1
|
Chen T, Wang Y, Chi X, Xiong L, Lu P, Wang X, Chen Y, Luo Q, Shen P, Xiao Y. Genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 carbapenem-resistant Klebsiella pneumoniae. Virulence 2024; 15:2349768. [PMID: 38736039 PMCID: PMC11093053 DOI: 10.1080/21505594.2024.2349768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
ST11 is the most common lineage among carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in Asia. Diverse morphotypes resulting from genetic mutations are associated with significant differences in microbial characteristics among K. pneumoniae isolates. Here, we investigated the genetic determinants and critical characteristics associated with distinct morphotypes of ST11 CRKP. An ST11-KL47 CRKP isolate carrying a pLVPK-like virulence plasmid was isolated from a patient with a bloodstream infection; the isolate had the "mcsw" morphotype. Two distinct morphotypes ("ntrd" and "msdw") were derived from this strain during in vitro passage. Whole genome sequencing was used to identify mutations that cause the distinct morphotypes of ST11 CRKP. Transmission electron microscopy, antimicrobial susceptibility tests, growth assays, biofilm formation, virulence assays, membrane permeability assays, and RNA-seq analysis were used to investigate the specific characteristics associated with different morphotypes of ST11 CRKP. Compared with the parental mcsw morphotype, the ntrd morphotype resulted from mutation of genes involved in capsular polysaccharide biosynthesis (wza, wzc, and wbaP), a result validated by gene knockout experiments. This morphotype showed capsule deficiency and lower virulence potential, but higher biofilm production. By contrast, the msdw morphotype displayed competition deficiency and increased susceptibility to chlorhexidine and polymyxin B. Further analyses indicated that these characteristics were caused by interruption of the sigma factor gene rpoN by insertion mutations and deletion of the rpoN gene, which attenuated membrane integrity presumably by downregulating the phage shock protein operon. These data expand current understanding of genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 CRKP.
Collapse
Affiliation(s)
- Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Luying Xiong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| |
Collapse
|
2
|
Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024; 48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
Collapse
Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, 1 Shuizha West Road, Beijing 102300, P.R. China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, P.R. China
| | - Yu Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xinli Sun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Yi Ren
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| |
Collapse
|
3
|
Wang X, Liu M, Yu C, Li J, Zhou X. Biofilm formation: mechanistic insights and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:49. [PMID: 38097907 PMCID: PMC10721784 DOI: 10.1186/s43556-023-00164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
Biofilms are complex multicellular communities formed by bacteria, and their extracellular polymeric substances are observed as surface-attached or non-surface-attached aggregates. Many types of bacterial species found in living hosts or environments can form biofilms. These include pathogenic bacteria such as Pseudomonas, which can act as persistent infectious hosts and are responsible for a wide range of chronic diseases as well as the emergence of antibiotic resistance, thereby making them difficult to eliminate. Pseudomonas aeruginosa has emerged as a model organism for studying biofilm formation. In addition, other Pseudomonas utilize biofilm formation in plant colonization and environmental persistence. Biofilms are effective in aiding bacterial colonization, enhancing bacterial resistance to antimicrobial substances and host immune responses, and facilitating cell‒cell signalling exchanges between community bacteria. The lack of antibiotics targeting biofilms in the drug discovery process indicates the need to design new biofilm inhibitors as antimicrobial drugs using various strategies and targeting different stages of biofilm formation. Growing strategies that have been developed to combat biofilm formation include targeting bacterial enzymes, as well as those involved in the quorum sensing and adhesion pathways. In this review, with Pseudomonas as the primary subject of study, we review and discuss the mechanisms of bacterial biofilm formation and current therapeutic approaches, emphasizing the clinical issues associated with biofilm infections and focusing on current and emerging antibiotic biofilm strategies.
Collapse
Affiliation(s)
- Xinyu Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ming Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chuanjiang Yu
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
4
|
Jacquiod S, Olsen NMC, Blouin M, Røder HL, Burmølle M. Genotypic variations and interspecific interactions modify gene expression and biofilm formation of Xanthomonas retroflexus. Environ Microbiol 2023; 25:3225-3238. [PMID: 37740256 DOI: 10.1111/1462-2920.16503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 09/24/2023]
Abstract
Multispecies biofilms are important models for studying the evolution of microbial interactions. Co-cultivation of Xanthomonas retroflexus (XR) and Paenibacillus amylolyticus (PA) systemically leads to the appearance of an XR wrinkled mutant (XRW), increasing biofilm production. The nature of this new interaction and the role of each partner remain unclear. We tested the involvement of secreted molecular cues in this interaction by exposing XR and XRW to PA or its supernatant and analysing the response using RNA-seq, colony-forming unit (CFU) estimates, biofilm quantification, and microscopy. Compared to wild type, the mutations in XRW altered its gene expression and increased its CFU number. These changes matched the reported effects for one of the mutated genes: a response regulator part of a two-component system involved in environmental sensing. When XRW was co-cultured with PA or its supernatant, the mutations effects on XRW gene expression were masked, except for genes involved in sedentary lifestyle, being consistent with the higher biofilm production. It appears that the higher biofilm production was the result of the interaction between the genetic context (mutations) and the biotic environment (PA signals). Regulatory genes involved in environmental sensing need to be considered to shed further light on microbial interactions.
Collapse
Affiliation(s)
- Samuel Jacquiod
- Agroécologie, INRAE, Institut Agro Dijon, Université de Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Nanna Mee Coops Olsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Blouin
- Agroécologie, INRAE, Institut Agro Dijon, Université de Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Henriette Lyng Røder
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| |
Collapse
|
6
|
Brockhurst M, Cavet J, Diggle SP, Grainger D, Mangenelli R, Sychrova H, Martin-Verstraete I, Welch M, Palmer T, Thomas GH. Shaping microbiology for 75 years: highlights of research published in Microbiology. Part 2 - Communities and evolution. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37379228 DOI: 10.1099/mic.0.001357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Affiliation(s)
- Michael Brockhurst
- Division of Evolution, Infection and Genomics, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Jennifer Cavet
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Stephen P Diggle
- Center for Microbial Dynamics & Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David Grainger
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Hana Sychrova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, UK
| |
Collapse
|
7
|
Moshynets OV, Pokholenko I, Iungin O, Potters G, Spiers AJ. eDNA, Amyloid Fibers and Membrane Vesicles Identified in Pseudomonas fluorescens SBW25 Biofilms. Int J Mol Sci 2022; 23:ijms232315096. [PMID: 36499433 PMCID: PMC9738004 DOI: 10.3390/ijms232315096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas fluorescens SBW25 is a model soil- and plant-associated bacterium capable of forming a variety of air-liquid interface biofilms in experimental microcosms and on plant surfaces. Previous investigations have shown that cellulose is the primary structural matrix component in the robust and well-attached Wrinkly Spreader biofilm, as well as in the fragile Viscous Mass biofilm. Here, we demonstrate that both biofilms include extracellular DNA (eDNA) which can be visualized using confocal laser scanning microscopy (CLSM), quantified by absorbance measurements, and degraded by DNase I treatment. This eDNA plays an important role in cell attachment and biofilm development. However, exogenous high-molecular-weight DNA appears to decrease the strength and attachment levels of mature Wrinkly Spreader biofilms, whereas low-molecular-weight DNA appears to have little effect. Further investigation with CLSM using an amyloid-specific fluorophore suggests that the Wrinkly Spreader biofilm might also include Fap fibers, which might be involved in attachment and contribute to biofilm strength. The robust nature of the Wrinkly Spreader biofilm also allowed us, using MALDI-TOF mass spectrometry, to identify matrix-associated proteins unable to diffuse out of the structure, as well as membrane vesicles which had a different protein profile compared to the matrix-associated proteins. CLSM and DNase I treatment suggest that some vesicles were also associated with eDNA. These findings add to our understanding of the matrix components in this model pseudomonad, and, as found in other biofilms, biofilm-specific products and material from lysed cells contribute to these structures through a range of complex interactions.
Collapse
Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Ianina Pokholenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Kyiv National University of Technologies and Design, 01011 Kyiv, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, 2030 Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, 2000 Antwerp, Belgium
- Correspondence:
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| |
Collapse
|
8
|
Illuminating the signalomics of microbial biofilm on plant surfaces. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
9
|
Sharma S, Meena M, Marwal A, Swapnil P. Biofilm matrix proteins. APPLICATION OF BIOFILMS IN APPLIED MICROBIOLOGY 2022:51-64. [DOI: 10.1016/b978-0-323-90513-8.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
|
10
|
Eco-evolutionary interaction between microbiome presence and rapid biofilm evolution determines plant host fitness. Nat Ecol Evol 2021; 5:670-676. [PMID: 33707690 DOI: 10.1038/s41559-021-01406-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
Microbiomes are important to the survival and reproduction of their hosts. Although ecological and evolutionary processes can happen simultaneously in microbiomes, little is known about how microbiome eco-evolutionary dynamics determine host fitness. Here we show, using experimental evolution, that fitness of the aquatic plant Lemna minor is modified by interactions between the microbiome and the evolution of one member, Pseudomonas fluorescens. Microbiome presence promotes P. fluorescens' rapid evolution to form biofilm, which reciprocally alters the microbiome's species composition. These eco-evolutionary dynamics modify the host's multigenerational fitness. The microbiome and non-evolving P. fluorescens together promote host fitness, whereas the microbiome with P. fluorescens that evolves biofilm reduces the beneficial impact on host fitness. Additional experiments suggest that the microbial effect on host fitness may occur through changes in microbiome production of auxin, a plant growth hormone. Our study, therefore, experimentally demonstrates the importance of the eco-evolutionary dynamics in microbiomes for host-microbiome interactions.
Collapse
|
11
|
Fanelli F, Caputo L, Quintieri L. Phenotypic and genomic characterization of Pseudomonas putida ITEM 17297 spoiler of fresh vegetables: Focus on biofilm and antibiotic resistance interaction. Curr Res Food Sci 2021; 4:74-82. [PMID: 33718885 PMCID: PMC7932912 DOI: 10.1016/j.crfs.2021.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
Pseudomonas putida is widely recognized as a spoiler of fresh foods under cold storage, and recently associated also with infections in clinical settings. The presence of antibiotic resistance genes (ARGs) could be acquired and transmitted by horizontal genetic transfer and further increase the risk associated with its persistence in food and the need to be deeper investigated. Thus, in this work we presented a genomic and phenotypic analysis of the psychrotrophic P. putida ITEM 17297 to provide new insight into AR mechanisms by this species until now widely studied only for its spoilage traits. ITEM 17297 displayed resistance to several classes of antibiotics and it also formed huge amounts of biofilm; this latter registered increases at 15 °C in comparison to the optimum growth condition (30 °C). After ITEM 17297 biofilms exposure to antibiotic concentrations higher than 10-fold their MIC values no eradication occurred; interestingly, biomasses of biofilm cultivated at 15 °C increased their amount in a dose-dependent manner. Genomic analyses revealed determinants (RND-systems, ABC-transporters, and MFS-efflux pumps) for multi-drugs resistance (β-lactams, macrolides, nalidixic acid, tetracycline, fusidic acid and bacitracin) and a novel ampC allele. Biofilm and motility related pathways were depicted underlying their contribution to AR. Based on these results, underestimated psychrotrophic pseudomonas, such as the herein studied ITEM 17297 strain, might assume relevance in relation to the risk associated with the transfer of antimicrobial resistance genes to humans through cold stored contaminated foods. P. putida biofilm and AR related molecular targets herein identified will provide a basis to clarify the interaction between AR and biofilm formation and to develop novel strategies to counteract the persistence of multidrug resistant P. putida in the food chain. Multidrug resistant Pseudomonas putida ITEM 17297 was isolated from fresh vegetables. Determinants for AR and biofilm formation were identified by genomic analysis. Biofilm increased more than 10-fold antibiotic MIC value of planktonic cells. Cold adapted biofilm increased its biomass under CHL, NA, and ERY pressure. New insight into the risk for P. putida spread in the food chain were provided.
Collapse
Affiliation(s)
- Francesca Fanelli
- Institute of Sciences of Food Production, National Research Council of Italy, V. G. Amendola 122/O, 70126, Bari, Italy
| | - Leonardo Caputo
- Institute of Sciences of Food Production, National Research Council of Italy, V. G. Amendola 122/O, 70126, Bari, Italy
| | - Laura Quintieri
- Institute of Sciences of Food Production, National Research Council of Italy, V. G. Amendola 122/O, 70126, Bari, Italy
| |
Collapse
|
12
|
|
13
|
Heredia-Ponce Z, Gutiérrez-Barranquero JA, Purtschert-Montenegro G, Eberl L, de Vicente A, Cazorla FM. Role of extracellular matrix components in the formation of biofilms and their contribution to the biocontrol activity of Pseudomonas chlororaphis PCL1606. Environ Microbiol 2020; 23:2086-2101. [PMID: 33314481 DOI: 10.1111/1462-2920.15355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022]
Abstract
Pseudomonas chlororaphis PCL1606 (PcPCL1606) displays plant-colonizing features and exhibits antagonistic traits against soil-borne phytopathogenic fungi. Biofilm formation could be relevant for the PcPCL1606 lifestyle, and in this study the role of some putative extracellular matrix components (EMC; Fap-like fibre, alginate and Psl-like polysaccharides) in the biofilm architecture and biocontrol activity of this bacterium were determined. EMC such as the Fap-like fibre and alginate polysaccharide play secondary roles in biofilm formation in PcPCL1606, because they are not fundamental to its biofilm architecture in flow cell chamber, but synergistically they have shown to favour bacterial competition during biofilm formation. Conversely, studies on Psl-like polysaccharide have revealed that it may contain mannose, and that it is strongly involved in the PcPCL1606 biofilm architecture and niche competition. Furthermore, the Fap-like fibre and Psl-like exopolysaccharide play roles in early surface attachment and contribute to biocontrol activity against the white root rot disease caused by Rosellinia necatrix in avocado plants. These results constitute the first report regarding the study of the extracellular matrix of the PcPCL1606 strain and highlight the importance of a putative Fap-like fibre and Psl-like exopolysaccharide produced by PcPCL1606 in the biofilm formation process and interactions with the host plant root.
Collapse
Affiliation(s)
- Zaira Heredia-Ponce
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - José Antonio Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | | | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| |
Collapse
|
14
|
Quorum quenching by 2-Hydroxyanisole extracted from Solanum torvum on Pseudomonas aeruginosa and its inhibitory action upon LasR protein. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
15
|
Koza A, Jerdan R, Cameron S, Spiers AJ. Three biofilm types produced by a model pseudomonad are differentiated by structural characteristics and fitness advantage. MICROBIOLOGY-SGM 2020; 166:707-716. [PMID: 32520698 DOI: 10.1099/mic.0.000938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Model bacterial biofilm systems suggest that bacteria produce one type of biofilm, which is then modified by environmental and physiological factors, although the diversification of developing populations might result in the appearance of adaptive mutants producing altered structures with improved fitness advantage. Here we compare the air-liquid (A-L) interface viscous mass (VM) biofilm produced by Pseudomonas fluorescens SBW25 and the wrinkly spreader (WS) and complementary biofilm-forming strain (CBFS) biofilm types produced by adaptive SBW25 mutants in order to better understand the link between these physical structures and the fitness advantage they provide in experimental microcosms. WS, CBFS and VM biofilms can be differentiated by strength, attachment levels and rheology, as well as by strain characteristics associated with biofilm formation. Competitive fitness assays demonstrate that they provide similar advantages under static growth conditions but respond differently to increasing levels of physical disturbance. Pairwise competitions between biofilms suggest that these strains must be competing for at least two growth-limiting resources at the A-L interface, most probably O2 and nutrients, although VM and CBFS cells located lower down in the liquid column might provide an additional fitness advantage through the colonization of a less competitive zone below the biofilm. Our comparison of different SBW25 biofilm types illustrates more generally how varied biofilm characteristics and fitness advantage could become among adaptive mutants arising from an ancestral biofilm-forming strain and raises the question of how significant these changes might be in a range of medical, biotechnological and industrial contexts where diversification and change may be problematic.
Collapse
Affiliation(s)
- Anna Koza
- School of Applied Sciences, Abertay University, Bell Street, Dundee DD1 1HG, UK
| | - Robyn Jerdan
- School of Applied Sciences, Abertay University, Bell Street, Dundee DD1 1HG, UK
| | - Scott Cameron
- School of Applied Sciences, Abertay University, Bell Street, Dundee DD1 1HG, UK
| | - Andrew J Spiers
- School of Applied Sciences, Abertay University, Bell Street, Dundee DD1 1HG, UK
| |
Collapse
|
16
|
Jana S, Charlton SGV, Eland LE, Burgess JG, Wipat A, Curtis TP, Chen J. Nonlinear rheological characteristics of single species bacterial biofilms. NPJ Biofilms Microbiomes 2020; 6:19. [PMID: 32286319 PMCID: PMC7156450 DOI: 10.1038/s41522-020-0126-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions and exhibit resistance to physical as well as chemical perturbations. In dynamic environments, where periodic or aperiodic flows over surfaces are involved, biofilms can be subjected to large shear forces. The ability to withstand these forces, which is often attributed to the resilience of the extracellular matrix. This attribute of the extracellular matrix is referred to as viscoelasticity and is a result of self-assembly and cross-linking of multiple polymeric components that are secreted by the microbes. We aim to understand the viscoelastic characteristic of biofilms subjected to large shear forces by performing Large Amplitude Oscillatory Shear (LAOS) experiments on four species of bacterial biofilms: Bacillus subtilis, Comamonas denitrificans, Pseudomonas fluorescens and Pseudomonas aeruginosa. We find that nonlinear viscoelastic measures such as intracycle strain stiffening and intracycle shear thickening for each of the tested species, exhibit subtle or distinct differences in the plot of strain amplitude versus frequency (Pipkin diagram). The biofilms also exhibit variability in the onset of nonlinear behaviour and energy dissipation characteristics, which could be a result of heterogeneity of the extracellular matrix constituents of the different biofilms. The results provide insight into the nonlinear rheological behaviour of biofilms as they are subjected to large strains or strain rates; a situation that is commonly encountered in nature, but rarely investigated.
Collapse
Affiliation(s)
- Saikat Jana
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK.
| | | | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK.
| |
Collapse
|
17
|
Jerdan R, Kuśmierska A, Petric M, Spiers AJ. Penetrating the air-liquid interface is the key to colonization and wrinkly spreader fitness. MICROBIOLOGY-SGM 2020; 165:1061-1074. [PMID: 31436522 DOI: 10.1099/mic.0.000844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In radiating populations of Pseudomonas fluorescens SBW25, adaptive wrinkly spreader (WS) mutants are able to gain access to the air-liquid (A-L) interface of static liquid microcosms and achieve a significant competitive fitness advantage over other non-biofilm-forming competitors. Aerotaxis and flagella-based swimming allows SBW25 cells to move into the high-O2 region located at the top of the liquid column and maintain their position by countering the effects of random cell diffusion, convection and disturbance (i.e. physical displacement). However, wild-type cells showed significantly lower levels of enrichment in this region compared to the archetypal WS, indicating that WS cells employ an additional mechanism to transfer to the A-L interface where displacement is no longer an issue and a biofilm can develop at the top of the liquid column. Preliminary experiments suggest that this might be achieved through the expression of an as yet unidentified surface active agent that is weakly associated with WS cells and alters liquid surface tension, as determined by quantitative tensiometry. The effect of physical displacement on the colonization of the high-O2 region and A-L interface was reduced through the addition of agar or polyethylene glycol to increase liquid viscosity, and under these conditions the competitive fitness of the WS was significantly reduced. These observations suggest that the ability to transfer to the A-L interface from the high-O2 region and remain there without further expenditure of energy (through, for example, the deployment of flagella) is a key evolutionary innovation of the WS, as it allows subsequent biofilm development and significant population increase, thereby affording these adaptive mutants a competitive fitness advantage over non-biofilm-forming competitors located within the liquid column.
Collapse
Affiliation(s)
- Robyn Jerdan
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kuśmierska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.,School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Marija Petric
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Andrew J Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| |
Collapse
|
18
|
Noirot-Gros MF, Forrester S, Malato G, Larsen PE, Noirot P. CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens. Sci Rep 2019; 9:15954. [PMID: 31685917 PMCID: PMC6828691 DOI: 10.1038/s41598-019-52400-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial biofilm formation involves signaling and regulatory pathways that control the transition from motile to sessile lifestyle, production of extracellular polymeric matrix, and maturation of the biofilm 3D structure. Biofilms are extensively studied because of their importance in biomedical, ecological and industrial settings. Gene inactivation is a powerful approach for functional studies but it is often labor intensive, limiting systematic gene surveys to the most tractable bacterial hosts. Here, we adapted the CRISPR interference (CRISPRi) system for use in diverse strain isolates of P. fluorescens, SBW25, WH6 and Pf0-1. We found that CRISPRi is applicable to study complex phenotypes such as cell morphology, motility and biofilm formation over extended periods of time. In SBW25, CRISPRi-mediated silencing of genes encoding the GacA/S two-component system and regulatory proteins associated with the cylic di-GMP signaling messenger produced swarming and biofilm phenotypes similar to those obtained after gene inactivation. Combined with detailed confocal microscopy of biofilms, our study also revealed novel phenotypes associated with extracellular matrix biosynthesis as well as the potent inhibition of SBW25 biofilm formation mediated by the PFLU1114 operon. We conclude that CRISPRi is a reliable and scalable approach to investigate gene networks in the diverse P. fluorescens group.
Collapse
Affiliation(s)
| | - Sara Forrester
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| | - Grace Malato
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States.,Department of Bioengineering, University of Illinois Chicago, Chicago, IL60607, United States
| | - Philippe Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| |
Collapse
|
19
|
Zee PC, Fukami T. Priority effects are weakened by a short, but not long, history of sympatric evolution. Proc Biol Sci 2019; 285:rspb.2017.1722. [PMID: 29386363 DOI: 10.1098/rspb.2017.1722] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/08/2018] [Indexed: 11/12/2022] Open
Abstract
Priority effects, or the effects of species arrival history on local species abundances, have been documented in a range of taxa. However, factors determining the extent to which priority effects affect community assembly remain unclear. Using laboratory populations of the bacterium Pseudomonas fluorescens, we examined whether shared evolutionary history affected the strength of priority effects. We hypothesized that sympatric evolution of populations belonging to the same guild would lead to niche differentiation, resulting in phenotypic complementarity that weakens priority effects. Consistent with this hypothesis, we found that priority effects tended to be weaker in sympatrically evolved pairs of immigrating populations than in allopatrically evolved pairs. Furthermore, priority effects were weaker under higher phenotypic complementarity. However, these patterns were observed only in populations with a relatively short history of sympatric evolution, and disappeared when populations had evolved together for a long time. Together, our results suggest that the evolutionary history of organismal traits may dictate the strength of priority effects and, consequently, the extent of historical contingency in the assembly of ecological communities.
Collapse
Affiliation(s)
- Peter C Zee
- Department of Biology, Stanford University, Stanford, CA 94305, USA .,Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Tadashi Fukami
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
20
|
Cooper VS, Warren TM, Matela AM, Handwork M, Scarponi S. EvolvingSTEM: a microbial evolution-in-action curriculum that enhances learning of evolutionary biology and biotechnology. Evolution 2019; 12:12. [PMID: 32647555 PMCID: PMC7328067 DOI: 10.1186/s12052-019-0103-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/29/2019] [Indexed: 12/02/2022]
Abstract
Evolution is a central, unifying theory for all of life science, yet the subject is poorly represented in most secondary-school biology courses, especially in the United States. One challenge to learning evolution is that it is taught as a conceptual, retrospective subject with few tangible outcomes for students. These typical passive learning strategies lead to student disengagement with the material and misunderstanding of evolutionary concepts. To promote greater investment and comprehension, we developed EvolvingSTEM, an inquiry-based laboratory curriculum that demonstrates concepts of natural selection, heredity, and ecological diversity through experimental evolution of a benign bacterium. Students transfer populations of Pseudomonas fluorescens growing on plastic beads, which selects for biofilm formation and mutants with new, conspicuous phenotypes. We introduced our curriculum to four introductory high school biology classes alongside their standard curriculum materials and found that students who learned evolution through EvolvingSTEM scored significantly better on a common assessment targeted to Next Generation Science Standards than students taught only the standard curriculum. This latter group subsequently achieved similar scores once they too completed our curriculum. Our work demonstrates that inquiry-based, hands-on experiences with evolving bacterial populations can greatly enhance student learning of evolutionary concepts.
Collapse
Affiliation(s)
- Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA.,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH USA
| | - Taylor M Warren
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH USA
| | - Abigail M Matela
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA
| | | | | |
Collapse
|
21
|
Zhang QG, Lu HS, Buckling A. Temperature drives diversification in a model adaptive radiation. Proc Biol Sci 2018; 285:rspb.2018.1515. [PMID: 30185639 DOI: 10.1098/rspb.2018.1515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/15/2018] [Indexed: 01/10/2023] Open
Abstract
The warmer regions harbour more species, attributable to accelerated speciation and increased ecological opportunities for coexistence. While correlations between temperature and energy availability and habitat area have been suggested as major drivers of these biodiversity patterns, temperature can theoretically also have direct effects on the evolution of diversity. Here, we experimentally studied the evolution of diversity in a model adaptive radiation of the bacterium Pseudomonas fluorescens across a temperature gradient. Diversification increased at higher temperatures, driven by both faster generation of genetic variation and stronger diversifying selection. Specifically, low temperatures could limit the generation of diversity, suggested by the observation that supply of genetic variation through immigration increased diversity at low, but not high temperatures. The two major determinants of mutation supply, population size and mutation rate, both showed a positive temperature dependence. Stronger diversifying selection in warmer environments was suggested by promoted coexistence, and further explicitly inferred by the ability of evolved phenotypes to invade the ancestral type from rare. We discuss possible physiological and environmental mechanisms underlying the findings, most of which are likely to be general.
Collapse
Affiliation(s)
- Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Han-Shu Lu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
| |
Collapse
|
22
|
Noirot-Gros MF, Shinde S, Larsen PE, Zerbs S, Korajczyk PJ, Kemner KM, Noirot PH. Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation. Front Microbiol 2018; 9:853. [PMID: 29774013 PMCID: PMC5943511 DOI: 10.3389/fmicb.2018.00853] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/13/2018] [Indexed: 12/20/2022] Open
Abstract
Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots.
Collapse
Affiliation(s)
| | - Shalaka Shinde
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter J Korajczyk
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Philippe H Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| |
Collapse
|
23
|
García García T, Ventroux M, Derouiche A, Bidnenko V, Correia Santos S, Henry C, Mijakovic I, Noirot-Gros MF, Poncet S. Phosphorylation of the Bacillus subtilis Replication Controller YabA Plays a Role in Regulation of Sporulation and Biofilm Formation. Front Microbiol 2018; 9:486. [PMID: 29619013 PMCID: PMC5871692 DOI: 10.3389/fmicb.2018.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/01/2018] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis cells can adopt different life-styles in response to various environmental cues, including planktonic cells during vegetative growth, sessile cells during biofilm formation and sporulation. While switching life-styles, bacteria must coordinate the progression of their cell cycle with their physiological status. Our current understanding of the regulatory pathways controlling the decision-making processes and triggering developmental switches highlights a key role of protein phosphorylation. The regulatory mechanisms that integrate the bacterial chromosome replication status with sporulation involve checkpoint proteins that target the replication initiator DnaA or the kinase phosphorelay controlling the master regulator Spo0A. B. subtilis YabA is known to interact with DnaA to prevent over-initiation of replication during vegetative growth. Here, we report that YabA is phosphorylated by YabT, a Ser/Thr kinase expressed during sporulation and biofilm formation. The phosphorylation of YabA has no effect on replication initiation control but hyper-phosphorylation of YabA leads to an increase in sporulation efficiency and a strong inhibition of biofilm formation. We also provide evidence that YabA phosphorylation affects the level of Spo0A-P in cells. These results indicate that YabA is a multifunctional protein with a dual role in regulating replication initiation and life-style switching, thereby providing a potential mechanism for cross-talk and coordination of cellular processes during adaptation to environmental change.
Collapse
Affiliation(s)
| | - Magali Ventroux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sara Correia Santos
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | | | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
24
|
Benforte FC, Colonnella MA, Ricardi MM, Solar Venero EC, Lizarraga L, López NI, Tribelli PM. Novel role of the LPS core glycosyltransferase WapH for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis. PLoS One 2018; 13:e0192559. [PMID: 29415056 PMCID: PMC5802925 DOI: 10.1371/journal.pone.0192559] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/25/2018] [Indexed: 11/19/2022] Open
Abstract
Psychrotroph microorganisms have developed cellular mechanisms to cope with cold stress. Cell envelopes are key components for bacterial survival. Outer membrane is a constituent of Gram negative bacterial envelopes, consisting of several components, such as lipopolysaccharides (LPS). In this work we investigated the relevance of envelope characteristics for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis by analyzing a mini Tn5 wapH mutant strain, encoding a core LPS glycosyltransferase. Our results showed that wapH strain is impaired to grow under low temperature but not for cold survival. The mutation in wapH, provoked a strong aggregative phenotype and modifications of envelope nanomechanical properties such as lower flexibility and higher turgor pressure, cell permeability and surface area to volume ratio (S/V). Changes in these characteristics were also observed in the wild type strain grown at different temperatures, showing higher cell flexibility but lower turgor pressure under cold conditions. Cold shock experiments indicated that an acclimation period in the wild type is necessary for cell flexibility and S/V ratio adjustments. Alteration in cell-cell interaction capabilities was observed in wapH strain. Mixed cells of wild type and wapH strains, as well as those of the wild type strain grown at different temperatures, showed a mosaic pattern of aggregation. These results indicate that wapH mutation provoked marked envelope alterations showing that LPS core conservation appears as a novel essential feature for active growth under cold conditions.
Collapse
Affiliation(s)
- Florencia C. Benforte
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria A. Colonnella
- Centro de Investigaciones en Bionanociencias, CONICET, Buenos Aires, Argentina
| | - Martiniano M. Ricardi
- Instituto de Fisiología, Biología Molecular y Neurociencias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Leonardo Lizarraga
- Centro de Investigaciones en Bionanociencias, CONICET, Buenos Aires, Argentina
| | - Nancy I. López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
- * E-mail: (NIL); (PMT)
| | - Paula M. Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
- * E-mail: (NIL); (PMT)
| |
Collapse
|
25
|
Koza A, Kusmierska A, McLaughlin K, Moshynets O, Spiers AJ. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation. FEMS Microbiol Lett 2018; 364:3850210. [PMID: 28535292 DOI: 10.1093/femsle/fnx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
Collapse
Affiliation(s)
- Anna Koza
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kusmierska
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Kimberley McLaughlin
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kiev 03143, Ukraine
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| |
Collapse
|
26
|
Abstract
Because of ubiquity of thioesters, thioesterases play a critical role in metabolism, membrane biosynthesis, signal transduction, and gene regulation. In many bacteria, YbgC is such an enzyme, whose coding gene mostly resides in the tol-pal cluster. Although all other proteins encoded in the tol-pal cluster are clearly involved in maintaining cell envelope integrity and cell division, little is known about the physiological role of YbgC. In this study, we identify in Shewanella oneidensis, a γ-proteobacterium used as a research model for environmental microbes, YbgC as a motility regulator. The loss of YbgC results in enhanced motility, which is likely due to the increased rotation rate of the flagellum. The regulatory function of YbgC requires its thioesterase activity but could not be replaced by YbgC homologues of other bacteria. We further show that the regulation of YbgC is mediated by the second message c-di-GMP.
Collapse
|
27
|
Velmourougane K, Prasanna R, Saxena AK. Agriculturally important microbial biofilms: Present status and future prospects. J Basic Microbiol 2017; 57:548-573. [PMID: 28407275 DOI: 10.1002/jobm.201700046] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.
Collapse
Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nath Bhanjan, Uttar Pradesh, India
| |
Collapse
|
28
|
Biofilm formation and cellulose expression by Bordetella avium 197N, the causative agent of bordetellosis in birds and an opportunistic respiratory pathogen in humans. Res Microbiol 2017; 168:419-430. [PMID: 28131895 DOI: 10.1016/j.resmic.2017.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 02/08/2023]
Abstract
Although bacterial cellulose synthase (bcs) operons are widespread within the Proteobacteria phylum, subunits required for the partial-acetylation of the polymer appear to be restricted to a few γ-group soil, plant-associated and phytopathogenic pseudomonads, including Pseudomonas fluorescens SBW25 and several Pseudomonas syringae pathovars. However, a bcs operon with acetylation subunits has also been annotated in the unrelated β-group respiratory pathogen, Bordetella avium 197N. Our comparison of subunit protein sequences and GC content analyses confirms the close similarity between the B. avium 197N and pseudomonad operons and suggests that, in both cases, the cellulose synthase and acetylation subunits were acquired as a single unit. Using static liquid microcosms, we can confirm that B. avium 197N expresses low levels of cellulose in air-liquid interface biofilms and that biofilm strength and attachment levels could be increased by elevating c-di-GMP levels like the pseudomonads, but cellulose was not required for biofilm formation itself. The finding that B. avium 197N is capable of producing cellulose from a highly-conserved, but relatively uncommon bcs operon raises the question of what functional role this modified polymer plays during the infection of the upper respiratory tract or survival between hosts, and what environmental signals control its production.
Collapse
|
29
|
Tallawi M, Opitz M, Lieleg O. Modulation of the mechanical properties of bacterial biofilms in response to environmental challenges. Biomater Sci 2017; 5:887-900. [DOI: 10.1039/c6bm00832a] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this review, we highlight recent research on the relationship between biofilm matrix composition, biofilm mechanics and environmental stimuli.
Collapse
Affiliation(s)
- Marwa Tallawi
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technische Universität München
- Garching
- Germany
| | - Madeleine Opitz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technische Universität München
- Garching
- Germany
| |
Collapse
|
30
|
New Insights into the Effects of Several Environmental Parameters on the Relative Fitness of a Numerically Dominant Class of Evolved Niche Specialist. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2016; 2016:4846565. [PMID: 28101396 PMCID: PMC5214101 DOI: 10.1155/2016/4846565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/24/2016] [Indexed: 11/17/2022]
Abstract
Adaptive radiation in bacteria has been investigated using Wrinkly Spreaders (WS), a morphotype which colonises the air-liquid (A-L) interface of static microcosms by biofilm formation with a significant fitness advantage over competitors growing lower down in the O2-limited liquid column. Here, we investigate several environmental parameters which impact the ecological opportunity that the Wrinkly Spreaders exploit in this model system. Manipulation of surface area/volume ratios suggests that the size of the WS niche was not as important as the ability to dominate the A-L interface and restrict competitor growth. The value of this niche to the Wrinkly Spreaders, as determined by competitive fitness assays, was found to increase as O2 flux to the A-L interface was reduced, confirming that competition for O2 was the main driver of WS fitness. The effect of O2 on fitness was also found to be dependent on the availability of nutrients, reflecting the need to take up both for optimal growth. Finally, the meniscus trap, a high-O2 region formed by the interaction of the A-L interface with the vial walls, was also important for fitness during the early stages of biofilm formation. These findings reveal the complexity of this seemingly simple model system and illustrate how changes in environmental physicality alter ecological opportunity and the fitness of the adaptive morphotype.
Collapse
|
31
|
Day M. Yeast petites and small colony variants: for everything there is a season. ADVANCES IN APPLIED MICROBIOLOGY 2016; 85:1-41. [PMID: 23942147 DOI: 10.1016/b978-0-12-407672-3.00001-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The yeast petite mutant was first found in the yeast Saccharomyces cerevisiae. The colony is small because of a block in the aerobic respiratory chain pathway, which generates ATP. The petite yeasts are thus unable to grow on nonfermentable carbon sources (such as glycerol or ethanol), and form small anaerobic-sized colonies when grown in the presence of fermentable carbon sources (such as glucose). The petite phenotype results from mutations in the mitochondrial genome, loss of mitochondria, or mutations in the host cell genome. The latter mutations affect nuclear-encoded genes involved in oxidative phosphorylation and these mutants are termed neutral petites. They all produce wild-type progeny when crossed with a wild-type strain. The staphylococcal small colony variant (SCV) is a slow-growing mutant that typically exhibits the loss of many phenotypic characteristics and pathogenic traits. SCVs are mostly small, nonpigmented, and nonhaemolytic. Their small size is often due to an inability to synthesize electron transport chain components and so cannot generate ATP by oxidative phosphorylation. Evidence suggests that they are responsible for persistent and/or recurrent infections. This chapter compares the physiological and genetic basis of the petite mutants and SCVs. The review focuses principally on two representatives, the eukaryote S. cerevisiae and the prokaryote Staphylococcus aureus. There is, clearly, commonality in the physiological response. Interestingly, the similarity, based on their physiological states, has not been commented on previously. The finding of an overlapping physiological response that occurs across a taxonomic divide is novel.
Collapse
Affiliation(s)
- Martin Day
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.
| |
Collapse
|
32
|
Thakur P, Chawla R, Tanwar A, Chakotiya AS, Narula A, Goel R, Arora R, Sharma RK. Attenuation of adhesion, quorum sensing and biofilm mediated virulence of carbapenem resistant Escherichia coli by selected natural plant products. Microb Pathog 2016; 92:76-85. [PMID: 26792674 DOI: 10.1016/j.micpath.2016.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 12/31/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Abstract
The multi-drug resistance offered by Carbapenem Resistant Escherichia coli (Family: Enterobacteriaceae; Class: Gammaproteobacteria) against third line antibiotics can be attributed towards its ability to develop biofilm. Such process involves adhesion and quorum-sensing induced colonization leading to biomass development. The present study explored the anti-adhesion, anti-quorum sensing and anti-biofilm potential of 05 pre-standardized potent herbals. Berberis aristata (PTRC-2111-A) exhibited maximum potential in all these activities i.e. 91.3% ± 0.05% (Anti-adhesion), 96.06% ± 0.05% (Anti-Quorum sensing) and 51.3% ± 0.07% (Anti-Biofilm formation) respectively. Camellia sinensis (PTRC-31911-A) showed both anti-adhesion (84.1% ± 0.03%) and anti-quorum sensing (90.0%) potential while Holarrhena antidysenterica (PTRC-8111-A) showed only anti-quorum sensing potential as compared to standards/antibiotics. These findings were in line with the molecular docking analysis of phytoligands against Lux S and Pilin receptors. Furthermore, the pairwise correlation analysis of the tested activities with qualitative, quantitative and bioactivity functional descriptors revealed that an increased content of alkaloid, moderate content of flavonoids and decreased content of tannins supported all the three activities. In addition, nitric oxide and superoxide scavenging activity were found to be correlated with anti-quorum sensing activity. The findings indicated clearly that B. aristata (Family: Berberidaceae) and C. sinensis (Family: Theaceae) were potent herbal leads with significant therapeutic potential which further needs to be explored at pre-clinical level in the future.
Collapse
Affiliation(s)
- Pallavi Thakur
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
| | - Raman Chawla
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, Delhi, India.
| | - Ankit Tanwar
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
| | - Ankita Singh Chakotiya
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
| | - Alka Narula
- Department of Biotechnology, Jamia Hamdard, Delhi, India
| | - Rajeev Goel
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
| | - Rajesh Arora
- Office of DG (LS), Defence Research and Development Organisation, DRDO Bhawan, Delhi, India
| | - Rakesh Kumar Sharma
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
| |
Collapse
|
33
|
Surface Polysaccharide Mutants Reveal that Absence of O Antigen Reduces Biofilm Formation of Actinobacillus pleuropneumoniae. Infect Immun 2015; 84:127-37. [PMID: 26483403 DOI: 10.1128/iai.00912-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/12/2015] [Indexed: 12/24/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a Gram-negative bacterium belonging to the Pasteurellaceae family and the causative agent of porcine pleuropneumonia, a highly contagious lung disease causing important economic losses. Surface polysaccharides, including lipopolysaccharides (LPS) and capsular polysaccharides (CPS), are implicated in the adhesion and virulence of A. pleuropneumoniae, but their role in biofilm formation is still unclear. In this study, we investigated the requirement for these surface polysaccharides in biofilm formation by A. pleuropneumoniae serotype 1. Well-characterized mutants were used: an O-antigen LPS mutant, a truncated core LPS mutant with an intact O antigen, a capsule mutant, and a poly-N-acetylglucosamine (PGA) mutant. We compared the amount of biofilm produced by the parental strain and the isogenic mutants using static and dynamic systems. Compared to the findings for the biofilm of the parental or other strains, the biofilm of the O antigen and the PGA mutants was dramatically reduced, and it had less cell-associated PGA. Real-time PCR analyses revealed a significant reduction in the level of pgaA, cpxR, and cpxA mRNA in the biofilm cells of the O-antigen mutant compared to that in the biofilm cells of the parental strain. Specific binding between PGA and LPS was consistently detected by surface plasmon resonance, but the lack of O antigen did not abolish these interactions. In conclusion, the absence of the O antigen reduces the ability of A. pleuropneumoniae to form a biofilm, and this is associated with the reduced expression and production of PGA.
Collapse
|
34
|
Liang ZX. The expanding roles of c-di-GMP in the biosynthesis of exopolysaccharides and secondary metabolites. Nat Prod Rep 2015; 32:663-83. [PMID: 25666534 DOI: 10.1039/c4np00086b] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cyclic dinucleotide c-di-GMP has emerged in the last decade as a prevalent intracellular messenger that orchestrates the transition between the motile and sessile lifestyles of many bacterial species. The motile-to-sessile transition is often associated with the formation of extracellular matrix-encased biofilm, an organized community of bacterial cells that often contributes to antibiotic resistance and host-pathogen interaction. It is increasingly clear that c-di-GMP controls motility, biofilm formation and bacterial pathogenicity partially through regulating the production of exopolysaccharides (EPS) and small-molecule secondary metabolites. This review summarizes our current understanding of the regulation of EPS biosynthesis by c-di-GMP in a diversity of bacterial species and highlights the emerging role of c-di-GMP in the biosynthesis of small-molecule secondary metabolites.
Collapse
Affiliation(s)
- Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551.
| |
Collapse
|
35
|
Hall JPJ, Harrison E, Lilley AK, Paterson S, Spiers AJ, Brockhurst MA. Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects. Environ Microbiol 2015; 17:5008-22. [PMID: 25969927 PMCID: PMC4989453 DOI: 10.1111/1462-2920.12901] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/20/2015] [Accepted: 05/05/2015] [Indexed: 01/26/2023]
Abstract
Plasmids are important mobile elements that can facilitate genetic exchange and local adaptation within microbial communities. We compared the sequences of four co‐occurring pQBR family environmental mercury resistance plasmids and measured their effects on competitive fitness of a Pseudomonas fluorescens
SBW25 host, which was isolated at the same field site. Fitness effects of carriage differed between plasmids and were strongly context dependent, varying with medium, plasmid status of competitor and levels of environmental mercury. The plasmids also varied widely in their rates of conjugation and segregational loss. We found that few of the plasmid‐borne accessory genes could be ascribed functions, although we identified a putative chemotaxis operon, a type IV pilus‐encoding cluster and a region encoding putative arylsulfatase enzymes, which were conserved across geographically distant isolates. One plasmid, pQBR55, conferred the ability to catabolize sucrose. Transposons, including the mercury resistance Tn5042, appeared to have been acquired by different pQBR plasmids by recombination, indicating an important role for horizontal gene transfer in the recent evolution of pQBR plasmids. Our findings demonstrate extensive genetic and phenotypic diversity among co‐occurring members of a plasmid community and suggest a role for environmental heterogeneity in the maintenance of plasmid diversity.
Collapse
Affiliation(s)
- James P J Hall
- Department of Biology, Wentworth Way, University of York, York, UK
| | - Ellie Harrison
- Department of Biology, Wentworth Way, University of York, York, UK
| | - Andrew K Lilley
- Pharmaceutical Science Research Division, King's College London, London, UK
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Andrew J Spiers
- The SIMBIOS Centre, School of Science, Engineering and Technology, Abertay University, Dundee, UK
| | | |
Collapse
|
36
|
Arrebola E, Carrión VJ, Gutiérrez-Barranquero JA, Pérez-García A, Rodríguez-Palenzuela P, Cazorla FM, de Vicente A. Cellulose production inPseudomonas syringaepv.syringae: a compromise between epiphytic and pathogenic lifestyles. FEMS Microbiol Ecol 2015; 91:fiv071. [DOI: 10.1093/femsec/fiv071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2015] [Indexed: 01/11/2023] Open
|
37
|
Udall YC, Deeni Y, Hapca SM, Raikes D, Spiers AJ. The evolution of biofilm-forming Wrinkly Spreaders in static microcosms and drip-fed columns selects for subtle differences in wrinkleality and fitness. FEMS Microbiol Ecol 2015; 91:fiv057. [DOI: 10.1093/femsec/fiv057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/30/2022] Open
|
38
|
O'Rourke D, FitzGerald CE, Traverse CC, Cooper VS. There and back again: consequences of biofilm specialization under selection for dispersal. Front Genet 2015; 6:18. [PMID: 25717335 PMCID: PMC4324302 DOI: 10.3389/fgene.2015.00018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/14/2015] [Indexed: 11/13/2022] Open
Abstract
Experimental evolution paired with modern sequencing can be a powerful approach to identify the mechanisms by which bacteria adapt to discrete environmental conditions found in nature or during infections. We used this approach to identify mechanisms enabling biofilm specialists of the opportunistic respiratory pathogen Burkholderia cenocepacia to regain planktonic fitness. Seven mutants producing wrinkly (W) small-colony variants by mutations in the wrinkly-spreader operon (wsp) cluster, but with varying duration of biofilm adaptation, served as ancestors of this experiment. Following planktonic growth, each W ancestor produced smooth (S) mutants with distinct fitness effects across planktonic, biofilm, and dispersal-phase environments. The causes of the S phenotype traced to mutations in three gene clusters: wsp, Bcen2424_1436, an uncharacterized two-component transcriptional regulator which appears to be critical for wsp signaling, and a cohort of genes involved in polysaccharide synthesis. The genetic pathway from W to S also associated with evolutionary history in the biofilm environment. W mutants isolated from long-term biofilm selection usually produced S types via secondary wsp mutations, whereas S types evolved from less adapted W ancestors by a wider scope of mutations. These different genetic pathways to suppress the W phenotype suggest that prolonged biofilm adaptation limits routes to subsequent planktonic adaptation, despite common initial mechanisms of biofilm adaptation. More generally, experimental evolution can be used as a nuanced screen for gain-of-function mutations in multiple conditions that illustrate tensions that bacteria may face in changing environments or hosts.
Collapse
Affiliation(s)
- Devon O'Rourke
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire Durham, NH, USA
| | - Cody E FitzGerald
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire Durham, NH, USA
| | - Charles C Traverse
- Department of Microbiology, University of Texas at Austin Austin, TX, USA
| | - Vaughn S Cooper
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire Durham, NH, USA
| |
Collapse
|
39
|
Laganà P, Caruso G, Mazzù F, Caruso G, Parisi S, Santi Delia A. Brief Notes About Biofilms. SPRINGERBRIEFS IN MOLECULAR SCIENCE 2015. [DOI: 10.1007/978-3-319-20559-5_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
40
|
Armitano J, Méjean V, Jourlin-Castelli C. Gram-negative bacteria can also form pellicles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:534-544. [PMID: 25756106 DOI: 10.1111/1758-2229.12171] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
There is a growing interest in the bacterial pellicle, a biofilm floating at the air-liquid interface. Pellicles have been well studied in the Gram-positive bacterium Bacillus subtilis, but far less in Gram-negative bacteria, where pellicle studies have mostly focused on matrix components rather than on the regulatory cascades involved. Several Gram-negative bacteria, including pathogenic bacteria, have been shown to be able to form a pellicle under static conditions. Here, we summarize the growing body of knowledge about pellicle formation in Gram-negative bacteria, especially about the components of the pellicle matrix. We also propose that the pellicle is a specific biofilm, and that its formation involves particular processes. Since this lifestyle concerns a growing number of bacteria, its properties undoubtedly deserve further investigation.
Collapse
|
41
|
Zhurina MV, Gannesen AV, Zdorovenko EL, Plakunov VK. Composition and functions of the extracellular polymer matrix of bacterial biofilms. Microbiology (Reading) 2014. [DOI: 10.1134/s002626171406023x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
42
|
Lipopolysaccharide O-chain core region required for cellular cohesion and compaction of in vitro and root biofilms developed by Rhizobium leguminosarum. Appl Environ Microbiol 2014; 81:1013-23. [PMID: 25416773 DOI: 10.1128/aem.03175-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The formation of biofilms is an important survival strategy allowing rhizobia to live on soil particles and plant roots. Within the microcolonies of the biofilm developed by Rhizobium leguminosarum, rhizobial cells interact tightly through lateral and polar connections, forming organized and compact cell aggregates. These microcolonies are embedded in a biofilm matrix, whose main component is the acidic exopolysaccharide (EPS). Our work shows that the O-chain core region of the R. leguminosarum lipopolysaccharide (LPS) (which stretches out of the cell surface) strongly influences bacterial adhesive properties and cell-cell cohesion. Mutants defective in the O chain or O-chain core moiety developed premature microcolonies in which lateral bacterial contacts were greatly reduced. Furthermore, cell-cell interactions within the microcolonies of the LPS mutants were mediated mostly through their poles, resulting in a biofilm with an altered three-dimensional structure and increased thickness. In addition, on the root epidermis and on root hairs, O-antigen core-defective strains showed altered biofilm patterns with the typical microcolony compaction impaired. Taken together, these results indicate that the surface-exposed moiety of the LPS is crucial for proper cell-to-cell interactions and for the formation of robust biofilms on different surfaces.
Collapse
|
43
|
Nait Chabane Y, Marti S, Rihouey C, Alexandre S, Hardouin J, Lesouhaitier O, Vila J, Kaplan JB, Jouenne T, Dé E. Characterisation of pellicles formed by Acinetobacter baumannii at the air-liquid interface. PLoS One 2014; 9:e111660. [PMID: 25360550 PMCID: PMC4216135 DOI: 10.1371/journal.pone.0111660] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/25/2014] [Indexed: 11/18/2022] Open
Abstract
The clinical importance of Acinetobacter baumannii is partly due to its natural ability to survive in the hospital environment. This persistence may be explained by its capacity to form biofilms and, interestingly, A. baumannii can form pellicles at the air-liquid interface more readily than other less pathogenic Acinetobacter species. Pellicles from twenty-six strains were morphologically classified into three groups: I) egg-shaped (27%); II) ball-shaped (50%); and III) irregular pellicles (23%). One strain representative of each group was further analysed by Brewster’s Angle Microscopy to follow pellicle development, demonstrating that their formation did not require anchoring to a solid surface. Total carbohydrate analysis of the matrix showed three main components: Glucose, GlcNAc and Kdo. Dispersin B, an enzyme that hydrolyzes poly-N-acetylglucosamine (PNAG) polysaccharide, inhibited A. baumannii pellicle formation, suggesting that this exopolysaccharide contributes to pellicle formation. Also associated with the pellicle matrix were three subunits of pili assembled by chaperon-usher systems: the major CsuA/B, A1S_1510 (presented 45% of identity with the main pilin F17-A from enterotoxigenic Escherichia coli pili) and A1S_2091. The presence of both PNAG polysaccharide and pili systems in matrix of pellicles might contribute to the virulence of this emerging pathogen.
Collapse
Affiliation(s)
- Yassine Nait Chabane
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
| | - Sara Marti
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
- * E-mail: (SM); (ED)
| | - Christophe Rihouey
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
| | - Stéphane Alexandre
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
| | - Julie Hardouin
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
| | - Olivier Lesouhaitier
- Laboratory of “Microbiologie Signaux et Micro-Environnement” - Equipe d’Accueil 4312, University of Rouen, Evreux, France
| | - Jordi Vila
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | - Jeffrey B. Kaplan
- Department of Biology, American University, Washington, District of Columbia, United States of America
| | - Thierry Jouenne
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- Unité Mixte de Recherche 6270 CNRS - Laboratory “Polymères, Biopolymères, Surfaces”, University of Rouen, Mont-Saint-Aignan, France
- * E-mail: (SM); (ED)
| |
Collapse
|
44
|
Cooper VS, Staples RK, Traverse CC, Ellis CN. Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms. Genomics 2014; 104:447-52. [PMID: 25263109 DOI: 10.1016/j.ygeno.2014.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 12/31/2022]
Abstract
A common phenotype within bacterial biofilms is the small, "wrinkly" colony, which may associate with worse prognoses from biofilm-associated infections. The mechanisms that produce these variants in Burkholderia are undefined. Here we report the mutational and ecological causes of wrinkly (W) colonies that evolved during experimental biofilm evolution of Burkholderia cenocepacia. Mutations clustered in a homologous pathway to the Pseudomonas wsp operon but with a distinct terminal signaling mechanism, and their parallel evolution suggested that they inhabited an equivalent biofilm niche. We tested this hypothesis of niche complementarity by measuring effects of substituting different W variants in the same evolved biofilm community. Despite phenotypic differences among W mutants growing alone, fitness of reconstituted mixed biofilms did not differ significantly. In conclusion, the evolution of small-colony variants in Burkholderia biofilms appears to be driven by an ecological opportunity that generates strong selection for constitutive wsp mutants to inhabit a common niche.
Collapse
Affiliation(s)
- Vaughn S Cooper
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03820, USA.
| | - Rachel K Staples
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Charles C Traverse
- Department of Microbiology, University of Texas at Austin, Austin, TX, USA
| | - Crystal N Ellis
- Massachusetts General Hospital, Department of Medicine, Division of Infectious Diseases, 55 Fruit Street, Boston, MA 02114, USA
| |
Collapse
|
45
|
Winkelströter LK, Teixeira FBDR, Silva EP, Alves VF, De Martinis ECP. Unraveling microbial biofilms of importance for food microbiology. MICROBIAL ECOLOGY 2014; 68:35-46. [PMID: 24370864 DOI: 10.1007/s00248-013-0347-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/06/2013] [Indexed: 06/03/2023]
Abstract
The presence of biofilms is a relevant risk factors in the food industry due to the potential contamination of food products with pathogenic and spoilage microorganisms. The majority of bacteria are able to adhere and to form biofilms, where they can persist and survive for days to weeks or even longer, depending on the microorganism and the environmental conditions. The biological cycle of biofilms includes several developmental phases such as: initial attachment, maturation, maintenance, and dispersal. Bacteria in biofilms are generally well protected against environmental stress, consequently, extremely difficult to eradicate and detect in food industry. In the present manuscript, some techniques and compounds used to control and to prevent the biofilm formation are presented and discussed. Moreover, a number of novel techniques have been recently employed to detect and evaluate bacteria attached to surfaces, including real-time polymerase chain reaction (PCR), DNA microarray and confocal laser scanning microscopy. Better knowledge on the architecture, physiology and molecular signaling in biofilms can contribute for preventing and controlling food-related spoilage and pathogenic bacteria. The present study highlights basic and applied concepts important for understanding the role of biofilms in bacterial survival, persistence and dissemination in food processing environments.
Collapse
Affiliation(s)
- Lizziane Kretli Winkelströter
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (FCFRP-USP), Av. do Café s/n, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | | | | | | | | |
Collapse
|
46
|
El-Kirat-Chatel S, Beaussart A, Boyd CD, O’Toole GA, Dufrêne YF. Single-cell and single-molecule analysis deciphers the localization, adhesion, and mechanics of the biofilm adhesin LapA. ACS Chem Biol 2014; 9:485-94. [PMID: 24556201 DOI: 10.1021/cb400794e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The large adhesin protein LapA mediates adhesion and biofilm formation by Pseudomonas fluorescens. Although adhesion is thought to involve the long multiple repeats of LapA, very little is known about the molecular mechanism by which this protein mediates attachment. Here we use atomic force microscopy to unravel the biophysical properties driving LapA-mediated adhesion. Single-cell force spectroscopy shows that expression of LapA on the cell surface via biofilm-inducing conditions (i.e., phosphate-rich medium) or deletion of the gene encoding the LapG protease (LapA+ mutant) increases the adhesion strength of P. fluorescens toward hydrophobic and hydrophilic substrates, consistent with the adherent phenotypes observed in these conditions. Substrate chemistry plays an unexpected role in modulating the mechanical response of LapA, with sequential unfolding of the multiple repeats occurring only on hydrophilic substrates. Biofilm induction also leads to shortening of the protein extensions, reflecting stiffening of their conformational properties. Using single-molecule force spectroscopy, we next demonstrate that the adhesin is randomly distributed on the surface of wild-type cells and can be released into the solution. For LapA+ mutant cells, we found that the adhesin massively accumulates on the cell surface without being released and that individual LapA repeats unfold when subjected to force. The remarkable adhesive and mechanical properties of LapA provide a molecular basis for the "multi-purpose" adhesion function of LapA, thereby making P. fluorescens capable of colonizing diverse environments.
Collapse
Affiliation(s)
- Sofiane El-Kirat-Chatel
- Institute
of Life Sciences, Université catholique de Louvain, Croix du
Sud, 1, bte L7.04.01, B-1348 Louvain-la-Neuve, Belgium
| | - Audrey Beaussart
- Institute
of Life Sciences, Université catholique de Louvain, Croix du
Sud, 1, bte L7.04.01, B-1348 Louvain-la-Neuve, Belgium
| | - Chelsea D. Boyd
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - George A. O’Toole
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Yves F. Dufrêne
- Institute
of Life Sciences, Université catholique de Louvain, Croix du
Sud, 1, bte L7.04.01, B-1348 Louvain-la-Neuve, Belgium
| |
Collapse
|
47
|
A new biofilm-associated colicin with increased efficiency against biofilm bacteria. ISME JOURNAL 2014; 8:1275-88. [PMID: 24451204 DOI: 10.1038/ismej.2013.238] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/26/2013] [Accepted: 11/30/2013] [Indexed: 11/08/2022]
Abstract
Formation of bacterial biofilm communities leads to profound physiological modifications and increased physical and metabolic exchanges between bacteria. It was previously shown that bioactive molecules produced within the biofilm environment contribute to bacterial interactions. Here we describe new pore-forming colicin R, specifically produced in biofilms formed by the natural isolate Escherichia coli ROAR029 but that cannot be detected under planktonic culture conditions. We demonstrate that an increased SOS stress response within mature biofilms induces SOS-dependent colicin R expression. We provide evidence that colicin R displays increased activity against E. coli strains that have a reduced lipopolysaccharide length, such as the pathogenic enteroaggregative E. coli LF82 clinical isolate, therefore pointing to lipopolysaccharide size as an important determinant for resistance to colicins. We show that colicin R toxicity toward E. coli LF82 is increased under biofilm conditions compared with planktonic susceptibility and that release of colicin R confers a strong competitive advantage in mixed biofilms by rapidly outcompeting sensitive neighboring bacteria. This work identifies the first biofilm-associated colicin that preferentially targets biofilm bacteria. Furthermore, it indicates that the study of antagonistic molecules produced in biofilm and multispecies contexts could reveal unsuspected, ecologically relevant bacterial interactions influencing population dynamics in natural environments.
Collapse
|
48
|
A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the wrinkly spreader. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2014; 2014:675432. [PMID: 24551477 PMCID: PMC3914426 DOI: 10.1155/2014/675432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/08/2013] [Indexed: 11/17/2022]
Abstract
Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm-forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments.
Collapse
|
49
|
Penterman J, Nguyen D, Anderson E, Staudinger BJ, Greenberg EP, Lam JS, Singh PK. Rapid evolution of culture-impaired bacteria during adaptation to biofilm growth. Cell Rep 2014; 6:293-300. [PMID: 24412364 DOI: 10.1016/j.celrep.2013.12.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 10/17/2013] [Accepted: 12/12/2013] [Indexed: 11/17/2022] Open
Abstract
Biofilm growth increases the fitness of bacteria in harsh conditions. However, bacteria from clinical and environmental biofilms can exhibit impaired growth in culture, even when the species involved are readily culturable and permissive conditions are used. Here, we show that culture-impaired variants of Pseudomonas aeruginosa arise rapidly and become abundant in laboratory biofilms. The culture-impaired phenotype is caused by mutations that alter the outer-membrane lipopolysaccharide structure. Within biofilms, the lipopolysaccharide mutations markedly increase bacterial fitness. However, outside the protected biofilm environment, the mutations sensitize the variants to killing by a self-produced antimicrobial agent. Thus, a biofilm-mediated adaptation produces a stark fitness trade-off that compromises bacterial survival in culture. Trade-offs like this could limit the ability of bacteria to transition between biofilm growth and the free-living state and produce bacterial populations that escape detection by culture-based sampling.
Collapse
Affiliation(s)
- Jon Penterman
- Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.
| | - Dao Nguyen
- Department of Medicine, McGill University, Montreal, QC H3G 1A4, Canada
| | - Erin Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Benjamin J Staudinger
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Everett P Greenberg
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Pradeep K Singh
- Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| |
Collapse
|
50
|
Rühs PA, Böni L, Fuller GG, Inglis RF, Fischer P. In-situ quantification of the interfacial rheological response of bacterial biofilms to environmental stimuli. PLoS One 2013; 8:e78524. [PMID: 24244319 PMCID: PMC3823922 DOI: 10.1371/journal.pone.0078524] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/20/2013] [Indexed: 11/28/2022] Open
Abstract
Understanding the numerous factors that can affect biofilm formation and stability remain poorly understood. One of the major limitations is the accurate measurement of biofilm stability and cohesiveness in real-time when exposed to changing environmental conditions. Here we present a novel method to measure biofilm strength: interfacial rheology. By culturing a range of bacterial biofilms on an air-liquid interface we were able to measure their viscoelastic growth profile during and after biofilm formation and subsequently alter growth conditions by adding surfactants or changing the nutrient composition of the growth medium. We found that different bacterial species had unique viscoelastic growth profiles, which was also highly dependent on the growth media used. We also found that we could reduce biofilm formation by the addition of surfactants or changing the pH, thereby altering the viscoelastic properties of the biofilm. Using this technique we were able to monitor changes in viscosity, elasticity and surface tension online, under constant and varying environmental conditions, thereby providing a complementary method to better understand the dynamics of both biofilm formation and dispersal.
Collapse
Affiliation(s)
- Patrick A. Rühs
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- * E-mail:
| | - Lukas Böni
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Gerald G. Fuller
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - R. Fredrik Inglis
- Department of Environmental Sciences and Department of Environmental Microbiology, ETH Zürich and EAWAG, Zürich, Switzerland
| | - Peter Fischer
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|