1
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Xiong X, Wan W, Ding B, Cai M, Lu M, Liu W. Type VI secretion system drives bacterial diversity and functions in multispecies biofilms. Microbiol Res 2024; 279:127570. [PMID: 38096690 DOI: 10.1016/j.micres.2023.127570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.
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Affiliation(s)
- Xiang Xiong
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Bangjing Ding
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Miaomiao Cai
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Mingzhu Lu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China.
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2
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Zarei M, Elmi Anvari S, Maktabi S, Saris PEJ, Yousefvand A. Identification, proteolytic activity quantification and biofilm-forming characterization of Gram-positive, proteolytic, psychrotrophic bacteria isolated from cold raw milk. PLoS One 2023; 18:e0290953. [PMID: 37703270 PMCID: PMC10499245 DOI: 10.1371/journal.pone.0290953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/19/2023] [Indexed: 09/15/2023] Open
Abstract
Psychrotrophic bacteria of raw milk face the dairy industry with significant spoilage and technological problems due to their ability to produce heat-resistant enzymes and biofilms. Despite extensive information about Gram-negative psychrotrophic bacteria in milk, little is known about Gram-positive psychrotrophic bacteria in milk, and their proteolytic activity and biofilm-forming characteristics. In the present study, Gram-positive, proteolytic, psychrotrophic bacteria of cold raw milk were identified, and their proteolytic activity and biofilm-forming capacity were quantified. In total, 12 genera and 22 species were represented among the bacterial isolates, however 50% belonged to three genera, namely Staphylococcus (19.4%), Bacillus (16.7%), and Enterococcus (13.9%). Different levels of proteolytic activity were detected in the identified isolates, even among the strains belonging to the same species. In addition, proteolytic activity was significantly higher at 25°C than at 7°C for all isolates. The crystal violet staining assay in polystyrene microtitre plates revealed a high level of variation in the biofilm-forming capacity at 7°C. After 72 hours of incubation, 11.1% of the strains did not produce a biofilm, while 27.8%, 52.8%, and 8.3% produced low, moderate, and high amounts of biofilm on polystyrene, respectively. The psychrotrophic bacteria were also able to produce biofilms on the surface of stainless steel coupons in ultra-high temperature milk after 72 h of incubation at 7°C; the number of attached cells ranged from 1.34 to 5.11 log cfu/cm2. These results expand the knowledge related to the proteolytic activity and biofilm-forming capacity of Gram-positive psychrotrophic milk bacteria.
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Affiliation(s)
- Mehdi Zarei
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sahar Elmi Anvari
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Siavash Maktabi
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Amin Yousefvand
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
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3
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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.
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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
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4
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Deng Y, Wang SY. Sorption of Cellulases in Biofilm Enhances Cellulose Degradation by Bacillus subtilis. Microorganisms 2022; 10:microorganisms10081505. [PMID: 35893563 PMCID: PMC9329931 DOI: 10.3390/microorganisms10081505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Biofilm commonly forms on the surfaces of cellulosic biomass but its roles in cellulose degradation remain largely unexplored. We used Bacillus subtilis to study possible mechanisms and the contributions of two major biofilm components, extracellular polysaccharides (EPS) and TasA protein, to submerged biofilm formation on cellulose and its degradation. We found that biofilm produced by B. subtilis is able to absorb exogenous cellulase added to the culture medium and also retain self-produced cellulase within the biofilm matrix. The bacteria that produced more biofilm degraded more cellulose compared to strains that produced less biofilm. Knockout strains that lacked both EPS and TasA formed a smaller amount of submerged biofilm on cellulose than the wild-type strain and also degraded less cellulose. Imaging of biofilm on cellulose suggests that bacteria, cellulose, and cellulases form cellulolytic biofilm complexes that facilitate synergistic cellulose degradation. This study brings additional insight into the important functions of biofilm in cellulose degradation and could potentiate the development of biofilm-based technology to enhance biomass degradation for biofuel production.
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Mazraeh D, Di Ventura B. Synthetic microbiology applications powered by light. Curr Opin Microbiol 2022; 68:102158. [PMID: 35660240 DOI: 10.1016/j.mib.2022.102158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Synthetic biology is a field of research in which molecular parts (mostly nucleic acids and proteins) are de novo created or modified and then used either alone or in combination to achieve new functions that can help solve the problems of our modern society. In synthetic microbiology, microbes are employed rather than other organisms or cell-free systems. Optogenetics, a relatively recently established technology that relies on the use of genetically encoded photosensitive proteins to control biological processes with high spatiotemporal precision, offers the possibility to empower synthetic (micro)biology applications due to the many positive features that light has as an external trigger. In this review, we describe recent synthetic microbiology applications that made use of optogenetics after briefly introducing the molecular mechanism behind some of the most employed optogenetic tools. We highlight the power and versatility of this technique, which opens up new horizons for both research and industry.
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Affiliation(s)
- Daniel Mazraeh
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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6
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Lin L. Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:14. [PMID: 35418100 PMCID: PMC8822760 DOI: 10.1186/s13068-022-02113-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
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7
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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]
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8
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Anaerobic granulation of single culture Clostridium beijerinckii. FOOD AND BIOPRODUCTS PROCESSING 2021. [DOI: 10.1016/j.fbp.2021.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Elisiário MP, De Wever H, Van Hecke W, Noorman H, Straathof AJJ. Membrane bioreactors for syngas permeation and fermentation. Crit Rev Biotechnol 2021; 42:856-872. [PMID: 34525894 DOI: 10.1080/07388551.2021.1965952] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Syngas fermentation to biofuels and chemicals is an emerging technology in the biobased economy. Mass transfer is usually limiting the syngas fermentation rate, due to the low aqueous solubilities of the gaseous substrates. Membrane bioreactors, as efficient gas-liquid contactors, are a promising configuration for overcoming this gas-to-liquid mass transfer limitation, so that sufficient productivity can be achieved. We summarize the published performances of these reactors. Moreover, we highlight numerous parameters settings that need to be used for the enhancement of membrane bioreactor performance. To facilitate this enhancement, we relate mass transfer and other performance indicators to the type of membrane material, module, and flow configuration. Hollow fiber modules with dense or asymmetric membranes on which biofilm might form seem suitable. A model-based approach is advocated to optimize their performance.
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Affiliation(s)
- Marina P Elisiário
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Heleen De Wever
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Wouter Van Hecke
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Henk Noorman
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,DSM Biotechnology Center, Delft, The Netherlands
| | - Adrie J J Straathof
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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10
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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]
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11
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Blackman LD, Qu Y, Cass P, Locock KES. Approaches for the inhibition and elimination of microbial biofilms using macromolecular agents. Chem Soc Rev 2021; 50:1587-1616. [PMID: 33403373 DOI: 10.1039/d0cs00986e] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biofilms are complex three-dimensional structures formed at interfaces by the vast majority of bacteria and fungi. These robust communities have an important detrimental impact on a wide range of industries and other facets of our daily lives, yet their removal is challenging owing to the high tolerance of biofilms towards conventional antimicrobial agents. This key issue has driven an urgent search for new innovative antibiofilm materials. Amongst these emerging approaches are highly promising materials that employ aqueous-soluble macromolecules, including peptides, proteins, synthetic polymers, and nanomaterials thereof, which exhibit a range of functionalities that can inhibit biofilm formation or detach and destroy organisms residing within established biofilms. In this Review, we outline the progress made in inhibiting and removing biofilms using macromolecular approaches, including a spotlight on cutting-edge materials that respond to environmental stimuli for "on-demand" antibiofilm activity, as well as synergistic multi-action antibiofilm materials. We also highlight materials that imitate and harness naturally derived species to achieve new and improved biomimetic and biohybrid antibiofilm materials. Finally, we share some speculative insights into possible future directions for this exciting and highly significant field of research.
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Affiliation(s)
- Lewis D Blackman
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia.
| | - Yue Qu
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia and Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Peter Cass
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia.
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12
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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.
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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
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13
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Dubbin K, Dong Z, Park DM, Alvarado J, Su J, Wasson E, Robertson C, Jackson J, Bose A, Moya ML, Jiao Y, Hynes WF. Projection Microstereolithographic Microbial Bioprinting for Engineered Biofilms. NANO LETTERS 2021; 21:1352-1359. [PMID: 33508203 DOI: 10.1021/acs.nanolett.0c04100] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbes are critical drivers of all ecosystems and many biogeochemical processes, yet little is known about how the three-dimensional (3D) organization of these dynamic organisms contributes to their overall function. To probe how biofilm structure affects microbial activity, we developed a technique for patterning microbes in 3D geometries using projection stereolithography to bioprint microbes within hydrogel architectures. Bacteria were printed and monitored for biomass accumulation, demonstrating postprint viability of cells using this technique. We verified our ability to integrate biological and geometric complexity by fabricating a printed biofilm with two E. coli strains expressing different fluorescence. Finally, we examined the target application of microbial absorption of metal ions to investigate geometric effects on both the metal sequestration efficiency and the uranium sensing capability of patterned engineered Caulobacter crescentus strains. This work represents the first demonstration of the stereolithographic printing of microbials and presents opportunities for future work of engineered biofilms and other complex 3D structured cultures.
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Affiliation(s)
- Karen Dubbin
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ziye Dong
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Dan M Park
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Javier Alvarado
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jimmy Su
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Elisa Wasson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Claire Robertson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Julie Jackson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Arpita Bose
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Monica L Moya
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Yongqin Jiao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - William F Hynes
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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14
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Recupido F, Toscano G, Tatè R, Petala M, Caserta S, Karapantsios TD, Guido S. The role of flow in bacterial biofilm morphology and wetting properties. Colloids Surf B Biointerfaces 2020; 192:111047. [PMID: 32388030 DOI: 10.1016/j.colsurfb.2020.111047] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 02/06/2023]
Abstract
Biofilms are bacterial communities embedded in an extracellular matrix, able to adhere to surfaces. Different experimental set-ups are widely used for in vitro biofilm cultivation; however, a well-defined comparison among different culture conditions, especially suited to interfacial characterization, is still lacking in the literature. The main objective of this work is to study the role of flow on biofilm formation, morphology and interfacial properties. Three different in vitro setups, corresponding to stagnant, shaking, and laminar flow conditions (custom-made flow cell), are used in this work to grow single strain biofilms of Pseudomonas fluorescens AR 11 on glass coupons. Results show that flow conditions significantly influenced biofilm formation kinetics, affecting mass transfer and cell attachment/detachment processes. Distinct morphological patterns are found under different flow regimes. Static contact angle data do not depend significantly on biofilm growth conditions in the parametric range investigated in this work.
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Affiliation(s)
- Federica Recupido
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124, Thessaloniki, Greece; Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples, Federico II, Piazzale V. Tecchio 80, 80125, Naples, Italy
| | - Giuseppe Toscano
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples, Federico II, Piazzale V. Tecchio 80, 80125, Naples, Italy
| | - Rosarita Tatè
- Institute of Genetics and Biophysics: "A. Buzzati-Traverso" (IGB-CNR), Pietro Castellino 111, 80131, Naples, Italy
| | - Maria Petala
- Department of Civil Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Sergio Caserta
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples, Federico II, Piazzale V. Tecchio 80, 80125, Naples, Italy; CEINGE, Advanced Biotechnologies, 80145, Naples, Italy.
| | - Thodoris D Karapantsios
- Division of Chemical Technology, School of Chemistry, Aristotle University of Thessaloniki, University Box 116, 54124, Thessaloniki, Greece.
| | - Stefano Guido
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples, Federico II, Piazzale V. Tecchio 80, 80125, Naples, Italy; CEINGE, Advanced Biotechnologies, 80145, Naples, Italy
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15
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Deconstruction of plant biomass by a Cellulomonas strain isolated from an ultra-basic (lignin-stripping) spring. Arch Microbiol 2020; 202:1077-1084. [PMID: 32030461 DOI: 10.1007/s00203-020-01816-z] [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: 11/29/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 10/25/2022]
Abstract
Plant material falling into the ultra-basic (pH 11.5-11.9) springs within The Cedars, an actively serpentinizing site in Sonoma County, California, is subject to conditions that mimic the industrial pretreatment of lignocellulosic biomass for biofuel production. We sought to obtain hemicellulolytic/cellulolytic bacteria from The Cedars springs that are capable of withstanding the extreme alkaline conditions wherein calcium hydroxide-rich water removes lignin, making cell wall polysaccharides more accessible to microorganisms and their enzymes. We enriched for such bacteria by adding plant debris from the springs into a synthetic alkaline medium with ground tissue of the biofuel crop switchgrass (Panicum virgatum L.) as the sole source of carbon. From the enrichment culture we isolated the facultative anaerobic bacterium Cellulomonas sp. strain FA1 (NBRC 114238), which tolerates high pH and catabolizes the major plant cell wall-associated polysaccharides cellulose, pectin, and hemicellulose. Strain FA1 in monoculture colonized the plant material and degraded switchgrass at a faster rate than the community from which it was derived. Cells of strain FA1 could be acclimated through subculturing to grow at a maximal concentration of 13.4% ethanol. A strain FA1-encoded β-1, 4-endoxylanase expressed in E. coli was active at a broad pH range, displaying near maximal activity at pH 6-9. Discovery of this bacterium illustrates the value of extreme alkaline springs in the search for microorganisms with potential for consolidated bioprocessing of plant biomass to biofuels and other valuable bio-inspired products.
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Enzyme-based strategy to eradicate monospecies Macrococcus caseolyticus biofilm contamination in dairy industries. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2019.104560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Liu D, Yang Z, Chen Y, Zhuang W, Niu H, Wu J, Ying H. Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:315. [PMID: 30479660 PMCID: PMC6245871 DOI: 10.1186/s13068-018-1316-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Biofilms are cell communities wherein cells are embedded in a self-produced extracellular polymeric substances (EPS). The biofilm of Clostridium acetobutylicum confers the cells superior phenotypes and has been extensively exploited to produce a variety of liquid biofuels and bulk chemicals. However, little has been known about the physiology of C. acetobutylicum in biofilm as well as the composition and biosynthesis of the EPS. Thus, this study is focused on revealing the cell physiology and EPS composition of C. acetobutylicum biofilm. RESULTS Here, we revealed a novel lifestyle of C. acetobutylicum in biofilm: elimination of sporulation and vegetative growth. Extracellular polymeric substances and wire-like structures were also observed in the biofilm. Furthermore, for the first time, the biofilm polysaccharides and proteins were isolated and characterized. The biofilm contained three heteropolysaccharides. The major fraction consisted of predominantly glucose, mannose and aminoglucose. Also, a great variety of proteins including many non-classically secreted proteins moonlighting as adhesins were found considerably present in the biofilm, with GroEL, a S-layer protein and rubrerythrin being the most abundant ones. CONCLUSIONS This study evidenced that vegetative C. acetobutylicum cells rather than commonly assumed spore-forming cells were essentially the solvent-forming cells. The abundant non-classically secreted moonlighting proteins might be important for the biofilm formation. This study provides the first physiological and molecular insights into C. acetobutylicum biofilm which should be valuable for understanding and development of the biofilm-based processes.
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Affiliation(s)
- Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
- Jiangsu National Synergetic Innovation Center for Advance Material (SICAM), No. 30, Puzhu South Road, Nanjing, 211800 China
| | - Zhengjiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
- Jiangsu National Synergetic Innovation Center for Advance Material (SICAM), No. 30, Puzhu South Road, Nanjing, 211800 China
| | - Wei Zhuang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
- Jiangsu National Synergetic Innovation Center for Advance Material (SICAM), No. 30, Puzhu South Road, Nanjing, 211800 China
| | - Huanqing Niu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
- Jiangsu National Synergetic Innovation Center for Advance Material (SICAM), No. 30, Puzhu South Road, Nanjing, 211800 China
| | - Jinglan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
- Jiangsu National Synergetic Innovation Center for Advance Material (SICAM), No. 30, Puzhu South Road, Nanjing, 211800 China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211800 China
- Jiangsu National Synergetic Innovation Center for Advance Material (SICAM), No. 30, Puzhu South Road, Nanjing, 211800 China
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Yuan L, Sadiq FA, Burmølle M, Liu T, He G. Insights into Bacterial Milk Spoilage with Particular Emphasis on the Roles of Heat-Stable Enzymes, Biofilms, and Quorum Sensing. J Food Prot 2018; 81:1651-1660. [PMID: 30207500 DOI: 10.4315/0362-028x.jfp-18-094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Milk spoilage caused by psychrotrophic bacteria and their heat-stable enzymes is a serious challenge for the dairy industry. In many studies, spoilage has been explored based on the simplistic view of undesirable enzymes produced by planktonic cells. Recently, biofilms and quorum sensing (QS) have been suggested as important factors in the deterioration of milk, which opens new avenues for investigation of the processes and challenges. Production and heat stability of enzymes are enhanced in biofilms, mainly because of inherent differences in physiological states and protective shielding by extracellular polymeric substances. QS plays a key role in modulating expression of hydrolytic enzymes and biofilm formation. To date, few studies have been conducted to investigate the complex interplays of enzyme production, biofilm formation, and QS. This review provides novel insights into milk spoilage with particular emphasis on the roles of biofilms and QS and summarizes potential effective strategies for controlling the spoilage of milk.
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Affiliation(s)
- Lei Yuan
- 1 College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Faizan A Sadiq
- 1 College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Mette Burmølle
- 2 Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Tongjie Liu
- 1 College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Guoqing He
- 1 College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China; and
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Mixotrophic Microalgae Biofilm: A Novel Algae Cultivation Strategy for Improved Productivity and Cost-efficiency of Biofuel Feedstock Production. Sci Rep 2018; 8:12528. [PMID: 30131525 PMCID: PMC6104096 DOI: 10.1038/s41598-018-31016-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/09/2018] [Indexed: 11/17/2022] Open
Abstract
In this work, we studied a novel algae cultivation strategy, mixotrophic microalgae biofilm, to improve the productivity and cost-efficiency of algal biofuel production. In contrast to previous methods, this improved approach can achieve high productivity at low cost by harnessing the benefits of mixotrophic growth’s high efficiency, i.e., capable of subsisting on inorganic and organic carbons thus unaffected by limited light, and microalgae biofilm’s low harvesting cost. Our results, as one of the first studies of this type, proved that microalgae biofilms under mixotrophic condition exhibited significantly higher productivity and quality of biofuel feedstock: 2–3 times higher of biomass yield, 2–10 times higher of lipid accumulation, and 40–60% lower of ash content when compared to microalgae biofilms under autotrophic condition. In addition, we investigated the impact of cell-surface properties (hydrophobicity and roughness) on the growth activities of microalgae biofilms and found that the productivity of mixotrophic biofilms was significantly correlated with the surface hydrophobicity. Finally, our work demonstrated the applicability of integrating this novel cultivation method with wastewater for maximum efficiency. This study opens a new possibility to solve the long-lasting challenges of algal biofuel feedstock production, i.e., low productivity and high cost of algal cultivation.
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Schlafer S, Kamp A, Garcia JE. A confocal microscopy based method to monitor extracellular pH in fungal biofilms. FEMS Yeast Res 2018; 18:4978430. [DOI: 10.1093/femsyr/foy049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/17/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sebastian Schlafer
- Department of Dentistry and Oral Health, Aarhus University, Vennelyst Boulevard 9, 8000 Aarhus, Denmark
- Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus, Denmark
| | - Javier E Garcia
- Department of Dentistry and Oral Health, Aarhus University, Vennelyst Boulevard 9, 8000 Aarhus, Denmark
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State of the art on granular sludge by using bibliometric analysis. Appl Microbiol Biotechnol 2018; 102:3453-3473. [PMID: 29497798 DOI: 10.1007/s00253-018-8844-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
Abstract
With rapid industrialization and urbanization in the nineteenth century, the activated sludge process (ASP) has experienced significant steps forward in the face of greater awareness of and sensitivity toward water-related environmental problems. Compared with conventional flocculent ASP, the major advantages of granular sludge are characterized by space saving and resource recovery, where the methane and hydrogen recovery in anaerobic granular and 50% more space saving, 30-50% of energy consumption reduction, 75% of footprint cutting, and even alginate recovery in aerobic granular. Numerous engineers and scientists have made great efforts to explore the superiority over the last 40 years. Therefore, a bibliometric analysis was desired to trace the global trends of granular sludge research from 1992 to 2016 indexed in the SCI-EXPANDED. Articles were published in 276 journals across 44 subject categories spanning 1420 institutes across 68 countries. Bioresource Technology (293, 11.9%), Water Research (235, 9.6%), and Applied Microbiology and Biotechnology (127, 5.2%) dominated in top three journals. The Engineering (991, 40.3%), China (906, 36.9%), and Harbin Inst Technol, China (114, 4.6%) were the most productive subject category, country, and institution, respectively. The hotspot is the emerging techniques depended on granular reactors in response to the desired removal requirements and bio-energy production (primarily in anaerobic granular sludge). In view of advanced and novel bio-analytical methods, the characteristics, functions, and mechanisms for microbial granular were further revealed in improving and innovating the granulation techniques. Therefore, a promising technique armed with strengthened treatment efficiency and efficient resource and bio-energy recovery can be achieved.
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Adhesion forces of the sea-water bacterium Paracoccus seriniphilus on titanium: Influence of microstructures and environmental conditions. Biointerphases 2017; 12:05G606. [PMID: 29108418 DOI: 10.1116/1.5002676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The bacterial attachment to surfaces is the first step of biofilm formation. This attachment is governed by adhesion forces which act between the bacterium and the substrate. Such forces can be measured by single cell force spectroscopy, where a single bacterium is attached to a cantilever of a scanning force microscope, and force-distance curves are measured. For the productive sea-water bacterium Paracoccus seriniphilus, pH dependent measurements reveal the highest adhesion forces at pH 4. Adhesion forces measured at salinities between 0% and 4.5% NaCl are in general higher for higher salinity. However, there is an exception for 0.9% where a higher adhesion force was measured than expected. These results are in line with zeta potential measurements of the bacterium, which also show an exceptionally low zeta potential at 0.9% NaCl. In the absence of macromolecular interactions, the adhesion forces are thus governed by (unspecific) electrostatic interactions, which can be adjusted by pH and ionic strength. It is further shown that microstructures on the titanium surface increase the adhesion force. Growth medium reduces the interaction forces dramatically, most probably through macromolecular bridging.
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Xiros C, Studer MH. A Multispecies Fungal Biofilm Approach to Enhance the Celluloyltic Efficiency of Membrane Reactors for Consolidated Bioprocessing of Plant Biomass. Front Microbiol 2017; 8:1930. [PMID: 29067006 PMCID: PMC5641325 DOI: 10.3389/fmicb.2017.01930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/21/2017] [Indexed: 01/06/2023] Open
Abstract
The constraints and advantages in cellulolytic enzymes production by fungal biofilms for a consolidated bioconversion process were investigated during this study. The biofilm cultivations were carried out in reactors designed for consolidated bioprocessing Multispecies Biofilm Membrane reactors, (MBM) where an aerobic fungal biofilm produces the lignocellulolytic enzymes while a fermenting microorganism forms the fermentation product at anaerobic conditions. It was shown that although mycelial growth was limited in the MBM reactors compared to submerged cultivations, the secretion of cellulolytic enzymes per cell dry weight was higher. When Trichoderma reesei was used as the sole enzyme producer, cellobiose accumulated in the liquid medium as the result of the deficiency of β-glucosidase in the fungal secretome. To enhance β-glucosidase activity, T. reesei was co-cultivated with A. phoenicis which is a β-glucosidase overproducer. The two fungi formed a multispecies biofilm which produced a balanced cellulolytic cocktail for the saccharification of plant biomass. The mixed biofilm reached a 2.5 fold increase in β-glucosidase production, compared to the single T. reesei biofilm. The enzymatic systems of single and mixed biofilms were evaluated regarding their efficiency on cellulosic substrates degradation. Washed solids from steam pretreated beechwood, as well as microcrystalline cellulose were used as the substrates. The enzymatic system of the multispecies biofilm released four times more glucose than the enzymatic system of T. reesei alone from both substrates and hydrolyzed 78 and 60% of the cellulose content of washed solids from beechwood and microcrystalline cellulose, respectively.
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Affiliation(s)
- Charilaos Xiros
- Laboratory for Bioenergy and Biochemicals, School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Bern, Switzerland
| | - Michael H Studer
- Laboratory for Bioenergy and Biochemicals, School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Bern, Switzerland
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25
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Leng RA. Biofilm compartmentalisation of the rumen microbiome: modification of fermentation and degradation of dietary toxins. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an17382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many deleterious chemicals in plant materials ingested by ruminants produce clinical effects, varying from losses of production efficiency through to death. Many of the effects are insidious, often going unrecognised by animal managers. When secondary plant compounds enter the rumen, they may undergo modification by rumen microbes, which often removes the deleterious compounds, but in specific instances, the deleterious effect may be enhanced. Improved understanding of rumen ecology, particularly concerning the biofilm mode of microbial fermentation, has led to major advances in our understanding of fermentation. In the present review, the potential impact of the physical structuring of the rumen microbiome is discussed in relation to how several economically important secondary plant compounds and other toxins are metabolised by the rumen microbiome and how their toxic effects may be remedied by providing inert particles with a large surface area to weight ratio in the diet. These particles provide additional surfaces for attachment of rumen microorganisms that help alleviate toxicity problems associated with deleterious compounds, including fluoroacetate, mimosine, mycotoxins, cyanoglycosides and hydrogen cyanide. The review first summarises the basic science of biofilm formation and describes the properties of biofilms and their roles in the rumen. It then addresses how biofilms on inert solids and fermentable particulates may assist in detoxification of potentially toxic compounds. A hypothesis that explains how nitrate poisoning may occur as a result of compartmentalisation of nitrate and nitrite reduction in the rumen is included.
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Wang ZW, Xu F, Manchala KR, Sun Y, Li Y. Fractal-like kinetics of the solid-state anaerobic digestion. WASTE MANAGEMENT (NEW YORK, N.Y.) 2016; 53:55-61. [PMID: 27132655 DOI: 10.1016/j.wasman.2016.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
Total solid content (TS) negatively impacts the methane production efficiency (MPE) of solid-state anaerobic digestion (SS-AD), to which the classic mass action-based kinetics failed to provide a unified explanation. This study revealed that SS-AD reactions actually follow the fractal-like kinetics in light of the surface reactions in crowded SS-AD environment packed with heterogeneous media. The fractal characteristics of the SS-AD kinetics were found increasingly pronounced as TS increased. This study represents the first attempt to resolve the dilemma in SS-AD kinetics with the application of fractal theory. Employing this new concept allows explaining the reduced MPE at high TS and offers an easy assessment of the fractal characteristics of the SS-AD media.
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Affiliation(s)
- Zhi-Wu Wang
- Department of Civil and Environmental Engineering, Virginia Tech, Occoquan Laboratory, 9408 Prince William Street, Manassas, VA 20110, USA.
| | - Fuqing Xu
- Department of Food, Agricultural and Biological Engineering, The Ohio State University/Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691, USA
| | - Karthik R Manchala
- Department of Civil and Environmental Engineering, Virginia Tech, Occoquan Laboratory, 9408 Prince William Street, Manassas, VA 20110, USA
| | - Yewei Sun
- Department of Civil and Environmental Engineering, Virginia Tech, Occoquan Laboratory, 9408 Prince William Street, Manassas, VA 20110, USA
| | - Yebo Li
- Department of Food, Agricultural and Biological Engineering, The Ohio State University/Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691, USA
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Corral-Lugo A, De la Torre J, Matilla MA, Fernández M, Morel B, Espinosa-Urgel M, Krell T. Assessment of the contribution of chemoreceptor-based signalling to biofilm formation. Environ Microbiol 2016; 18:3355-3372. [PMID: 26662997 DOI: 10.1111/1462-2920.13170] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/30/2015] [Indexed: 12/01/2022]
Abstract
Although it is well established that one- and two-component regulatory systems participate in regulating biofilm formation, there also exists evidence suggesting that chemosensory pathways are also involved. However, little information exists about which chemoreceptors and signals modulate this process. Here we report the generation of the complete set of chemoreceptor mutants of Pseudomonas putida KT2440 and the identification of four mutants with significantly altered biofilm phenotypes. These receptors are a WspA homologue of Pseudomonas aeruginosa, previously identified to control biofilm formation by regulating c-di-GMP levels, and three uncharacterized chemoreceptors. One of these receptors, named McpU, was found to mediate chemotaxis towards different polyamines. The functional annotation of McpU was initiated by high-throughput thermal shift assays of the receptor ligand binding domain (LBD). Isothermal titration calorimetry showed that McpU-LBD specifically binds putrescine, cadaverine and spermidine, indicating that McpU represents a novel chemoreceptor type. Another uncharacterized receptor, named McpA, specifically binds 12 different proteinogenic amino acids and mediates chemotaxis towards these compounds. We also show that mutants in McpU and WspA-Pp have a significantly reduced ability to colonize plant roots. Data agree with other reports showing that polyamines are signal molecules involved in the regulation of bacteria-plant communication and biofilm formation.
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Affiliation(s)
- Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Jesús De la Torre
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain.
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Martinez JS, Kelly KD, Ghoussoub YE, Delgado JD, Keller III TCS, Schlenoff JB. Cell resistant zwitterionic polyelectrolyte coating promotes bacterial attachment: an adhesion contradiction. Biomater Sci 2016; 4:689-98. [DOI: 10.1039/c5bm00585j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Polymers of various architectures with zwitterionic functionality have recently been shown to effectively suppress nonspecific fouling of surfaces by proteins and prokaryotic (bacteria) or eukaryotic (mammalian) cells as well as other microorganisms and environmental contaminants.
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Affiliation(s)
| | - Kristopher D. Kelly
- Department of Chemistry and Biochemistry
- The Florida State University
- Tallahassee
- USA
| | - Yara E. Ghoussoub
- Department of Chemistry and Biochemistry
- The Florida State University
- Tallahassee
- USA
| | - Jose D. Delgado
- Department of Chemistry and Biochemistry
- The Florida State University
- Tallahassee
- USA
| | | | - Joseph B. Schlenoff
- Department of Chemistry and Biochemistry
- The Florida State University
- Tallahassee
- USA
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Morrell-Falvey JL, Elkins JG, Wang ZW. Determination of the cellulase activity distribution in Clostridium thermocellum and Caldicellulosiruptor obsidiansis cultures using a fluorescent substrate. J Environ Sci (China) 2015; 34:212-218. [PMID: 26257364 DOI: 10.1016/j.jes.2015.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 06/04/2023]
Abstract
This study took advantage of resorufin cellobioside as a fluorescent substrate to determine the distribution of cellulase activity in cellulosic biomass fermentation systems. Cellulolytic biofilms were found to express nearly four orders greater cellulase activity compared to planktonic cultures of Clostridium thermocellum and Caldicellulosiruptor obsidiansis, which can be primarily attributed to the high cell concentration and surface attachment. The formation of biofilms results in cellulases being secreted close to their substrates, which appears to be an energetically favorable stategy for insoluble substrate utilization. For the same reason, cellulases should be closely associated with the surfaces of suspended cell in soluble substrate-fed culture, which has been verified with cellobiose-fed cultures of C. thermocellum and C. obsidiansis. This study addressed the importance of cellulase activity distribution in cellulosic biomass fermentation, and provided theoretical foundation for the leading role of biofilm in cellulose degradation. System optimization and reactor designs that promote biofilm formation in cellulosic biomass hydrolysis may promise an improved cellulosic biofuel process.
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Affiliation(s)
- Jennifer L Morrell-Falvey
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James G Elkins
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zhi-Wu Wang
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Ohio State University ATI, 1328 Dover Rd, Wooster, OH 44691, USA.
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T OO, T OF. Synergistic effect of methane emission through ruminant production. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajar2014.8686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Todhanakasem T, Narkmit T, Areerat K, Thanonkeo P. Fermentation of rice bran hydrolysate to ethanol using Zymomonas mobilis biofilm immobilization on DEAE-cellulose. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Munir RI, Schellenberg J, Henrissat B, Verbeke TJ, Sparling R, Levin DB. Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability. PLoS One 2014; 9:e104260. [PMID: 25101643 PMCID: PMC4125193 DOI: 10.1371/journal.pone.0104260] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 07/11/2014] [Indexed: 02/06/2023] Open
Abstract
Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active enzymes (CAZymes), sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199) and carbohydrate binding modules (95) were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly.
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Affiliation(s)
- Riffat I. Munir
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John Schellenberg
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Tobin J. Verbeke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David B. Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Zuroff TR, Gu W, Fore RL, Leschine SB, Curtis WR. Insights into Clostridium phytofermentans biofilm formation: aggregation, microcolony development and the role of extracellular DNA. MICROBIOLOGY-SGM 2014; 160:1134-1143. [PMID: 24625451 DOI: 10.1099/mic.0.078014-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biofilm formation is a critical component to the lifestyle of many naturally occurring cellulose-degrading microbes. In this work, cellular aggregation and biofilm formation of Clostridium phytofermentans, a cellulolytic anaerobic bacterium, was investigated using a combination of microscopy and analytical techniques. Aggregates included thread-like linkages and a DNA/protein-rich extracellular matrix when grown on soluble cellobiose. Similar dense biofilms formed on the surface of the model cellulosic substrate Whatman no. 1 filter paper. Following initially dispersed attachment, microcolonies of ~500 µm diameter formed on the filter paper after 6 days. Enzymic treatment of both the biofilm and cellular aggregates with DNase and proteinase resulted in significant loss of rigidity, pointing to the key role of extracellular DNA and proteins in the biofilm structure. A high-throughput biofilm assay was adapted for studying potential regulators of biofilm formation. Various media manipulations were shown to greatly impact biofilm formation, including repression in the presence of glucose but not the β(1→4)-linked disaccharide cellobiose, implicating a balance of hydrolytic activity and assimilation to maintain biofilm integrity. Using the microtitre plate biofilm assay, DNase and proteinase dispersed ~60 and 30 % of mature biofilms, respectively, whilst RNase had no impact. This work suggests that Clostridium phytofermentans has evolved a DNA/protein-rich biofilm matrix complementing its cellulolytic nature. These insights add to our current understanding of natural ecosystems as well as strategies for efficient bioprocess design.
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Affiliation(s)
- Trevor R Zuroff
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Weimin Gu
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Rachel L Fore
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susan B Leschine
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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Teh KH, Lindsay D, Palmer J, Andrewes P, Bremer P, Flint S. Proteolysis in ultra-heat-treated skim milk after exposure to multispecies biofilms under conditions modelling a milk tanker. INT J DAIRY TECHNOL 2014. [DOI: 10.1111/1471-0307.12114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Koon Hoong Teh
- Institute of Food, Nutrition and Human Health; Massey University; Private Bag 11222 Palmerston North New Zealand
- Fonterra Research Centre; Private Bag 11029 Palmerston North New Zealand
| | - Denise Lindsay
- Fonterra Research Centre; Private Bag 11029 Palmerston North New Zealand
| | - Jon Palmer
- Institute of Food, Nutrition and Human Health; Massey University; Private Bag 11222 Palmerston North New Zealand
| | - Paul Andrewes
- Fonterra Research Centre; Private Bag 11029 Palmerston North New Zealand
| | - Phil Bremer
- Department of Food Science; University of Otago; PO Box 56 Dunedin New Zealand
| | - Steve Flint
- Institute of Food, Nutrition and Human Health; Massey University; Private Bag 11222 Palmerston North New Zealand
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37
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Wang ZW, Li Y. A theoretical derivation of the Contois equation for kinetic modeling of the microbial degradation of insoluble substrates. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Lipolysis within single culture and co-culture biofilms of dairy origin. Int J Food Microbiol 2013; 163:129-35. [DOI: 10.1016/j.ijfoodmicro.2013.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 11/16/2022]
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Ronan P, Yeung CW, Schellenberg J, Sparling R, Wolfaardt GM, Hausner M. A versatile and robust aerotolerant microbial community capable of cellulosic ethanol production. BIORESOURCE TECHNOLOGY 2013; 129:156-163. [PMID: 23238345 DOI: 10.1016/j.biortech.2012.10.164] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 06/01/2023]
Abstract
The use of microbial communities in the conversion of cellulosic materials to bio-ethanol has the potential to improve the economic competitiveness of this biofuel and subsequently lessen our dependency on fossil fuel-based energy sources. Interactions between functionally different microbial groups within a community can expand habitat range, including the creation of anaerobic microenvironments. Currently, research focussing on exploring the nature of the interactions occurring during cellulose degradation and ethanol production within mixed microbial communities has been limited. The aim of this study was to enrich and characterize a cellulolytic bacterial community, and determine if ethanol is a major soluble end-product. Cellulolytic activity by the community was observed in both non-reduced and pre-reduced media, with ethanol and acetate being major fermentation products. Similar results were obtained when sterile wastewater extract was provided as nutrient. Several community members showed high similarity to Clostridium species with overlapping metabolic capabilities, suggesting clostridial functional redundancy.
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Affiliation(s)
- Patrick Ronan
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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Teodósio JS, Simões M, Alves MA, Melo LF, Mergulhão FJ. Setup and validation of flow cell systems for biofouling simulation in industrial settings. ScientificWorldJournal 2012; 2012:361496. [PMID: 22666110 PMCID: PMC3361220 DOI: 10.1100/2012/361496] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/18/2011] [Indexed: 11/17/2022] Open
Abstract
A biofouling simulation system consisting of a flow cell and a recirculation tank was used. The fluid circulates at a flow rate of 350 L· h⁻¹ in a semicircular flow cell with hydraulic diameter of 18.3 mm, corresponding to an average velocity of 0.275 m· s⁻¹. Using computational fluid dynamics for flow simulation, an average wall shear stress of 0.4 Pa was predicted. The validity of the numerical simulations was visually confirmed by inorganic deposit formation (using kaolin particles) and also by direct observation of pathlines of tracer PVC particles using streak photography. Furthermore, the validity of chemostat assumptions was verified by residence time analysis. The system was used to assess the influence of the dilution rate on biofilm formation by Escherichia coli JM109(DE3). Two dilution rates of 0.013 and 0.0043 h⁻¹ were tested and the results show that the planktonic cell concentration is increased at the lower dilution rate and that no significant changes were detected on the amount of biofilm formed in both conditions.
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Affiliation(s)
- Joana S Teodósio
- LEPAE-Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
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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]
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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.
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Mangwani N, Dash HR, Chauhan A, Das S. Bacterial Quorum Sensing: Functional Features and Potential Applications in Biotechnology. J Mol Microbiol Biotechnol 2012; 22:215-27. [DOI: 10.1159/000341847] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Teh KH, Flint S, Palmer J, Lindsay D, Andrewes P, Bremer P. Thermo-resistant enzyme-producing bacteria isolated from the internal surfaces of raw milk tankers. Int Dairy J 2011. [DOI: 10.1016/j.idairyj.2011.04.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gardner JG, Zeitler LA, Wigstrom WJS, Engel KC, Keating DH. A high-throughput solid phase screening method for identification of lignocellulose-degrading bacteria from environmental isolates. Biotechnol Lett 2011; 34:81-9. [PMID: 21904949 DOI: 10.1007/s10529-011-0742-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 08/24/2011] [Indexed: 11/25/2022]
Abstract
The development of cost-effective biofuels will require improvements in the efficiency of biomass deconstruction, a process typically carried out by lignocellulose-degrading enzymes. Environmental microbes represent an abundant and diverse source of lignocelluloses-degrading enzymes for use in biotechnology. However, identification of microorganisms that possess these enzymes has been slowed by a lack of rapid screening methodologies, particularly those that utilize native lignocellulosic substrates. In this report, we describe a new, solid-phase screening system for the identification of microbes capable of lignocellulose degradation. The critical component of this screening system is the use of acrylamide, instead of agar, as the solidifying agent. Our results show that this screening method allows for the identification of Gram-positive and Gram-negative bacteria that possess cellulose and hemicellulose degrading activities from environmental isolates.
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Affiliation(s)
- Jeffrey G Gardner
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 3554 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706, USA
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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.
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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
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Wang ZW, Hamilton-Brehm SD, Lochner A, Elkins JG, Morrell-Falvey JL. Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis. BIORESOURCE TECHNOLOGY 2011; 102:3155-3162. [PMID: 21075617 DOI: 10.1016/j.biortech.2010.10.104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 05/30/2023]
Abstract
In this study, a hydrolysate diffusion and utilization model was developed to examine factors influencing cellulolytic biofilm morphology. Model simulations using Caldicellulosiruptor obsidiansis revealed that the cellulolytic biofilm needs to generate more hydrolysate than it consumes to establish a higher than bulk solution intra-biofilm substrate concentration to support its growth. This produces a hydrolysate surplus that diffuses through the thin biofilm structure into the bulk solution, which gives rise to a uniform growth rate and hence the homogeneous morphology of the cellulolytic biofilm. Model predictions were tested against experimental data from a cellulose-fermenting bioreactor and the results were consistent with the model prediction and indicated that only a small fraction (10-12%) of the soluble hydrolysis products are utilized by the biofilm. The factors determining the rate-limiting step of cellulolytic biofilm growth are also analyzed and discussed.
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Affiliation(s)
- Zhi-Wu Wang
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Factors affecting accumulation and degradation of curdlan, trehalose and glycogen in cultures of Cellulomonas flavigena strain KU (ATCC 53703). Antonie van Leeuwenhoek 2010; 99:681-95. [PMID: 21190083 DOI: 10.1007/s10482-010-9544-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 12/10/2010] [Indexed: 10/18/2022]
Abstract
Cellulomonas flavigena strain KU (ATCC 53703) is a cellulolytic, Gram-positive bacterium which produces large quantities of an insoluble exopolysaccharide (EPS) when grown in minimal media with a high carbon-to-nitrogen (C/N) ratio. Earlier studies proved the EPS is structurally identical to the linear β-1,3-glucan known as curdlan and provided evidence that the EPS functions as a carbon and energy reserve compound. We now report that C. flavigena KU also accumulates two intracellular, glucose-storage carbohydrates under conditions of carbon and energy excess. These carbohydrates were partially purified and identified as the disaccharide trehalose and a glycogen/amylopectin-type polysaccharide. A novel method is described for the sequential fractionation and quantitative determination of all three carbohydrates from culture samples. This fractionation protocol was used to examine the effects of C/N ratio and osmolarity on the accumulation of cellular carbohydrates in batch culture. Increasing the C/N of the growth medium caused a significant accumulation of curdlan and glycogen but had a relatively minor effect on accumulation of trehalose. In contrast, trehalose levels increased in response to increasing osmolarity, while curdlan levels declined and glycogen levels were generally unaffected. During starvation for an exogenous source of carbon and energy, only curdlan and glycogen showed substantial degradation within the first 24 h. These results support the conclusion that extracellular curdlan and intracellular glycogen can both serve as short-term reserve compounds for C. flavigena KU and that trehalose appears to accumulate as a compatible solute in response to osmotic stress.
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