturing systems, respectively. Interestingly, the consortial interactions also produced biofilms with predictable, self-assembling, laminated microstructures. This study establishes a metabolic engineering paradigm which can be easily adapted to existing E. coli based bioprocesses to improve productivity based on a robust ecological theme.
Collapse
Affiliation(s)
- Hans C Bernstein
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
| | | | | |
Collapse
|
124
|
Staying alive: new perspectives on cell immobilization for biosensing purposes. Anal Bioanal Chem 2011; 402:1785-97. [PMID: 21922308 DOI: 10.1007/s00216-011-5364-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/10/2011] [Accepted: 08/24/2011] [Indexed: 01/09/2023]
|
125
|
Wang X, Wood TK. Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microbiol 2011; 77:5577-83. [PMID: 21685157 PMCID: PMC3165247 DOI: 10.1128/aem.05068-11] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In many genomes, toxin-antitoxin (TA) systems have been identified; however, their role in cell physiology has been unclear. Here we examine the evidence that TA systems are involved in biofilm formation and persister cell formation and that these systems may be important regulators of the switch from the planktonic to the biofilm lifestyle as a stress response by their control of secondary messenger 3',5'-cyclic diguanylic acid. Specifically, upon stress, the sequence-specific mRNA interferases MqsR and MazF mediate cell survival. In addition, we propose that TA systems are not redundant, as they may have developed to respond to specific stresses.
Collapse
Affiliation(s)
- Xiaoxue Wang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
- Key Laboratory of Marine Bio-Resource Sustainable Utilization, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Thomas K. Wood
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
| |
Collapse
|
126
|
Tsoligkas AN, Winn M, Bowen J, Overton TW, Simmons MJH, Goss RJM. Engineering biofilms for biocatalysis. Chembiochem 2011; 12:1391-5. [PMID: 21608096 DOI: 10.1002/cbic.201100200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas N Tsoligkas
- School of Chemical Engineering, Birmingham University, Edgbaston, Birmingham, UK
| | | | | | | | | | | |
Collapse
|
127
|
Almeida C, Azevedo NF, Santos S, Keevil CW, Vieira MJ. Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH). PLoS One 2011; 6:e14786. [PMID: 21479268 PMCID: PMC3066202 DOI: 10.1371/journal.pone.0014786] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 10/11/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Our current understanding of biofilms indicates that these structures are typically composed of many different microbial species. However, the lack of reliable techniques for the discrimination of each population has meant that studies focusing on multi-species biofilms are scarce and typically generate qualitative rather than quantitative data. METHODOLOGY/PRINCIPAL FINDINGS We employ peptide nucleic acid fluorescence in situ hybridization (PNA FISH) methods to quantify and visualize mixed biofilm populations. As a case study, we present the characterization of Salmonella enterica/Listeria monocytogenes/Escherichia coli single, dual and tri-species biofilms in seven different support materials. Ex-situ, we were able to monitor quantitatively the populations of ∼56 mixed species biofilms up to 48 h, regardless of the support material. In situ, a correct quantification remained more elusive, but a qualitative understanding of biofilm structure and composition is clearly possible by confocal laser scanning microscopy (CLSM) at least up to 192 h. Combining the data obtained from PNA FISH/CLSM with data from other established techniques and from calculated microbial parameters, we were able to develop a model for this tri-species biofilm. The higher growth rate and exopolymer production ability of E. coli probably led this microorganism to outcompete the other two [average cell numbers (cells/cm(2)) for 48 h biofilm: E. coli 2,1 × 10(8) (± 2,4 × 10(7)); L. monocytogenes 6,8 × 10(7) (± 9,4 × 10(6)); and S. enterica 1,4 × 10(6) (± 4,1 × 10(5))]. This overgrowth was confirmed by CSLM, with two well-defined layers being easily identified: the top one with E. coli, and the bottom one with mixed regions of L. monocytogenes and S. enterica. SIGNIFICANCE While PNA FISH has been described previously for the qualitative study of biofilm populations, the present investigation demonstrates that it can also be used for the accurate quantification and spatial distribution of species in polymicrobial communities. Thus, it facilitates the understanding of interspecies interactions and how these are affected by changes in the surrounding environment.
Collapse
Affiliation(s)
- Carina Almeida
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Nuno F. Azevedo
- Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sílvio Santos
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
| | - Charles W. Keevil
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Maria J. Vieira
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
| |
Collapse
|
128
|
Abstract
Bacteria prefer to grow attached to themselves or an interface, and it is important for an array of applications to make biofilms disperse. Here we report simultaneously the discovery and protein engineering of BdcA (formerly YjgI) for biofilm dispersal using the universal signal 3,5-cyclic diguanylic acid (c-di-GMP). The bdcA deletion reduced biofilm dispersal, and production of BdcA increased biofilm dispersal to wild-type level. Since BdcA increases motility and extracellular DNA production while decreasing exopolysaccharide, cell length and aggregation, we reasoned that BdcA decreases the concentration of c-di-GMP, the intracellular messenger that controls cell motility through flagellar rotation and biofilm formation through synthesis of curli and cellulose. Consistently, c-di-GMP levels increase upon deleting bdcA, and purified BdcA binds c-di-GMP but does not act as a phosphodiesterase. Additionally, BdcR (formerly YjgJ) is a negative regulator of bdcA. To increase biofilm dispersal, we used protein engineering to evolve BdcA for greater c-di-GMP binding and found that the single amino acid change E50Q causes nearly complete removal of biofilms via dispersal without affecting initial biofilm formation.
Collapse
Affiliation(s)
- Qun Ma
- Department of Chemical Engineering, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122
| | - Zhonghua Yang
- Department of Chemical Engineering, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122
- College of Chemical Engineering and Technology, Wuhan University of Science and Technology, Wuhan 430081
| | - Mingming Pu
- Department of Chemical Engineering, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology, and Biotechnology and Brown University, Providence, RI 02912
| | - Thomas K. Wood
- Department of Chemical Engineering, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122
- Department of Biology, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122
- Department of Civil Engineering, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122
| |
Collapse
|
129
|
Wood TK, Hong SH, Ma Q. Engineering biofilm formation and dispersal. Trends Biotechnol 2010; 29:87-94. [PMID: 21131080 DOI: 10.1016/j.tibtech.2010.11.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/01/2010] [Accepted: 11/03/2010] [Indexed: 02/07/2023]
Abstract
Anywhere water is in the liquid state, bacteria will exist as biofilms, which are complex communities of cells that are cemented together. Although frequently associated with disease and biofouling, biofilms are also important for engineering applications, such as bioremediation, biocatalysis and microbial fuel cells. Here, we review approaches to alter genetic circuits and cell signaling towards controlling biofilm formation, and emphasize utilizing these tools for engineering applications. Based on a better understanding of the genetic basis of biofilm formation, we find that biofilms might be controlled by manipulating extracellular signals, and that they might be dispersed using conserved intracellular signals and regulators. Biofilms could also be formed at specific locations where they might be engineered to make chemicals or treat human disease.
Collapse
Affiliation(s)
- Thomas K Wood
- Department of Chemical Engineering, 220 Jack E. Brown Building, Texas A & M University, College Station, TX 77843-3122, USA.
| | | | | |
Collapse
|
130
|
|
131
|
The impact of Ivan Málek’s continuous culture concept on bioprocessing. J Ind Microbiol Biotechnol 2010; 37:1249-56. [DOI: 10.1007/s10295-010-0881-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/16/2010] [Indexed: 10/18/2022]
|
132
|
Castellón E, Chavarría M, de Lorenzo V, Zayat M, Levy D. An electro-optical device from a biofilm structure created by bacterial activity. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:4846-4850. [PMID: 20717993 DOI: 10.1002/adma.201001986] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Erick Castellón
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | |
Collapse
|
133
|
Sabra W, Dietz D, Tjahjasari D, Zeng AP. Biosystems analysis and engineering of microbial consortia for industrial biotechnology. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000111] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
134
|
Lang K, Bühler K, Schmid A. Utilization of Biofilms as Biocatalysts for Chemical Synthesis. CHEM-ING-TECH 2010. [DOI: 10.1002/cite.201050488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
135
|
Halan B, Schmid A, Buehler K. Maximizing the productivity of catalytic biofilms on solid supports in membrane aerated reactors. Biotechnol Bioeng 2010; 106:516-27. [PMID: 20229513 DOI: 10.1002/bit.22732] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A new solid support membrane aerated biofilm reactor was designed for the synthesis of enantiopure (S)-styrene oxide utilizing Pseudomonas sp. strain VLB120DeltaC growing in a biofilm as biocatalyst. In analogy to traditional packed bed systems, maximizing the volumetric oxygen mass transfer capability (k(L)a) was identified as the most critical issue enabling a consistent productivity, as this parameter was shown to directly influence biofilm growth and biotransformation performance. A microporous ceramic unit was identified as an ideal microenvironment for biofilm growth and for efficient oxygen transfer. A uniform and dense biofilm developed on this matrix. Due to this dual function, the reactor configuration could be significantly simplified by eliminating additional packing materials, as used in traditional packed bed reactors. Up to now, a maximum productivity of 28 g L(ab) (-1) day(-1) was achieved by integrating an in situ substrate feed and an in situ product recovery technique based on a silicone membrane. The system was stable for more than 30 days before it was actively terminated.
Collapse
Affiliation(s)
- Babu Halan
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse. 66, Dortmund 44227, Germany
| | | | | |
Collapse
|
136
|
Constructing multispecies biofilms with defined compositions by sequential deposition of bacteria. Appl Microbiol Biotechnol 2010; 86:1941-6. [DOI: 10.1007/s00253-010-2473-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/25/2010] [Accepted: 01/26/2010] [Indexed: 11/26/2022]
|