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Liu X, Li Y, Guo Y, Zeng Z, Li B, Wood TK, Cai X, Wang X. Physiological Function of Rac Prophage During Biofilm Formation and Regulation of Rac Excision in Escherichia coli K-12. Sci Rep 2015; 5:16074. [PMID: 26530864 PMCID: PMC4632033 DOI: 10.1038/srep16074] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022] Open
Abstract
Rac or rac-like prophage harbors many genes with important physiological functions, while it remains excision-proficient in several bacterial strains including Escherichia coli, Salmonella spp. and Shigella spp. Here, we found that rac excision is induced during biofilm formation, and the isogenic stain without rac is more motile and forms more biofilms in nutrient-rich medium at early stages in E. coli K-12. Additionally, the presence of rac genes increases cell lysis during biofilm development. In most E. coli strains, rac is integrated into the ttcA gene which encodes a tRNA-thioltransferase. Rac excision in E. coli K-12 leads to a functional change of TtcA, which results in reduced fitness in the presence of carbenicillin. Additionally, we demonstrate that YdaQ (renamed as XisR) is the excisionase of rac in E. coli K-12, and that rac excision is induced by the stationary sigma factor RpoS through inducing xisR expression. Taken together, our results reveal that upon rac integration, not only are new genes introduced into the host, but also there is a functional change in a host enzyme. Hence, rac excision is tightly regulated by host factors to control its stability in the host genome under different stress conditions.
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Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Zhenshun Zeng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baiyuan Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-4400.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802-4400
| | - Xingsheng Cai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
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Abstract
Worldwide, infectious diseases are one of the leading causes of death among children. At least 65% of all infections are caused by the biofilm mode of bacterial growth. Bacteria colonise surfaces and grow as multicellular biofilm communities surrounded by a polymeric matrix as a common survival strategy. These sessile communities endow bacteria with high tolerance to antimicrobial agents and hence cause persistent and chronic bacterial infections, such as dental caries, periodontitis, otitis media, cystic fibrosis and pneumonia. The highly complex nature and the rapid adaptability of the biofilm population impede our understanding of the process of biofilm formation, but an important role for oxygen-binding proteins herein is clear. Much research on this bacterial lifestyle is already performed, from genome/proteome analysis to in vivo antibiotic susceptibility testing, but without significant progress in biofilm treatment or eradication. This review will present the multiple challenges of biofilm research and discuss possibilities to cross these barriers in future experimental studies.
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Affiliation(s)
- Joke Donné
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Abstract
E. coli is a relevant model organism for the study of the molecular mechanisms underlying surface colonization. This process requires two essential steps: adhesion to a surface, followed by cell-cell adhesion counteracting the shear forces of the environment, with both steps contributing to the formation of a biofilm. This review provides an overview of the current knowledge of the genetic analyses aiming at identifying factors involved in both of these two highly related biological processes, with a particular emphasis on studies performed in Escherichia coli K-12. Bacterial adhesion to abiotic surfaces is likely to be highly dependent on the physicochemical and electrostatic interactions between the bacterial envelope and the substrate, which is itself often conditioned by the fluids to which it is exposed. Genetic analyses have revealed the diversity of genetic factors in E. coli that participate in colonization and biofilm formation on abiotic surfaces. The study of surface colonization and biofilm formation represents a rapidly expanding field of investigation. The use of E. coli K-12 to investigate the genetic basis of bacterial interactions with surfaces has led to the identification of a large repertoire of adhesins whose expression is subject to a complex interplay between regulatory networks. Understanding how E. coli K-12 behaves in complex biofilm communities will certainly contribute to an understanding of how natural commensal and pathogenic E. coli isolates develop.
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Oliveira NM, Martinez-Garcia E, Xavier J, Durham WM, Kolter R, Kim W, Foster KR. Biofilm Formation As a Response to Ecological Competition. PLoS Biol 2015; 13:e1002191. [PMID: 26158271 PMCID: PMC4497666 DOI: 10.1371/journal.pbio.1002191] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/29/2015] [Indexed: 12/28/2022] Open
Abstract
Bacteria form dense surface-associated communities known as biofilms that are central to their persistence and how they affect us. Biofilm formation is commonly viewed as a cooperative enterprise, where strains and species work together for a common goal. Here we explore an alternative model: biofilm formation is a response to ecological competition. We co-cultured a diverse collection of natural isolates of the opportunistic pathogen Pseudomonas aeruginosa and studied the effect on biofilm formation. We show that strain mixing reliably increases biofilm formation compared to unmixed conditions. Importantly, strain mixing leads to strong competition: one strain dominates and largely excludes the other from the biofilm. Furthermore, we show that pyocins, narrow-spectrum antibiotics made by other P. aeruginosa strains, can stimulate biofilm formation by increasing the attachment of cells. Side-by-side comparisons using microfluidic assays suggest that the increase in biofilm occurs due to a general response to cellular damage: a comparable biofilm response occurs for pyocins that disrupt membranes as for commercial antibiotics that damage DNA, inhibit protein synthesis or transcription. Our data show that bacteria increase biofilm formation in response to ecological competition that is detected by antibiotic stress. This is inconsistent with the idea that sub-lethal concentrations of antibiotics are cooperative signals that coordinate microbial communities, as is often concluded. Instead, our work is consistent with competition sensing where low-levels of antibiotics are used to detect and respond to the competing genotypes that produce them. Mixing natural isolates of the pathogenic bacterium Pseudomonas aeruginosa shows that the formation of biofilm is a response to antibiotic stress from competing genotypes. Bacteria often attach to each other and to surfaces and make biofilms. These dense communities occur everywhere, including on us and inside us, where they are central to both health and disease. Biofilm formation is often viewed as the coordinated action of multiple strains that work together in order to prosper and protect each other. In this study, we provide evidence for a very different view: biofilms are formed when bacterial strains compete with one another. We mixed together different strains of the widespread pathogen Pseudomonas aeruginosa and found that pairs often make bigger biofilms than either one alone. Rather than working together, however, we show that one strain normally kills the other off and that biofilm formation is actually a response to the damage of antibiotic warfare. Our work helps to explain the widespread observation that treating bacteria with clinical antibiotics can stimulate biofilm formation. When we treat bacteria, they respond as if the attack is coming from a foreign strain that must be outnumbered and outcompeted in a biofilm.
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Affiliation(s)
- Nuno M. Oliveira
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
| | - Esteban Martinez-Garcia
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Joao Xavier
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- Memorial Sloan-Kettering Cancer Center, Computational Biology Program, New York, New York, United States of America
| | | | - Roberto Kolter
- Harvard Medical School, Department of Microbiology and Immunobiology, Boston, Massachusetts, United States of America
| | - Wook Kim
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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55
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Thuptimdang P, Limpiyakorn T, McEvoy J, Prüß BM, Khan E. Effect of silver nanoparticles on Pseudomonas putida biofilms at different stages of maturity. JOURNAL OF HAZARDOUS MATERIALS 2015; 290:127-133. [PMID: 25756827 DOI: 10.1016/j.jhazmat.2015.02.073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
This study determined the effect of silver nanoparticles (AgNPs) on Pseudomonas putida KT2440 biofilms at different stages of maturity. Three biofilm stages (1-3, representing early to late stages of development) were identified from bacterial adenosine triphosphate (ATP) activity under static (96-well plate) and dynamic conditions (Center for Disease Control and Prevention biofilm reactor). Extracellular polymeric substance (EPS) levels, measured using crystal violet and total carbohydrate assays, and expression of the EPS-associated genes, csgA and alg8, supported the conclusion that biofilms at later stages were older than those at earlier stages. More mature biofilms (stages 2 and 3) showed little to no reduction in ATP activity following exposure to AgNPs. In contrast, the same treatment reduced ATP activity by more than 90% in the less mature stage 1 biofilms. Regardless of maturity, biofilms with EPS stripped off were more susceptible to AgNPs than controls with intact EPS, demonstrating that EPS is critical for biofilm tolerance of AgNPs. The findings from this study show that stage of maturity is an important factor to consider when studying effect of AgNPs on biofilms.
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Affiliation(s)
- Pumis Thuptimdang
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management, Bangkok 10330, Thailand.
| | - Tawan Limpiyakorn
- Center of Excellence on Hazardous Substance Management, Bangkok 10330, Thailand; Department of Environmental Engineering, Chulalongkorn University, Bangkok 10330, Thailand; Research Unit Control of Emerging Micropollutants in Environment, Chulalongkorn University, Bangkok 10330, Thailand.
| | - John McEvoy
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA.
| | - Birgit M Prüß
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA.
| | - Eakalak Khan
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND 58108, USA.
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Dharmaprakash A, Thandavarayan R, Joseph I, Thomas S. Development of broad-spectrum antibiofilm drugs: strategies and challenges. Future Microbiol 2015; 10:1035-48. [DOI: 10.2217/fmb.15.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT The severity of many chronic bacterial infections is mainly due to the biofilm mode of life adapted by pathogenic bacteria. The bacteria in biofilm-stage exhibit high resistance to host immune responses and antimicrobials, which complicates the treatment process and results in life threatening conditions. Most of the chronic infections are polymicrobial in nature. In order to combat the polymicrobial biofilm infections and to increase the efficiency of antimicrobials, there is an urgent need for broad-spectrum antibiofilm drugs. This review discusses the clinical needs and current status of broad-spectrum antibiofilm drugs with special emphasis on prospective strategies and hurdles in the process of new drug discovery.
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Affiliation(s)
- Akhilandeswarre Dharmaprakash
- Cholera & Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695 014, Kerala, India
| | | | - Iype Joseph
- Pathogen Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695 014, Kerala, India
| | - Sabu Thomas
- Cholera & Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695 014, Kerala, India
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57
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Wilkins M, Hall-Stoodley L, Allan RN, Faust SN. New approaches to the treatment of biofilm-related infections. J Infect 2014; 69 Suppl 1:S47-52. [DOI: 10.1016/j.jinf.2014.07.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
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58
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In vivo expression of Streptococcus pyogenes immunogenic proteins during tibial foreign body infection. Infect Immun 2014; 82:3891-9. [PMID: 25001603 DOI: 10.1128/iai.01831-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Group A streptococcus (GAS) is an important human pathogen that causes a number of diseases with a wide range of severities. While all known strains of GAS are still sensitive to penicillin, there have been reports of antibiotic treatment failure in as many as 20% to 40% of cases. Biofilm formation has been implicated as a possible cause for these failures. A biofilm is a microbially derived, sessile community where cells grow attached to a surface or as a bacterial conglomerate and surrounded by a complex extracellular matrix. While the ability of group A streptococcus to form biofilms in the laboratory has been shown, there is a lack of understanding of the role of GAS biofilms during an infection. We hypothesized that during infections, GAS exhibits a biofilm phenotype, complete with unique protein expression. To test this hypothesis, a rabbit model of GAS osteomyelitis was developed. A rabbit was inoculated with GAS using an infected indwelling device. Following the infection, blood and tissue samples were collected. Histological samples of the infected tibia were prepared, and the formation of a biofilm in vivo was visualized using peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) and confocal microscopy. In addition, Western blotting with convalescent rabbit serum detected cell wall proteins expressed in vitro under biofilm and planktonic growth conditions. Immunogenic proteins were then identified using matrix-assisted laser desorption ionization-time of flight tandem mass spectrometry (MALDI-TOF/TOF MS). These identities, along with the in vivo results, support the hypothesis that GAS forms biofilms during an infection. This unique phenotype should be taken into consideration when designing a vaccine or any other treatment for group A streptococcus infections.
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59
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Bacteriocin expression in sessile and planktonic populations of Escherichia coli. J Antibiot (Tokyo) 2014; 68:52-5. [DOI: 10.1038/ja.2014.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 05/20/2014] [Accepted: 05/28/2014] [Indexed: 11/08/2022]
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60
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Identification of genes induced in Vibrio cholerae in a dynamic biofilm system. Int J Med Microbiol 2014; 304:749-63. [PMID: 24962154 PMCID: PMC4101255 DOI: 10.1016/j.ijmm.2014.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/23/2014] [Accepted: 05/25/2014] [Indexed: 12/13/2022] Open
Abstract
The facultative human pathogen Vibrio cholerae, the causative agent of the severe secretory diarrheal disease cholera, persists in its aquatic reservoirs in biofilms during interepidemic periods. Biofilm is a likely form in which clinically relevant V. cholerae is taken up by humans, providing an infective dose. Thus, a better understanding of biofilm formation of V. cholerae is relevant for the ecology and epidemiology of cholera as well as a target to control the disease. Most previous studies have investigated static biofilms of V. cholerae and elucidated structural prerequisites like flagella, pili and a biofilm matrix including extracellular DNA, numerous matrix proteins and exopolysaccharide, as well as the involvement of regulatory pathways like two-component systems, quorum sensing and c-di-GMP signaling. However, aquatic environments are more likely to reflect an open, dynamic system. Hence, we used a biofilm system with constant medium flow and a temporal controlled reporter-system of transcription to identify genes induced during dynamic biofilm formation. We identified genes known or predicted to be involved in c-di-GMP signaling, motility and chemotaxis, metabolism, and transport. Subsequent phenotypic characterization of mutants with independent mutations in candidate dynamic biofilm-induced genes revealed novel insights into the physiology of static and dynamic biofilm conditions. The results of this study also reinforce the hypotheses that distinct differences in regulatory mechanisms governing biofilm development are present under dynamic conditions compared to static conditions.
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61
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Serra DO, Hengge R. Stress responses go three dimensional - the spatial order of physiological differentiation in bacterial macrocolony biofilms. Environ Microbiol 2014; 16:1455-71. [PMID: 24725389 PMCID: PMC4238805 DOI: 10.1111/1462-2920.12483] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/28/2014] [Indexed: 11/30/2022]
Abstract
In natural habitats, bacteria often occur in multicellular communities characterized by a robust extracellular matrix of proteins, amyloid fibres, exopolysaccharides and extracellular DNA. These biofilms show pronounced stress resistance including a resilience against antibiotics that causes serious medical and technical problems. This review summarizes recent studies that have revealed clear spatial physiological differentiation, complex supracellular architecture and striking morphology in macrocolony biofilms. By responding to gradients of nutrients, oxygen, waste products and signalling compounds that build up in growing biofilms, various stress responses determine whether bacteria grow and proliferate or whether they enter into stationary phase and use their remaining resources for maintenance and survival. As a consequence, biofilms differentiate into at least two distinct layers of vegetatively growing and stationary phase cells that exhibit very different cellular physiology. This includes a stratification of matrix production with a major impact on microscopic architecture, biophysical properties and directly visible morphology of macrocolony biofilms. Using Escherichia coli as a model system, this review also describes our detailed current knowledge about the underlying molecular control networks – prominently featuring sigma factors, transcriptional cascades and second messengers – that drive this spatial differentiation and points out directions for future research.
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Affiliation(s)
- Diego O Serra
- Institute of Biology/Microbiology, Humboldt Universität zu Berlin, Chausseestr. 117, Berlin, 10115, Germany
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62
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Beliaev AS, Romine MF, Serres M, Bernstein HC, Linggi BE, Markillie LM, Isern NG, Chrisler WB, Kucek LA, Hill EA, Pinchuk GE, Bryant DA, Wiley HS, Fredrickson JK, Konopka A. Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing. ISME JOURNAL 2014; 8:2243-55. [PMID: 24781900 DOI: 10.1038/ismej.2014.69] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/10/2022]
Abstract
We used deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities, which was manifested through the transcriptional upregulation of transport and catabolic pathways. Although growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. These hypothesized interactions were inferred from the excretion of specific amino acids (for example, alanine and methionine) by the cyanobacterium, which correlated with the downregulation of the corresponding biosynthetic machinery in Shewanella W3-18-1. In addition, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation may indicate increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.
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Affiliation(s)
- Alexander S Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margie F Romine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margrethe Serres
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hans C Bernstein
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bryan E Linggi
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lye M Markillie
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nancy G Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Leo A Kucek
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Eric A Hill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Grigoriy E Pinchuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Donald A Bryant
- 1] Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA [2] Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jim K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Allan Konopka
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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63
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Flood BE, Bailey JV, Biddle JF. Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments. GEOBIOLOGY 2014; 12:119-132. [PMID: 24382125 DOI: 10.1111/gbi.12072] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 11/27/2013] [Indexed: 06/03/2023]
Abstract
Wrinkle structures are sedimentary features that are produced primarily through the trapping and binding of siliciclastic sediments by mat-forming micro-organisms. Wrinkle structures and related sedimentary structures in the rock record are commonly interpreted to represent the stabilizing influence of cyanobacteria on sediments because cyanobacteria are known to produce similar textures and structures in modern tidal flat settings. However, other extant bacteria such as filamentous representatives of the family Beggiatoaceae can also interact with sediments to produce sedimentary features that morphologically resemble many of those associated with cyanobacteria-dominated mats. While Beggiatoa spp. and cyanobacteria are metabolically and phylogenetically distant, genomic analyses show that the two groups share hundreds of homologous genes, likely as the result of horizontal gene transfer. The comparative genomics results described here suggest that some horizontally transferred genes may code for phenotypic traits such as filament formation, chemotaxis, and the production of extracellular polymeric substances that potentially underlie the similar biostabilizing influences of these organisms on sediments. We suggest that the ecological utility of certain basic life modes such as the construction of mats and biofilms, coupled with the lateral mobility of genes in the microbial world, introduces an element of uncertainty into the inference of specific phylogenetic origins from gross morphological features preserved in the ancient rock record.
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Affiliation(s)
- B E Flood
- Department of Earth Sciences, University of Minnesota- Twin Cities, Minneapolis, MN, USA
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64
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The Salmonella Spi1 virulence regulatory protein HilD directly activates transcription of the flagellar master operon flhDC. J Bacteriol 2014; 196:1448-57. [PMID: 24488311 DOI: 10.1128/jb.01438-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Infection of intestinal epithelial cells is dependent on the Salmonella enterica serovar Typhimurium pathogenicity island 1 (Spi1)-encoded type III injectisome system and flagellar motility. Thus, the expression of virulence and flagellar genes is subject to tight regulatory control mechanisms in order to ensure the correct spatiotemporal production of the respective gene products. In this work, we reveal a new level of cross-regulation between the Spi1 and flagellar regulatory systems. Transposon mutagenesis identified a class of mutants that prevented flhDC autorepression by overexpressing HilD. HilD, HilC, RtsA, and HilA comprise a positive regulatory circuit for the expression of the Spi1 genes. Here, we report a novel transcriptional cross talk between the Spi1 and flagellar regulons where HilD transcriptionally activates flhDC gene expression by binding to nucleotides -68 to -24 upstream from the P5 transcriptional start site. We additionally show that, in contrast to the results of a previous report, HilA does not affect flagellar gene expression. Finally, we discuss a model of the cross-regulation network between Spi1 and the flagellar system and propose a regulatory mechanism via the Spi1 master regulator HilD that would prime flagellar genes for rapid reactivation during host infection.
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65
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Bridier A, Briandet R. Contribution of confocal laser scanning microscopy in deciphering biofilm tridimensional structure and reactivity. Methods Mol Biol 2014; 1147:255-266. [PMID: 24664839 DOI: 10.1007/978-1-4939-0467-9_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Confocal laser scanning microscopy (CLSM) became in last years an invaluable technique to study biofilms since it enables researchers to explore noninvasively the dynamic architecture and the reactivity of these biological edifices. The constant development of fluorescent markers and genetic tools along with the improvement of spatial, spectral, and temporal resolution of imaging facilities offers new opportunities to better decipher microbial biofilm properties. In this contribution, we proposed to describe the contribution of CLSM to the study of biofilm architecture and reactivity throughout two different illustrative approaches.
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66
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TerAvest MA, He Z, Rosenbaum MA, Martens EC, Cotta MA, Gordon JI, Angenent LT. Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats. Biotechnol Bioeng 2013; 111:165-73. [PMID: 23996813 DOI: 10.1002/bit.24994] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/21/2013] [Accepted: 06/25/2013] [Indexed: 11/12/2022]
Abstract
Bacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host-derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, including the factors that allow it to maintain itself in the gut. Biofilm formation may be a mechanism for bacterial retention in the gut. Therefore, we used custom GeneChips to compare the transcriptomes of biofilm and planktonic B. thetaiotaomicron during growth in mono-colonized chemostats. We identified 1,154 genes with a fold-change greater than 2, with confidence greater than or equal to 95%. Among the prominent changes observed in biofilm populations were: (i) greater expression of genes in polysaccharide utilization loci that are involved in foraging of O-glycans normally found in the gut mucosa; and (ii) regulated expression of capsular polysaccharide biosynthesis loci. Hierarchical clustering of the data with different datasets, which were obtained during growth under a range of conditions in minimal media and in intestinal tracts of gnotobiotic mice, revealed that within this group of differentially expressed genes, biofilm communities were more similar to the in vivo samples than to planktonic cells and exhibited features of substrate limitation. The current study also validates the use of chemostats as an in vitro "gnotobiotic" model to study gene expression of attached populations of this bacterium. This is important to gut microbiota research, because bacterial attachment and the consequences of disruptions in attachment are difficult to study in vivo.
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Affiliation(s)
- Michaela A TerAvest
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, 14853
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67
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de la Fuente-Núñez C, Reffuveille F, Fernández L, Hancock REW. Bacterial biofilm development as a multicellular adaptation: antibiotic resistance and new therapeutic strategies. Curr Opin Microbiol 2013; 16:580-9. [PMID: 23880136 DOI: 10.1016/j.mib.2013.06.013] [Citation(s) in RCA: 495] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 12/20/2022]
Abstract
Bacteria have evolved the ability to form multicellular, surface-adherent communities called biofilms that allow survival in hostile environments. In clinical settings, bacteria are exposed to various sources of stress, including antibiotics, nutrient limitation, anaerobiosis, heat shock, etc., which in turn trigger adaptive responses in bacterial cells. The combination of this and other defense mechanisms results in the formation of highly (adaptively) resistant multicellular structures that are recalcitrant to host immune clearance mechanisms and very difficult to eradicate with the currently available antimicrobial agents, which are generally developed for the eradication of free-swimming (planktonic) bacteria. However, novel strategies that specifically target the biofilm mode of growth have been recently described, thus providing the basis for future anti-biofilm therapy.
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Affiliation(s)
- César de la Fuente-Núñez
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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68
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RflM functions as a transcriptional repressor in the autogenous control of the Salmonella Flagellar master operon flhDC. J Bacteriol 2013; 195:4274-82. [PMID: 23873910 DOI: 10.1128/jb.00728-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Motility of bacteria like Salmonella enterica is a highly regulated process that responds to a variety of internal and external stimuli. A hierarchy of three promoter classes characterizes the Salmonella flagellar system, and the onset of flagellar gene expression depends on the oligomeric regulatory complex and class 1 gene product FlhD(4)C(2). The flhDC promoter is a target for a broad range of transcriptional regulators that bind within the flhDC promoter region and either negatively or positively regulate flhDC operon transcription. In this work, we demonstrate that the RflM protein is a key component of flhDC regulation. Transposon mutagenesis was performed to investigate a previously described autoinhibitory effect of the flagellar master regulatory complex FlhD(4)C(2). RflM is a LuxR homolog that functions as a flagellar class 1 transcriptional repressor. RflM was found to be the negative regulator of flhDC expression that is responsible for the formerly described autoinhibitory effect of the FlhD(4)C(2) complex on flhDC operon transcription (K. Kutsukake, Mol. Gen. Genet. 254:440-448, 1997). We conclude that upon commencement of flagellar gene expression, the FlhD(4)C(2) complex initiates a regulatory feedback loop by activating rflM gene expression. rflM encodes a transcriptional repressor, RflM, which fine-tunes flhDC expression levels.
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69
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Anti-biofilm activity of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. Res Microbiol 2013; 164:450-6. [DOI: 10.1016/j.resmic.2013.01.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/24/2013] [Indexed: 01/05/2023]
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70
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Rizzello L, Cingolani R, Pompa PP. Nanotechnology tools for antibacterial materials. Nanomedicine (Lond) 2013; 8:807-21. [DOI: 10.2217/nnm.13.63] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The understanding of the interactions between biological systems and nanoengineered devices is crucial in several research fields, including tissue engineering, biomechanics, synthetic biology and biomedical devices. This review discusses the current knowledge of the interactions between bacteria and abiotic nanostructured substrates. First, the effects of randomly organized nanoscale topography on bacterial adhesion and persistence are described. Second, the interactions between microorganisms and highly organized/ordered micro- and nano-patterns are discussed. Finally, we survey the most promising approaches for the fabrication of silver polymeric nanocomposites, which have important applications as antimicrobial materials. The advantages, drawbacks and limitations of such nanotechnologies are critically discussed in view of potential future applications.
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Affiliation(s)
- Loris Rizzello
- Center for Bio-Molecular Nanotechnology, Istituto Italiano di Tecnologia, Via Barsanti, 1-73010 Arnesano (Lecce), Italy
| | - Roberto Cingolani
- Istituto Italiano di Tecnologia, Central Research Laboratories, Via Morego, 30-16136 Genova, Italy
| | - Pier Paolo Pompa
- Center for Bio-Molecular Nanotechnology, Istituto Italiano di Tecnologia, Via Barsanti, 1-73010 Arnesano (Lecce), Italy.
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Abstract
Bacterial extracellular polysaccharides have been shown to mediate many of the cell-to-cell and cell-to-surface interactions that are required for the formation, cohesion and stabilization of bacterial biofilms. However, recent studies have identified several bacterial polysaccharides that inhibit biofilm formation by a wide spectrum of bacteria and fungi both in vitro and in vivo. This review discusses the composition, modes of action and potential biological roles of antibiofilm polysaccharides recently identified in bacteria and eukarya. Some of these molecules may have technological applications as antibiofilm agents in industry and medicine.
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Affiliation(s)
- Olaya Rendueles
- Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, 25-28 rue du Dr Roux, F-75015 Paris, France
| | - Jeffrey B. Kaplan
- Department of Oral Biology, New Jersey Dental School, Newark, NJ 07103, USA
| | - Jean-Marc Ghigo
- Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, 25-28 rue du Dr Roux, F-75015 Paris, France
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Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. Appl Environ Microbiol 2012; 78:8311-20. [PMID: 23001650 DOI: 10.1128/aem.02516-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Members of the genus Sphingomonas are important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degrading Sphingomonas sp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity.
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73
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Marshall SH, Gómez FA, Ramírez R, Nilo L, Henríquez V. Biofilm generation by Piscirickettsia salmonis under growth stress conditions: a putative in vivo survival/persistence strategy in marine environments. Res Microbiol 2012; 163:557-66. [DOI: 10.1016/j.resmic.2012.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/28/2012] [Indexed: 10/28/2022]
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Costaglioli P, Barthe C, Claverol S, Brözel VS, Perrot M, Crouzet M, Bonneu M, Garbay B, Vilain S. Evidence for the involvement of the anthranilate degradation pathway in Pseudomonas aeruginosa biofilm formation. Microbiologyopen 2012; 1:326-39. [PMID: 23170231 PMCID: PMC3496976 DOI: 10.1002/mbo3.33] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/21/2012] [Accepted: 07/02/2012] [Indexed: 12/03/2022] Open
Abstract
Bacterial biofilms are complex cell communities found attached to surfaces and surrounded by an extracellular matrix composed of exopolysaccharides, DNA, and proteins. We investigated the whole-genome expression profile of Pseudomonas aeruginosa sessile cells (SCs) present in biofilms developed on a glass wool substratum. The transcriptome and proteome of SCs were compared with those of planktonic cell cultures. Principal component analysis revealed a biofilm-specific gene expression profile. Our study highlighted the overexpression of genes controlling the anthranilate degradation pathway in the SCs grown on glass wool for 24 h. In this condition, the metabolic pathway that uses anthranilate for Pseudomonas quinolone signal production was not activated, which suggested that anthranilate was primarily being consumed for energy metabolism. Transposon mutants defective for anthranilate degradation were analyzed in a simple assay of biofilm formation. The phenotypic analyses confirmed that P. aeruginosa biofilm formation partially depended on the activity of the anthranilate degradation pathway. This work points to a new feature concerning anthranilate metabolism in P. aeruginosa SCs.
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Affiliation(s)
- Patricia Costaglioli
- Biotechnologie des Protéines Recombinantes à Visée Santé, University Bordeaux EA4135, F-33000, Bordeaux, France
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75
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Alavi M, Stojadinovic A, Izadjoo M. An overview of biofilm and its detection in clinical samples. J Wound Care 2012; 21:376-83. [DOI: 10.12968/jowc.2012.21.8.376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- M.R. Alavi
- Diagnostics and Translational Research Center, Henry M. Jackson Foundation for Advancement of Military Medicine, Maryland, USA
- Combat Wound Initiative Program, Maryland, USA
| | - A. Stojadinovic
- Combat Wound Initiative Program, Maryland, USA
- Uniformed Services University of the Health Sciences, Maryland, USA
| | - M.J. Izadjoo
- Diagnostics and Translational Research Center, Henry M. Jackson Foundation for Advancement of Military Medicine, Maryland, USA
- Combat Wound Initiative Program, Maryland, USA
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76
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Phillips NJ, Steichen CT, Schilling B, Post DMB, Niles RK, Bair TB, Falsetta ML, Apicella MA, Gibson BW. Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins. PLoS One 2012; 7:e38303. [PMID: 22701624 PMCID: PMC3368942 DOI: 10.1371/journal.pone.0038303] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/03/2012] [Indexed: 02/07/2023] Open
Abstract
Neisseria gonorrhoeae, the causative agent of gonorrhea, can form biofilms in vitro and in vivo. In biofilms, the organism is more resistant to antibiotic treatment and can serve as a reservoir for chronic infection. We have used stable isotope labeling by amino acids in cell culture (SILAC) to compare protein expression in biofilm and planktonic organisms. Two parallel populations of N. gonorrhoeae strain 1291, which is an arginine auxotroph, were grown for 48 h in continuous-flow chambers over glass, one supplemented with (13)C(6)-arginine for planktonic organisms and the other with unlabeled arginine for biofilm growth. The biofilm and planktonic cells were harvested and lysed separately, and fractionated into three sequential protein extracts. Corresponding heavy (H) planktonic and light (L) biofilm protein extracts were mixed and separated by 1D SDS-PAGE gels, and samples were extensively analyzed by liquid chromatography-mass spectrometry. Overall, 757 proteins were identified, and 152 unique proteins met a 1.5-fold cutoff threshold for differential expression with p-values <0.05. Comparing biofilm to planktonic organisms, this set included 73 upregulated and 54 downregulated proteins. Nearly a third of the upregulated proteins were involved in energy metabolism, with cell envelope proteins making up the next largest group. Of the downregulated proteins, the largest groups were involved in protein synthesis and energy metabolism. These proteomics results were compared with our previously reported results from transcriptional profiling of gonococcal biofilms using microarrays. Nitrite reductase and cytochrome c peroxidase, key enzymes required for anaerobic growth, were detected as highly upregulated in both the proteomic and transcriptomic datasets. These and other protein expression changes observed in the present study were consistent with a shift to anaerobic respiration in gonococcal biofilms, although changes in membrane proteins not explicitly related to this shift may have other functions.
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Affiliation(s)
- Nancy J. Phillips
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher T. Steichen
- Department of Microbiology, College of Medicine, The University of Iowa, Iowa City, Iowa, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Deborah M. B. Post
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Richard K. Niles
- Department of Obstetrics, Gynecology, and Reproductive Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Thomas B. Bair
- Department of Microbiology, College of Medicine, The University of Iowa, Iowa City, Iowa, United States of America
| | - Megan L. Falsetta
- Department of Microbiology, College of Medicine, The University of Iowa, Iowa City, Iowa, United States of America
| | - Michael A. Apicella
- Department of Microbiology, College of Medicine, The University of Iowa, Iowa City, Iowa, United States of America
| | - Bradford W. Gibson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Buck Institute for Research on Aging, Novato, California, United States of America
- * E-mail:
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77
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Abstract
Infectious diseases can be difficult to cure, especially if the pathogen forms a biofilm. After decades of extensive research into the morphology, physiology and genomics of biofilm formation, attention has recently been directed toward the analysis of the cellular metabolome in order to understand the transformation of a planktonic cell to a biofilm. Metabolomics can play an invaluable role in enhancing our understanding of the underlying biological processes related to the structure, formation and antibiotic resistance of biofilms. A systematic view of metabolic pathways or processes responsible for regulating this 'social structure' of microorganisms may provide critical insights into biofilm-related drug resistance and lead to novel treatments. This review will discuss the development of NMR-based metabolomics as a technology to study medically relevant biofilms. Recent advancements from case studies reviewed in this manuscript have shown the potential of metabolomics to shed light on numerous biological problems related to biofilms.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
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78
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Dong L, Tong Z, Linghu D, Lin Y, Tao R, Liu J, Tian Y, Ni L. Effects of sub-minimum inhibitory concentrations of antimicrobial agents on Streptococcus mutans biofilm formation. Int J Antimicrob Agents 2012; 39:390-5. [DOI: 10.1016/j.ijantimicag.2012.01.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/10/2012] [Accepted: 01/18/2012] [Indexed: 11/26/2022]
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Stahlhut SG, Struve C, Krogfelt KA, Reisner A. Biofilm formation of Klebsiella pneumoniae on urethral catheters requires either type 1 or type 3 fimbriae. ACTA ACUST UNITED AC 2012; 65:350-9. [PMID: 22448614 PMCID: PMC3410544 DOI: 10.1111/j.1574-695x.2012.00965.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 02/17/2012] [Accepted: 03/20/2012] [Indexed: 01/29/2023]
Abstract
Urinary catheters are standard medical devices utilized in both hospital and nursing home settings, but are associated with a high frequency of catheter-associated urinary tract infections (CAUTI). In particular, biofilm formation on the catheter surface by uropathogens such as Klebsiella pneumoniae causes severe problems. Here we demonstrate that type 1 and type 3 fimbriae expressed by K. pneumoniae enhance biofilm formation on urinary catheters in a catheterized bladder model that mirrors the physico-chemical conditions present in catheterized patients. Furthermore, we show that both fimbrial types are able to functionally compensate for each other during biofilm formation on urinary catheters. In situ monitoring of fimbrial expression revealed that neither of the two fimbrial types is expressed when cells are grown planktonically. Interestingly, during biofilm formation on catheters, both fimbrial types are expressed, suggesting that they are both important in promoting biofilm formation on catheters. Additionally, transformed into and expressed by a nonfimbriated Escherichia coli strain, both fimbrial types significantly increased biofilm formation on catheters compared with the wild-type E. coli strain. The widespread occurrence of the two fimbrial types in different species of pathogenic bacteria stresses the need for further assessment of their role during urinary tract infections.
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Affiliation(s)
- Steen G Stahlhut
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
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80
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Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics 2012; 13:138. [PMID: 22507456 PMCID: PMC3431258 DOI: 10.1186/1471-2164-13-138] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 02/27/2012] [Indexed: 11/10/2022] Open
Abstract
Background Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. Results The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Conclusions Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
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Affiliation(s)
- Melinda E Clark
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
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81
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Yersinia--flea interactions and the evolution of the arthropod-borne transmission route of plague. Curr Opin Microbiol 2012; 15:239-46. [PMID: 22406208 DOI: 10.1016/j.mib.2012.02.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/14/2012] [Accepted: 02/16/2012] [Indexed: 02/06/2023]
Abstract
Yersinia pestis, the causative agent of plague, is unique among the enteric group of Gram-negative bacteria in relying on a blood-feeding insect for transmission. The Yersinia-flea interactions that enable plague transmission cycles have had profound historical consequences as manifested by human plague pandemics. The arthropod-borne transmission route was a radical ecologic change from the food-borne and water-borne transmission route of Yersinia pseudotuberculosis, from which Y. pestis diverged only within the last 20000 years. Thus, the interactions of Y. pestis with its flea vector that lead to colonization and successful transmission are the result of a recent evolutionary adaptation that required relatively few genetic changes. These changes from the Y. pseudotuberculosis progenitor included loss of insecticidal activity, increased resistance to antibacterial factors in the flea midgut, and extending Yersinia biofilm-forming ability to the flea host environment.
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Parker ZM, Pendergraft SS, Sobieraj J, McGinnis MM, Karatan E. Elevated levels of the norspermidine synthesis enzyme NspC enhance Vibrio cholerae biofilm formation without affecting intracellular norspermidine concentrations. FEMS Microbiol Lett 2012; 329:18-27. [PMID: 22239666 DOI: 10.1111/j.1574-6968.2012.02498.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/15/2011] [Accepted: 01/04/2012] [Indexed: 11/30/2022] Open
Abstract
Biofilm formation in Vibrio cholerae is in part regulated by norspermidine, a polyamine synthesized by the enzyme carboxynorspermidine decarboxylase (NspC). The absence of norspermidine in the cell leads to a marked reduction in V. cholerae biofilm formation by an unknown mechanism. In this work, we show that overexpression of nspC results in large increases in biofilm formation and vps gene expression as well as a significant decrease in motility. Interestingly, increased NspC levels do not lead to increased concentrations of norspermidine in the cell. Our results show that NspC levels inversely regulate biofilm and motility and implicate the presence of an effective feedback mechanism maintaining norspermidine homeostasis in V. cholerae. Moreover, we provide evidence that NspC and the norspermidine sensor protein, NspS, provide independent and distinct inputs into the biofilm regulatory network.
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Affiliation(s)
- Zachary M Parker
- Department of Biology, Appalachian State University, Boone, NC 27599, USA
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83
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Park SH, Cheon HL, Park KH, Chung MS, Choi SH, Ryu S, Kang DH. Inactivation of biofilm cells of foodborne pathogen by aerosolized sanitizers. Int J Food Microbiol 2011; 154:130-4. [PMID: 22264420 DOI: 10.1016/j.ijfoodmicro.2011.12.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 12/01/2011] [Accepted: 12/11/2011] [Indexed: 11/30/2022]
Abstract
The objective of this study was to determine the effect of aerosolized sanitizers on the inactivation of Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes biofilms. Biofilms were formed on a stainless steel and polyvinyl chloride (PVC) coupon by using a mixture of three strains each of three foodborne pathogens. Six day old biofilms on stainless steel and PVC coupons were treated with aerosolized sodium hypochlorite (SHC; 100 ppm) and peracetic acid (100, 200, and 400 ppm) in a model cabinet for 5, 10, 30, and 50 min. Treatment with 100 ppm PAA was more effective than the same concentration of SHC with increasing treatment time. Exposure to 100 ppm SHC and PAA for 50 min significantly (p<0.05) reduced biofilm cells of three foodborne pathogens (0.50 to 3.63 log CFU/coupon and 2.83 to more than 5.78 log CFU/coupon, respectively) compared to the control treatment. Exposure to 200 and 400 ppm PAA was more effective in reducing biofilm cells. Biofilm cells were reduced to below the detection limit (1.48 log CFU/coupon) between 10 and 30 min of exposure. The results of this study suggest that aerosolized sanitizers have a potential as a biofilm control method in the food industry.
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Affiliation(s)
- Sang-Hyun Park
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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84
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Abstract
In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in Escherichia coli depends on the σS (RpoS) subunit of RNA polymerase. σS is closely related to the vegetative sigma factor σ70 (RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σS is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σS levels, which mainly rely on the rapid inhibition of σS proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σS directly or indirectly activates more than 500 genes. Additional signal input is integrated by σS cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σS. At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σS is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σS to specific environmental niches.
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85
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Bridier A, Briandet R, Thomas V, Dubois-Brissonnet F. Resistance of bacterial biofilms to disinfectants: a review. BIOFOULING 2011; 27:1017-32. [PMID: 22011093 DOI: 10.1080/08927014.2011.626899] [Citation(s) in RCA: 533] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A biofilm can be defined as a community of microorganisms adhering to a surface and surrounded by a complex matrix of extrapolymeric substances. It is now generally accepted that the biofilm growth mode induces microbial resistance to disinfection that can lead to substantial economic and health concerns. Although the precise origin of such resistance remains unclear, different studies have shown that it is a multifactorial process involving the spatial organization of the biofilm. This review will discuss the mechanisms identified as playing a role in biofilm resistance to disinfectants, as well as novel anti-biofilm strategies that have recently been explored.
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Affiliation(s)
- A Bridier
- AgroParisTech, UMR MICALIS, F-91300 Massy, France
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86
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Shalá AA, Restrepo S, González Barrios AF. A network model for biofilm development in Escherichia coli K-12. Theor Biol Med Model 2011; 8:34. [PMID: 21939518 PMCID: PMC3224578 DOI: 10.1186/1742-4682-8-34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 09/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In nature, bacteria often exist as biofilms. Biofilms are communities of microorganisms attached to a surface. It is clear that biofilm-grown cells harbor properties remarkably distinct from planktonic cells. Biofilms frequently complicate treatments of infections by protecting bacteria from the immune system, decreasing antibiotic efficacy and dispersing planktonic cells to distant body sites. In this work, we employed enhanced Boolean algebra to model biofilm formation. RESULTS The network obtained describes biofilm formation successfully, assuming - in accordance with the literature - that when the negative regulators (RscCD and EnvZ/OmpR) are off, the positive regulator (FlhDC) is on. The network was modeled under three different conditions through time with satisfactory outcomes. Each cluster was constructed using the K-means/medians Clustering Support algorithm on the basis of published Affymetrix microarray gene expression data from biofilm-forming bacteria and the planktonic state over four time points for Escherichia coli K-12. CONCLUSIONS The different phenotypes obtained demonstrate that the network model of biofilm formation can simulate the formation or repression of biofilm efficiently in E. coli K-12.
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Affiliation(s)
- Andrew A Shalá
- Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, Colombia
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87
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Korolev KS, Xavier JB, Nelson DR, Foster KR. A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies. Am Nat 2011; 178:538-52. [PMID: 21956031 DOI: 10.1086/661897] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.
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Affiliation(s)
- Kirill S Korolev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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88
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Koerdt A, Orell A, Pham TK, Mukherjee J, Wlodkowski A, Karunakaran E, Biggs CA, Wright PC, Albers SV. Macromolecular fingerprinting of sulfolobus species in biofilm: a transcriptomic and proteomic approach combined with spectroscopic analysis. J Proteome Res 2011; 10:4105-19. [PMID: 21761944 PMCID: PMC3166137 DOI: 10.1021/pr2003006] [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] [Indexed: 11/29/2022]
Abstract
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Microorganisms in nature often live in surface-associated sessile communities, encased in a self-produced matrix, referred to as biofilms. Biofilms have been well studied in bacteria but in a limited way for archaea. We have recently characterized biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus, and S. tokodaii. These strains form different communities ranging from simple carpet structures in S. solfataricus to high density tower-like structures in S. acidocaldarius under static condition. Here, we combine spectroscopic, proteomic, and transcriptomic analyses to describe physiological and regulatory features associated with biofilms. Spectroscopic analysis reveals that in comparison to planktonic life-style, biofilm life-style has distinctive influence on the physiology of each Sulfolobus spp. Proteomic and transcriptomic data show that biofilm-forming life-style is strain specific (eg ca. 15% of the S. acidocaldarius genes were differently expressed, S. solfataricus and S. tokodaii had ∼3.4 and ∼1%, respectively). The -omic data showed that regulated ORFs were widely distributed in basic cellular functions, including surface modifications. Several regulated genes are common to biofilm-forming cells in all three species. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, indicating their possible roles as a key regulatory factor in biofilm development. S. acidocaldarius, S. solfataricus, and S. tokodaii strains were grown independently as biofilms. Comparison between planktonic and biofilm cell popupations of all three strains was performed by spectroscopic analysis (FTIR and XPS), iTRAQ proteomics, and RNA microarrays. To highlight common features in biofilm formation among the Sulfolobus strains, the data is presented as a comparative analysis. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, suggesting their roles as key regulatory factor in biofilm development.
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Affiliation(s)
- Andrea Koerdt
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
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89
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Karunakaran E, Mukherjee J, Ramalingam B, Biggs CA. "Biofilmology": a multidisciplinary review of the study of microbial biofilms. Appl Microbiol Biotechnol 2011; 90:1869-81. [PMID: 21538113 DOI: 10.1007/s00253-011-3293-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 03/26/2011] [Accepted: 03/27/2011] [Indexed: 11/29/2022]
Abstract
The observation of biofilm formation is not a new phenomenon. The prevalence and significance of biofilm and aggregate formation in various processes have encouraged extensive research in this field for more than 40 years. In this review, we highlight techniques from different disciplines that have been used to successfully describe the extracellular, surface and intracellular elements that are predominant in understanding biofilm formation. To reduce the complexities involved in studying biofilms, researchers in the past have generally taken a parts-based, disciplinary specific approach to understand the different components of biofilms in isolation from one another. Recently, a few studies have looked into combining the different techniques to achieve a more holistic understanding of biofilms, yet this approach is still in its infancy. In order to attain a global understanding of the processes involved in the formation of biofilms and to formulate effective biofilm control strategies, researchers in the next decade should recognise that the study of biofilms, i.e. biofilmology, has evolved into a discipline in its own right and that mutual cooperation between the various disciplines towards a multidisciplinary research vision is vital in this field.
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Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, ChELSI Institute, The University of Sheffield, Sheffield, UK
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90
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Falsetta ML, Steichen CT, McEwan AG, Cho C, Ketterer M, Shao J, Hunt J, Jennings MP, Apicella MA. The Composition and Metabolic Phenotype of Neisseria gonorrhoeae Biofilms. Front Microbiol 2011; 2:75. [PMID: 21833322 PMCID: PMC3153042 DOI: 10.3389/fmicb.2011.00075] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 03/30/2011] [Indexed: 12/02/2022] Open
Abstract
Neisseria gonorrhoeae has been shown to form biofilms during cervical infection. Thus, biofilm formation may play an important role in the infection of women. The ability of N. gonorrhoeae to form membrane blebs is crucial to biofilm formation. Blebs contain DNA and outer membrane structures, which have been shown to be major constituents of the biofilm matrix. The organism expresses a DNA thermonuclease that is involved in remodeling of the biofilm matrix. Comparison of the transcriptional profiles of gonococcal biofilms and planktonic runoff indicate that genes involved in anaerobic metabolism and oxidative stress tolerance are more highly expressed in biofilm. The expression of aniA, ccp, and norB, which encode nitrite reductase, cytochrome c peroxidase, and nitric oxide reductase respectively, is required for mature biofilm formation over glass and human cervical cells. In addition, anaerobic respiration occurs in the substratum of gonococcal biofilms and disruption of the norB gene required for anaerobic respiration, results in a severe biofilm attenuation phenotype. It has been demonstrated that accumulation of nitric oxide (NO) contributes to the phenotype of a norB mutant and can retard biofilm formation. However, NO can also enhance biofilm formation, and this is largely dependent on the concentration and donation rate or steady-state kinetics of NO. The majority of the genes involved in gonococcal oxidative stress tolerance are also required for normal biofilm formation, as mutations in the following genes result in attenuated biofilm formation over cervical cells and/or glass: oxyR, gor, prx, mntABC, trxB, and estD. Overall, biofilm formation appears to be an adaptation for coping with the environmental stresses present in the female genitourinary tract. Therefore, this review will discuss the studies, which describe the composition and metabolic phenotype of gonococcal biofilms.
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Affiliation(s)
- Megan L Falsetta
- Department of Microbiology, The University of Iowa Iowa City, IA, USA
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91
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Lauchnor EG, Radniecki TS, Semprini L. Inhibition and gene expression of Nitrosomonas europaea biofilms exposed to phenol and toluene. Biotechnol Bioeng 2010; 108:750-7. [PMID: 21404249 DOI: 10.1002/bit.22999] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/23/2010] [Accepted: 10/26/2010] [Indexed: 11/08/2022]
Abstract
Pure culture biofilms of the ammonia-oxidizing bacterium Nitrosomonas europaea were grown in a Drip Flow Biofilm Reactor and exposed to the aromatic hydrocarbons phenol and toluene. Ammonia oxidation rates, as measured by nitrite production in the biofilms, were inhibited 50% when exposed to 56 µM phenol or 100 µM toluene, while 50% inhibition of suspended cells occurred at 8 µM phenol or 20 µM toluene. Biofilm-grown cells dispersed into liquid medium and immediately exposed to phenol or toluene experienced similar inhibition levels as batch grown cells, indicating that mass transfer may be a factor in N. europaea biofilm resistance. Whole genome microarray analysis of gene expression was used to detect genes up-regulated in biofilms during toluene and phenol exposure. Two genes, a putative pirin protein (NE1545) and a putative inner membrane protein (NE1546) were up-regulated during phenol exposure, but no genes were up-regulated during toluene exposure. Using qRT-PCR, up-regulation of NE1545 was detected in biofilms and suspended cells exposed to a range of phenol concentrations and levels of inhibition. In the biofilms, NE1545 expression was up-regulated an average of 13-fold over the range of phenol concentrations tested, and was essentially independent of phenol concentration. However, the expression of NE1545 in suspended cells increased from 20-fold at 7 µM phenol up to 80-fold at 30 µM phenol. This study demonstrates that biofilms of N. europaea are more resistant than suspended cells to inhibition of ammonia oxidation by phenol and toluene, even though the global transcriptional responses to the inhibitors do not differ in N. europaea between the suspended and attached growth states.
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Affiliation(s)
- Ellen G Lauchnor
- School of Chemical, Biological and Environmental Engineering, 102 Gleeson Hall, Oregon State University, Corvallis, Oregon 97331, USA
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92
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Duval JF, Gaboriaud F. Progress in electrohydrodynamics of soft microbial particle interphases. Curr Opin Colloid Interface Sci 2010. [DOI: 10.1016/j.cocis.2009.12.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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93
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Coenye T. Response of sessile cells to stress: from changes in gene expression to phenotypic adaptation. ACTA ACUST UNITED AC 2010; 59:239-52. [PMID: 20482621 DOI: 10.1111/j.1574-695x.2010.00682.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A better understanding of the genotypic and phenotypic adaptation of sessile (biofilm-associated) microorganisms to various forms of stress is required in order to develop more effective antibiofilm strategies. This review presents an overview of what high-throughput transcriptomic analyses have taught us concerning the response of various clinically relevant microorganisms (including Pseudomonas aeruginosa, Burkholderia cenocepacia and Candida albicans) to treatment with antibiotics or disinfectants. In addition, several problems associated with identifying gene expression patterns in biofilms in general and their implications for identifying the response to stress are discussed (with a focus on heterogeneity in microbial biofilms and the role of small RNAs in microbial group behavior).
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium.
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94
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Franks AE. Transcriptional analysis in microbial fuel cells: common pitfalls in global gene expression studies of microbial biofilms. FEMS Microbiol Lett 2010; 307:111-2. [PMID: 20455951 DOI: 10.1111/j.1574-6968.2010.01975.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ashley E Franks
- Department of Microbiology, University of Massachusetts, Amherst, MA 01002, USA.
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95
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Bhomkar P, Materi W, Semenchenko V, Wishart DS. Transcriptional response of E. coli upon FimH-mediated fimbrial adhesion. GENE REGULATION AND SYSTEMS BIOLOGY 2010; 4:1-17. [PMID: 20458372 PMCID: PMC2865769 DOI: 10.4137/grsb.s4525] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Functionalities which may be genetically programmed into a bacterium are limited by its range of possible activities and its sensory capabilities. Therefore, enhancing the bacterial sensory repertoire is a crucial step for expanded utility in potential biomedical, industrial or environmental applications. Using microarray and qRT-PCR analyses, we have investigated transcription in E. coli (strain CSH50) following FimH-mediated adhesion to biocompatible substrates. Specifically, wild-type FimH-mediated adhesion of E. coli to mannose agarose beads and His-tagged FimH-mediated adhesion to Ni2+-NTA beads both led to induction of ahpCF, dps, grxA and marRAB genes among bound cells relative to unbound cells. The strongly-induced genes are known to be regulated by OxyR or SoxS cytoplasmic redox sensors. Some differentially altered genes also overlapped with those implicated in biofilm formation. This study provides an insight into transcriptional events following FimH-mediated adhesion and may provide a platform for elucidation of the signaling circuit necessary for engineering a synthetic attachment response in E. coli.
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Affiliation(s)
- Prasanna Bhomkar
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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96
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Lee J, Kim IS, Yu HW. Flow Cytometric Detection of Bacillus spoOA Gene in Biofilm Using Quantum Dot Labeling. Anal Chem 2010; 82:2836-43. [DOI: 10.1021/ac902807n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jinwook Lee
- Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea
| | - In S. Kim
- Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea
| | - Hye-Weon Yu
- Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea
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97
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Müsken M, Di Fiore S, Dötsch A, Fischer R, Häussler S. Genetic determinants of Pseudomonas aeruginosa biofilm establishment. Microbiology (Reading) 2010; 156:431-441. [DOI: 10.1099/mic.0.033290-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The establishment of bacterial biofilms on surfaces is a complex process that requires various factors for each consecutive developmental step. Here we report the screening of the comprehensive Harvard Pseudomonas aeruginosa PA14 mutant library for mutants exhibiting an altered biofilm phenotype. We analysed the capability of all mutants to form biofilms at the bottom of a 96-well plate by the use of an automated confocal laser-scanning microscope and found 394 and 285 genetic determinants of reduced and enhanced biofilm production, respectively. Overall, 67 % of the identified mutants were affected within genes encoding hypothetical proteins, indicating that novel developmental pathways are likely to be dissected in the future. Nevertheless, a common theme that emerged from the analysis of the genes with a predicted function is that the establishment of a biofilm requires regulatory components that are involved in survival under microaerophilic growth conditions, arginine metabolism, alkyl-quinolone signalling, pH homeostasis and the DNA repair system.
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Affiliation(s)
- Mathias Müsken
- Chronic Pseudomonas Infection Research Group, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Stefano Di Fiore
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeck Str. 6, D-52704 Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, D-52704 Aachen, Germany
| | - Andreas Dötsch
- Chronic Pseudomonas Infection Research Group, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeck Str. 6, D-52704 Aachen, Germany
| | - Susanne Häussler
- Twincore, Center for Experimental and Clinical Infection Research, a joint venture of the Helmholtz Center for Infection Research and the Medical School Hannover, Feodor Lynen Strasse 7, D-30265 Hannover, Germany
- Chronic Pseudomonas Infection Research Group, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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98
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Hamilton S, Bongaerts RJM, Mulholland F, Cochrane B, Porter J, Lucchini S, Lappin-Scott HM, Hinton JCD. The transcriptional programme of Salmonella enterica serovar Typhimurium reveals a key role for tryptophan metabolism in biofilms. BMC Genomics 2009; 10:599. [PMID: 20003355 PMCID: PMC2805695 DOI: 10.1186/1471-2164-10-599] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 12/11/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Biofilm formation enhances the capacity of pathogenic Salmonella bacteria to survive stresses that are commonly encountered within food processing and during host infection. The persistence of Salmonella within the food chain has become a major health concern, as biofilms can serve as a reservoir for the contamination of food products. While the molecular mechanisms required for the survival of bacteria on surfaces are not fully understood, transcriptional studies of other bacteria have demonstrated that biofilm growth triggers the expression of specific sets of genes, compared with planktonic cells. Until now, most gene expression studies of Salmonella have focused on the effect of infection-relevant stressors on virulence or the comparison of mutant and wild-type bacteria. However little is known about the physiological responses taking place inside a Salmonella biofilm. RESULTS We have determined the transcriptomic and proteomic profiles of biofilms of Salmonella enterica serovar Typhimurium. We discovered that 124 detectable proteins were differentially expressed in the biofilm compared with planktonic cells, and that 10% of the S. Typhimurium genome (433 genes) showed a 2-fold or more change in the biofilm compared with planktonic cells. The genes that were significantly up-regulated implicated certain cellular processes in biofilm development including amino acid metabolism, cell motility, global regulation and tolerance to stress. We found that the most highly down-regulated genes in the biofilm were located on Salmonella Pathogenicity Island 2 (SPI2), and that a functional SPI2 secretion system regulator (ssrA) was required for S. Typhimurium biofilm formation. We identified STM0341 as a gene of unknown function that was needed for biofilm growth. Genes involved in tryptophan (trp) biosynthesis and transport were up-regulated in the biofilm. Deletion of trpE led to decreased bacterial attachment and this biofilm defect was restored by exogenous tryptophan or indole. CONCLUSIONS Biofilm growth of S. Typhimurium causes distinct changes in gene and protein expression. Our results show that aromatic amino acids make an important contribution to biofilm formation and reveal a link between SPI2 expression and surface-associated growth in S. Typhimurium.
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Affiliation(s)
- Shea Hamilton
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
- Department of Biological Sciences, University of Exeter, Exeter, EX4 4PS, UK
- Shea Hamilton, Faculty of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK; Brett Cochrane, Unilever SEAC, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Roy JM Bongaerts
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Francis Mulholland
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Brett Cochrane
- School of Biological Sciences, University of Southampton, Southampton, SO16 7PX, UK
- Shea Hamilton, Faculty of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK; Brett Cochrane, Unilever SEAC, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Jonathan Porter
- National Laboratory Service, Starcross Laboratory, Staplake Mount, Starcross, EX6 8PE, UK
| | - Sacha Lucchini
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | | | - Jay CD Hinton
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
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99
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Stankiewicz N, Gold A, Yüksel Y, Berensmeier S, Schwartz T. In vivo labeling and specific magnetic bead separation of RNA for biofilm characterization and stress-induced gene expression analysis in bacteria. J Microbiol Methods 2009; 79:344-52. [PMID: 19837116 DOI: 10.1016/j.mimet.2009.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/07/2009] [Accepted: 10/07/2009] [Indexed: 11/26/2022]
Abstract
The method of in vivo labeling and separation of bacterial RNA was developed as an approach to elucidating the stress response of natural bacterial populations. This technique is based on the incorporation of digoxigenin-11-uridine-5'-triphosphate (DIG-11-UTP) in the RNA of active bacteria. The digoxigenin fulfills a dual role as a label of de novo synthesized RNA and a target for magnetic bead separation from a total RNA extract. Depending on the growth conditions and the population's composition, the assembly rate of DIG-11-UTP ranged from 1.2% to 12.5% of the total RNA in gram-positive and gram-negative reference bacteria as well as in natural biofilms from drinking water, surface water, and lake sediment. Separation of DIG-RNA from total RNA extracts was performed with a biotinylated anti-digoxigenin antibody and streptavidin-functionalized magnetic particles. The average separation yield from total RNA extracts was about 95% of labeled RNA. The unspecific bindings of non-labeled nucleic acids were smaller than 0.2%, as was evaluated by spiking experiments with an unmarked DNA amplicon. Applicability of the method developed was demonstrated by rRNA-directed PCR-DGGE population analysis of natural biofilms and expression profiling of two stress-induced genes (vanA and rpoS) in reference bacteria.
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Affiliation(s)
- Nikolai Stankiewicz
- Karlsruhe Institute of Technology - KIT (former: Forschungszentrum Karlsruhe), Institute of Functional Interfaces (IFG), Microbiology of Natural and Technical Interfaces Department, P.O. Box 3640, D-76021 Karlsruhe, Germany
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100
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Lakins MA, Marrison JL, O'Toole PJ, van der Woude MW. Exploiting advances in imaging technology to study biofilms by applying multiphoton laser scanning microscopy as an imaging and manipulation tool. J Microsc 2009; 235:128-37. [PMID: 19659907 DOI: 10.1111/j.1365-2818.2009.03190.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Biofilms are an important element of the natural ecosystems but can be detrimental in health care and industrial settings. To improve our ability to combat biofilms, we need to understand the processes that facilitate their formation and dispersal. One approach that has proven to be invaluable is to image biofilms as they grow. Here we describe tools and protocols to visualize biofilms with multiphoton laser scanning microscopy, compare this with single photon laser scanning confocal microscopy and highlight best working procedures. Furthermore, we describe how with multiphoton laser scanning microscopy the laser can be used to manipulate the biofilm, specifically to achieve localized bleaching, killing or ablation within the biofilm biomass. These applications open novel ways to study the dynamics of biofilm formation, regeneration and dispersal.
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Affiliation(s)
- M A Lakins
- Centre of Immunology and Infection, Department of Biology, University of York and The Hull York Medical School, York YO10 5YW, UK
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