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Al-Tameemi Z, Rodríguez-Verdugo A. Microbial diversification is maintained in an experimentally evolved synthetic community. mSystems 2024; 9:e0105324. [PMID: 39404341 PMCID: PMC11575400 DOI: 10.1128/msystems.01053-24] [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: 08/05/2024] [Accepted: 09/11/2024] [Indexed: 11/20/2024] Open
Abstract
Microbial communities are incredibly diverse. Yet, the eco-evolutionary processes originating and maintaining this diversity remain understudied. Here, we investigate the patterns of diversification for Pseudomonas putida evolving in isolation and with Acinetobacter johnsonii leaking resources used by P. putida. We experimentally evolved four experimental replicates in monoculture and co-culture for 200 generations. We observed that P. putida diversified into two distinct morphotypes that differed from their ancestor by single-point mutations. One of the most prominent mutations hit the fleQ gene encoding the master regulator of flagella and biofilm formation. We experimentally confirmed that fleQ mutants were unable to swim and formed less biofilm than their ancestor, but they also produced higher yields. Interestingly, the fleQ genotype and other mutations swept to fixation in monocultures but not in co-cultures. In co-cultures, the two lineages stably coexisted for approximately 150 generations. We hypothesized that A. johnsonii modulates the coexistence of the two lineages through frequency-dependent selection. However, invasion experiments with two genotypes in monoculture and co-culture did not support this hypothesis. Finally, we conducted an evolutionary "replay" experiment to assess whether the presence or absence of A. johnsonii influenced the coexistence of morphotypes at the population level. Interestingly, A. johnsonii had a stabilizing effect on the co-culture. Overall, our study suggests that interspecies interactions play an important role in shaping patterns of diversification in microbial communities. IMPORTANCE In nature, bacteria live in microbial communities and interact with other species, for example, through the exchange of resources leaked into the external environment (i.e., cross-feeding interactions). The role that these cross-feeding interactions play in shaping patterns of diversification remains understudied. Using a simple bacterial system in which one species cross-feeds resources to a second species (commensal species), we showed that the commensal species diversified into two subpopulations that persisted only when the cross-feeder partner was present. We further observed loss-of-function mutations in flagellar genes that were fixed in monocultures but not in co-cultures. Our findings suggest that cross-feeding species influence patterns of diversification of other species. Given that nutrient leakage is pervasive in microbial communities, the findings from this study have the potential to extend beyond our specific bacterial system. Importantly, our study has contributed to answering the larger question of whether species evolved differently in isolation versus when interacting with other species.
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Affiliation(s)
- Zahraa Al-Tameemi
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
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2
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Yang S, Li X, Cang W, Mu D, Ji S, An Y, Wu R, Wu J. Biofilm tolerance, resistance and infections increasing threat of public health. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:233-247. [PMID: 37933277 PMCID: PMC10625689 DOI: 10.15698/mic2023.11.807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 11/08/2023]
Abstract
Microbial biofilms can cause chronic infection. In the clinical setting, the biofilm-related infections usually persist and reoccur; the main reason is the increased antibiotic resistance of biofilms. Traditional antibiotic therapy is not effective and might increase the threat of antibiotic resistance to public health. Therefore, it is urgent to study the tolerance and resistance mechanism of biofilms to antibiotics and find effective therapies for biofilm-related infections. The tolerance mechanism and host reaction of biofilm to antibiotics are reviewed, and bacterial biofilm related diseases formed by human pathogens are discussed thoroughly. The review also explored the role of biofilms in the development of bacterial resistance mechanisms and proposed therapeutic intervention strategies for biofilm related diseases.
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Affiliation(s)
- Shanshan Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Xinfei Li
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
| | - Weihe Cang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
| | - Delun Mu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Yuejia An
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
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3
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Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P. Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia. MICROBIAL ECOLOGY 2023; 86:2305-2319. [PMID: 37209180 PMCID: PMC10640420 DOI: 10.1007/s00248-023-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.
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Affiliation(s)
- Ema Kostešić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Mitrović
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | | | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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4
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Malviya J, Alameri AA, Al-Janabi SS, Fawzi OF, Azzawi AL, Obaid RF, Alsudani AA, Alkhayyat AS, Gupta J, Mustafa YF, Karampoor S, Mirzaei R. Metabolomic profiling of bacterial biofilm: trends, challenges, and an emerging antibiofilm target. World J Microbiol Biotechnol 2023; 39:212. [PMID: 37256458 DOI: 10.1007/s11274-023-03651-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023]
Abstract
Biofilm-related infections substantially contribute to bacterial illnesses, with estimates indicating that at least 80% of such diseases are linked to biofilms. Biofilms exhibit unique metabolic patterns that set them apart from their planktonic counterparts, resulting in significant metabolic reprogramming during biofilm formation. Differential glycolytic enzymes suggest that central metabolic processes are markedly different in biofilms and planktonic cells. The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is highly expressed in Staphylococcus aureus biofilm progenitors, indicating that changes in glycolysis activity play a role in biofilm development. Notably, an important consideration is a correlation between elevated cyclic di-guanylate monophosphate (c-di-GMP) activity and biofilm formation in various bacteria. C-di-GMP plays a critical role in maintaining the persistence of Pseudomonas aeruginosa biofilms by regulating alginate production, a significant biofilm matrix component. Furthermore, it has been demonstrated that S. aureus biofilm development is initiated by several tricarboxylic acid (TCA) intermediates in a FnbA-dependent manner. Finally, Glucose 6-phosphatase (G6P) boosts the phosphorylation of histidine-containing protein (HPr) by increasing the activity of HPr kinase, enhancing its interaction with CcpA, and resulting in biofilm development through polysaccharide intercellular adhesion (PIA) accumulation and icaADBC transcription. Therefore, studying the metabolic changes associated with biofilm development is crucial for understanding the complex mechanisms involved in biofilm formation and identifying potential targets for intervention. Accordingly, this review aims to provide a comprehensive overview of recent advances in metabolomic profiling of biofilms, including emerging trends, prevailing challenges, and the identification of potential targets for anti-biofilm strategies.
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Affiliation(s)
- Jitendra Malviya
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, India
| | - Ameer A Alameri
- Department of Chemistry, College of Science, University of Babylon, Babylon, Iraq
| | - Saif S Al-Janabi
- Medical Laboratory Techniques Department, Al-Maarif University College, Ramadi, Iraq
| | | | | | - Rasha Fadhel Obaid
- Department of Biomedical Engineering, Al-Mustaqbal University College, Babylon, Iraq
| | - Ali A Alsudani
- College of Science, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Ameer S Alkhayyat
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, U. P., India
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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5
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Pouget C, Dunyach-Remy C, Magnan C, Pantel A, Sotto A, Lavigne JP. Polymicrobial Biofilm Organization of Staphylococcus aureus and Pseudomonas aeruginosa in a Chronic Wound Environment. Int J Mol Sci 2022; 23:ijms231810761. [PMID: 36142675 PMCID: PMC9504628 DOI: 10.3390/ijms231810761] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Biofilm on the skin surface of chronic wounds is an important step that involves difficulties in wound healing. The polymicrobial nature inside this pathogenic biofilm is key to understanding the chronicity of the lesion. Few in vitro models have been developed to study bacterial interactions inside this chronic wound. We evaluated the biofilm formation and the evolution of bacteria released from this biofilm on the two main bacteria isolated in this condition, Staphylococcus aureus and Pseudomonas aeruginosa, using a dynamic system (BioFlux™ 200) and a chronic wound-like medium (CWM) that mimics the chronic wound environment. We observed that all species constituted a faster biofilm in the CWM compared to a traditional culture medium (p < 0.01). The percentages of biofilm formation were significantly higher in the mixed biofilm compared to those determined for the bacterial species alone (p < 0.01). Biofilm organization was a non-random structure where S. aureus aggregates were located close to the wound surface, whereas P. aeruginosa was located deeper in the wound bed. Planktonic biofilm-detached bacteria showed decreased growth, overexpression of genes encoding biofilm formation, and an increase in the mature biofilm biomass formed. Our data confirmed the impact of the chronic wound environment on biofilm formation and on bacterial lifecycle inside the biofilm.
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Affiliation(s)
- Cassandra Pouget
- Bacterial Virulence and Chronic Infections, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University Montpellier, CEDEX 09, 30029 Nîmes, France
| | - Catherine Dunyach-Remy
- Bacterial Virulence and Chronic Infections, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University Montpellier, CEDEX 09, 30029 Nîmes, France
| | - Chloé Magnan
- Bacterial Virulence and Chronic Infections, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University Montpellier, CEDEX 09, 30029 Nîmes, France
| | - Alix Pantel
- Bacterial Virulence and Chronic Infections, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University Montpellier, CEDEX 09, 30029 Nîmes, France
| | - Albert Sotto
- Bacterial Virulence and Chronic Infections, INSERM U1047, Department of Infectious Diseases, CHU Nîmes, University Montpellier, CEDEX 09, 30029 Nîmes, France
| | - Jean-Philippe Lavigne
- Bacterial Virulence and Chronic Infections, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University Montpellier, CEDEX 09, 30029 Nîmes, France
- Correspondence: ; Tel.: +33-466-683-202
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6
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The symbiosis among, and the storage stabilities of, starter lactic acid bacterial strains in biofilms. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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7
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Liu T, Yang R, Zhou J, Lu X, Yuan Z, Wei X, Guo L. Interactions Between Streptococcus gordonii and Fusobacterium nucleatum Altered Bacterial Transcriptional Profiling and Attenuated the Immune Responses of Macrophages. Front Cell Infect Microbiol 2022; 11:783323. [PMID: 35071038 PMCID: PMC8776643 DOI: 10.3389/fcimb.2021.783323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
Interspecies coaggregation promotes transcriptional changes in oral bacteria, affecting bacterial pathogenicity. Streptococcus gordonii (S. gordonii) and Fusobacterium nucleatum (F. nucleatum) are common oral inhabitants. The present study investigated the transcriptional profiling of S. gordonii and F. nucleatum subsp. polymorphum in response to the dual-species coaggregation using RNA-seq. Macrophages were infected with both species to explore the influence of bacterial coaggregation on both species' abilities to survive within macrophages and induce inflammatory responses. Results indicated that, after the 30-min dual-species coaggregation, 116 genes were significantly up-regulated, and 151 genes were significantly down-regulated in S. gordonii; 97 genes were significantly down-regulated, and 114 genes were significantly up-regulated in F. nucleatum subsp. polymorphum. Multiple S. gordonii genes were involved in the biosynthesis and export of cell-wall proteins and carbohydrate metabolism. F. nucleatum subsp. polymorphum genes were mostly associated with translation and protein export. The coaggregation led to decreased expression levels of genes associated with lipopolysaccharide and peptidoglycan biosynthesis. Coaggregation between S. gordonii and F. nucleatum subsp. polymorphum significantly promoted both species' intracellular survival within macrophages and attenuated the production of pro-inflammatory cytokines IL-6 and IL-1β. Physical interactions between these two species promoted a symbiotic lifestyle and repressed macrophage's killing and pro-inflammatory responses.
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Affiliation(s)
- Tingjun Liu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Ruiqi Yang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Jiani Zhou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xianjun Lu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Zijian Yuan
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xi Wei
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Lihong Guo
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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8
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Cruz A, Condinho M, Carvalho B, Arraiano CM, Pobre V, Pinto SN. The Two Weapons against Bacterial Biofilms: Detection and Treatment. Antibiotics (Basel) 2021; 10:1482. [PMID: 34943694 PMCID: PMC8698905 DOI: 10.3390/antibiotics10121482] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial biofilms are defined as complex aggregates of bacteria that grow attached to surfaces or are associated with interfaces. Bacteria within biofilms are embedded in a self-produced extracellular matrix made of polysaccharides, nucleic acids, and proteins. It is recognized that bacterial biofilms are responsible for the majority of microbial infections that occur in the human body, and that biofilm-related infections are extremely difficult to treat. This is related with the fact that microbial cells in biofilms exhibit increased resistance levels to antibiotics in comparison with planktonic (free-floating) cells. In the last years, the introduction into the market of novel compounds that can overcome the resistance to antimicrobial agents associated with biofilm infection has slowed down. If this situation is not altered, millions of lives are at risk, and this will also strongly affect the world economy. As such, research into the identification and eradication of biofilms is important for the future of human health. In this sense, this article provides an overview of techniques developed to detect and imaging biofilms as well as recent strategies that can be applied to treat biofilms during the several biofilm formation steps.
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Affiliation(s)
- Adriana Cruz
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Manuel Condinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Beatriz Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Sandra N. Pinto
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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9
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Abstract
Microbial communities are constantly challenged with environmental stressors, such as antimicrobials, pollutants, and global warming. How do they respond to these changes? Answering this question is crucial given that microbial communities perform essential functions for life on Earth. Our research aims to understand and predict communities' responses to change by addressing the following questions. (i) How do eco-evolutionary feedbacks influence microbial community dynamics? (ii) How do multiple interacting species in a microbial community alter evolutionary processes? (iii) To what extent do microbial communities respond to change by ecological versus evolutionary processes? To answer these questions, we use microbial communities of reduced complexity coupled with experimental evolution, genome sequencing, and mathematical modeling. The overall expectation from this integrative research approach is to generate general concepts that extend beyond specific bacterial species and provide fundamental insights into the consequences of evolution on the functioning of whole microbial communities.
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10
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Genomic evolution of the marine bacterium Phaeobacter inhibens during biofilm growth. Appl Environ Microbiol 2021; 87:e0076921. [PMID: 34288701 DOI: 10.1128/aem.00769-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
P. inhibens 2.10 is an effective biofilm former on marine surfaces and has the ability to outcompete other microorganisms, possibly due to the production of the plasmid-encoded, secondary metabolite tropodithietic acid (TDA). P. inhibens 2.10 biofilms produce phenotypic variants with reduced competitiveness compared to the wild-type. In the present study, we used longitudinal, genome-wide deep sequencing to uncover the genetic foundation that contributes to the emergent phenotypic diversity in P. inhibens 2.10 biofilm dispersants. Our results show that phenotypic variation is not due to the loss of plasmid that encodes the genes for the TDA synthesis, but instead show that P. inhibens 2.10 biofilm populations become rapidly enriched in single nucleotide variations in genes involved in the synthesis of TDA. While variants in genes previously linked to other phenotypes, such as lipopolysaccharide production (i.e. rfbA) and celluar persistence (i.e. metG), also appear to be selected for during biofilm dispersal, the number and consistency of variations found for genes involved in TDA production suggest that this metabolite imposes a burden for P. inhibens 2.10 cells. Our results indicate a strong selection pressure for the loss of TDA in mono-species biofilm populations and provide insight into how competition (or lack thereof) in biofilms might shape genome evolution in bacteria. Importance Statement Biofilm formation and dispersal are important survival strategies for environmental bacteria. During biofilm dispersal cells often display stable and heritable variants from the parental biofilm. Phaeobacter inhibens is an effective colonizer of marine surfaces, in which a subpopulation of its biofilm dispersal cells displays a non-competitive phenotype. This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens, little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens, including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g. quorum sensing). This work is significant as it reveals how the biofilm-lifestyle might shape genome evolution in a cosmopolitan bacterium.
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11
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Structure and Fluorescence Intensity Measurements in Biofilms. Methods Mol Biol 2019. [PMID: 31432478 DOI: 10.1007/978-1-4939-9686-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
Abstract
Confocal laser scanning microscopy (CLSM) is one of the most relevant technologies for studying biofilms in situ. Several tools have been developed to investigate and quantify the architecture of biofilms. However, an approach to accurately quantify the intensity of a fluorescent signal over biofilm depth is still lacking. Here we present a tool developed in the ImageJ open-source software that can be used to extract both structure and fluorescence intensity from CLSM data: BIAM (Biofilm Intensity and Architecture Measurement). This is of utmost significance when studying the fundamental mechanisms of biofilm development, differentiation, and in situ gene expression or when aiming to understand the effect of external molecules on biofilm phenotypes.
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12
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Crabbé A, Jensen PØ, Bjarnsholt T, Coenye T. Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms. Trends Microbiol 2019; 27:850-863. [PMID: 31178124 DOI: 10.1016/j.tim.2019.05.003] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/25/2019] [Accepted: 05/07/2019] [Indexed: 01/04/2023]
Abstract
Active bacterial metabolism is a prerequisite for optimal activity of many classes of antibiotics. Hence, bacteria have developed strategies to reduce or modulate metabolic pathways to become tolerant. This review describes the tight relationship between metabolism and tolerance in bacterial biofilms, and how physicochemical properties of the microenvironment at the host-pathogen interface (such as oxygen and nutritional content) are key to this relationship. Understanding how metabolic adaptations lead to tolerance brings us to novel approaches to tackle antibiotic-tolerant biofilms. We describe the use of hyperbaric oxygen therapy, metabolism-stimulating metabolites, and alternative strategies to redirect bacterial metabolism towards an antibiotic-susceptible phenotype.
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Affiliation(s)
- Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Peter Østrup Jensen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark; Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.
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13
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Conforte VP, Yaryura PM, Bianco MI, Rodríguez MC, Daglio Y, Prieto E, Schilardi P, Vojnov AA. Changes in the physico-chemical properties of the xanthan produced byXanthomonas citrisubsp.citriin grapefruit leaf extract. Glycobiology 2019; 29:269-278. [DOI: 10.1093/glycob/cwy114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/19/2018] [Accepted: 01/03/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- Valeria P Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
| | - Pablo M Yaryura
- Centro de Investigaciones y Transferencia (CIT Villa María), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)—Instituto de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María. Av. Arturo Jauretche 1555, (5900), Villa María, Córdoba, Argentina
| | - María I Bianco
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
| | - María C Rodríguez
- niversidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Ciudad Universitaria-Pabellón 2, C1428EGA. Ciudad Autónoma de Buenos Aires, Argentina
| | - Yasmin Daglio
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)—Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Facultad de Ciencias Exactas y Naturales Pabellón II, 3er P, Ciudad Universitaria, 1428, Buenos Aires, Argentina
| | - Eduardo Prieto
- Universidad Nacional de La Plata (UNLP), Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Consejo Nacional de Investigaciones Científicas y Tecnológicas INIFTA—CONICET), Diagonal 113 y 64 S/N La Plata, Buenos Aires, Argentina
| | - Patricia Schilardi
- Universidad Nacional de La Plata (UNLP), Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Consejo Nacional de Investigaciones Científicas y Tecnológicas INIFTA—CONICET), Diagonal 113 y 64 S/N La Plata, Buenos Aires, Argentina
| | - Adrián A Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
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14
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Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
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Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
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15
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Matrix Polysaccharides and SiaD Diguanylate Cyclase Alter Community Structure and Competitiveness of Pseudomonas aeruginosa during Dual-Species Biofilm Development with Staphylococcus aureus. mBio 2018; 9:mBio.00585-18. [PMID: 30401769 PMCID: PMC6222129 DOI: 10.1128/mbio.00585-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacteria in natural and engineered environments form biofilms that include many different species. Microorganisms rely on a number of different strategies to manage social interactions with other species and to access resources, build biofilm consortia, and optimize growth. For example, Pseudomonas aeruginosa and Staphylococcus aureus are biofilm-forming bacteria that coinfect the lungs of cystic fibrosis patients and diabetic and chronic wounds. P. aeruginosa is known to antagonize S. aureus growth. However, many of the factors responsible for mixed-species interactions and outcomes such as infections are poorly understood. Biofilm bacteria are encased in a self-produced extracellular matrix that facilitates interspecies behavior and biofilm development. In this study, we examined the poorly understood roles of the major matrix biopolymers and their regulators in mixed-species biofilm interactions and development. Mixed-species biofilms display a number of emergent properties, including enhanced antimicrobial tolerance and communal metabolism. These properties may depend on interspecies relationships and the structure of the biofilm. However, the contribution of specific matrix components to emergent properties of mixed-species biofilms remains poorly understood. Using a dual-species biofilm community formed by the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus, we found that whilst neither Pel nor Psl polysaccharides, produced by P. aeruginosa, affect relative species abundance in mature P. aeruginosa and S. aureus biofilms, Psl production is associated with increased P. aeruginosa abundance and reduced S. aureus aggregation in the early stages of biofilm formation. Our data suggest that the competitive effect of Psl is not associated with its structural role in cross-linking the matrix and adhering to P. aeruginosa cells but is instead mediated through the activation of the diguanylate cyclase SiaD. This regulatory control was also found to be independent of the siderophore pyoverdine and Pseudomonas quinolone signal, which have previously been proposed to reduce S. aureus viability by inducing lactic acid fermentation-based growth. In contrast to the effect mediated by Psl, Pel reduced the effective crosslinking of the biofilm matrix and facilitated superdiffusivity in microcolony regions. These changes in matrix cross-linking enhance biofilm surface spreading and expansion of microcolonies in the later stages of biofilm development, improving overall dual-species biofilm growth and increasing biovolume severalfold. Thus, the biofilm matrix and regulators associated with matrix production play essential roles in mixed-species biofilm interactions.
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16
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Majzoub ME, McElroy K, Maczka M, Thomas T, Egan S. Causes and Consequences of a Variant Strain of Phaeobacter inhibens With Reduced Competition. Front Microbiol 2018; 9:2601. [PMID: 30450086 PMCID: PMC6224355 DOI: 10.3389/fmicb.2018.02601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/11/2018] [Indexed: 11/13/2022] Open
Abstract
Phaeobacter inhibens 2.10 is an effective biofilm former and colonizer of marine surfaces and has the ability to outcompete other microbiota. During biofilm dispersal P. inhibens 2.10 produces heritable phenotypic variants, including those that have a reduced ability to inhibit the co-occurring bacterium Pseudoalteromonas tunicata. However, the genetic changes that underpin the phenotypic variation and what the ecological consequences are for variants within the population are unclear. To answer these questions we sequenced the genomes of strain NCV12a1, a biofilm variant of P. inhibens 2.10 with reduced inhibitory activity and the P. inhibens 2.10 WT parental strain. Genome wide analysis revealed point mutations in genes involved in synthesis of the antibacterial compound tropodithietic acid (TDA) and indirectly in extracellular polymeric substances (EPS) production. However, confocal laser scanning microscopy analyses found little differences in biofilm growth between P. inhibens 2.10 WT (parental) and NCV12a1. P. inhibens NCV12a1 was also not outcompeted in co-cultured biofilms with P. tunicata, despite its reduced inhibitory activity, rather these biofilms were thicker than those produced when the WT strain was co-cultured with P. tunicata. Notably, dispersal populations from biofilms of P. inhibens NCV12a1 had a higher proportion of WT-like morphotypes when co-cultured with P. tunicata. These observations may explain why the otherwise non-inhibiting variant persists in the presence of a natural competitor, adding to our understanding of the relative importance of genetic diversification in microbial biofilms.
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Affiliation(s)
- Marwan E Majzoub
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Kerensa McElroy
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Michael Maczka
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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17
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Monmeyran A, Thomen P, Jonquière H, Sureau F, Li C, Plamont MA, Douarche C, Casella JF, Gautier A, Henry N. The inducible chemical-genetic fluorescent marker FAST outperforms classical fluorescent proteins in the quantitative reporting of bacterial biofilm dynamics. Sci Rep 2018; 8:10336. [PMID: 29985417 PMCID: PMC6037777 DOI: 10.1038/s41598-018-28643-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/26/2018] [Indexed: 01/10/2023] Open
Abstract
To increase our understanding of bacterial biofilm complexity, real- time quantitative analyses of the living community functions are required. To reach this goal, accurate fluorescent reporters are needed. In this paper, we used the classical fluorescent genetic reporters of the GFP family and demonstrated their limits in the context of a living biofilm. We showed that fluorescence signal saturated after only a few hours of growth and related this saturation to the reduction of oxygen concentration induced by bacterial consumption. This behaviour prevents the use of GFP-like fluorescent proteins for quantitative measurement in living biofilms. To overcome this limitation, we propose the use of a recently introduced small protein tag, FAST, which is fluorescent in the presence of an exogenously applied fluorogenic dye, enabling to avoid the oxygen sensitivity issue. We compared the ability of FAST to report on biofilm growth with that of GFP and mCherry, and demonstrated the superiority of the FAST:fluorogen probes for investigating dynamics in the complex environment of a living biofilm.
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Affiliation(s)
- Amaury Monmeyran
- Laboratoire Jean Perrin, CNRS UMR 8237 Sorbonne Université & UPMC Université Paris 06, F-75005, Paris, France
| | - Philippe Thomen
- Laboratoire Jean Perrin, CNRS UMR 8237 Sorbonne Université & UPMC Université Paris 06, F-75005, Paris, France
- Institut de Physique de Nice, UMR 7010, Université Nice Sophia Antipolis, Nice, France
| | - Hugo Jonquière
- Laboratoire Jean Perrin, CNRS UMR 8237 Sorbonne Université & UPMC Université Paris 06, F-75005, Paris, France
| | - Franck Sureau
- Laboratoire Jean Perrin, CNRS UMR 8237 Sorbonne Université & UPMC Université Paris 06, F-75005, Paris, France
| | - Chenge Li
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Carine Douarche
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Jean-François Casella
- Laboratoire Jean Perrin, CNRS UMR 8237 Sorbonne Université & UPMC Université Paris 06, F-75005, Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Nelly Henry
- Laboratoire Jean Perrin, CNRS UMR 8237 Sorbonne Université & UPMC Université Paris 06, F-75005, Paris, France.
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18
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Percival SL, Malone M, Mayer D, Salisbury AM, Schultz G. Role of anaerobes in polymicrobial communities and biofilms complicating diabetic foot ulcers. Int Wound J 2018; 15:776-782. [PMID: 29863794 DOI: 10.1111/iwj.12926] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/28/2018] [Indexed: 11/29/2022] Open
Abstract
Infected tissues in the feet of people with diabetes in the form of a diabetic foot ulcer (DFU) present a complex pathology for clinicians to manage. This is partly attributed to the multi-factorial nature of the disease, which may include; altered foot architecture leading to excessive plantar pressures and frictional forces peripheral arterial disease and loss of protective sensation. In addition, to the above co-morbid variables, it is understood that a delayed wound healing state may be perpetuated by the presence of microorganisms residing in the wound tissue. The microbiology of chronic DFUs has often been reported as being polymicrobial. Of growing interest is the presence and potential role of anaerobic microorganisms in the pathology of DFUs and how they may contribute to the infective process or delayed healing. The presence of anaerobes in DFUs has been greatly underestimated, largely due to the limitations of conventional culture methods in identifying them from samples. Advancements in molecular and microscopy techniques have extended our view of the wound microbiome in addition to observing the growth and behaviour (planktonic or biofilm) of microorganisms in situ. This review paper will reflect on the evidence for the role and significance of anaerobes in DFUs and infection. A focus of this review will be to explore recent advancements in molecular genomics and microscopy techniques in order to better assess the roles of anaerobic bacteria in chronic DFUs and in biofilm-based wound care.
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Affiliation(s)
- Steven L Percival
- 5D Health Protection Group Ltd, Centre of Excellence in Biofilm Science and Technologies (CEBST), Liverpool Bio-Innovation Hub, Liverpool, UK
| | - Matthew Malone
- Infectious Disease and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia.,High Risk Foot Service, Liverpool Hospital South Western Sydney LHD, Sydney, New South Wales, Australia
| | - Dieter Mayer
- Department of Surgery, HFR Fribourg - Cantonal Hospital, Fribourg, Switzerland
| | - Anne-Marie Salisbury
- 5D Health Protection Group Ltd, Centre of Excellence in Biofilm Science and Technologies (CEBST), Liverpool Bio-Innovation Hub, Liverpool, UK
| | - Gregory Schultz
- Institute for Wound Research, Department Obstetrics & Gynaecology, University of Florida, Gainesville, Florida
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19
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Falcone M, Ferrara S, Rossi E, Johansen HK, Molin S, Bertoni G. The Small RNA ErsA of Pseudomonas aeruginosa Contributes to Biofilm Development and Motility through Post-transcriptional Modulation of AmrZ. Front Microbiol 2018; 9:238. [PMID: 29497413 PMCID: PMC5819304 DOI: 10.3389/fmicb.2018.00238] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
The small RNA ErsA of Pseudomonas aeruginosa was previously suggested to be involved in biofilm formation via negative post-transcriptional regulation of the algC gene that encodes the virulence-associated enzyme AlgC, which provides sugar precursors for the synthesis of several polysaccharides. In this study, we show that a knock-out ersA mutant strain forms a flat and uniform biofilm, not characterized by mushroom-multicellular structures typical of a mature biofilm. Conversely, the knock-out mutant strain showed enhanced swarming and twitching motilities. To assess the influence of ErsA on the P. aeruginosa transcriptome, we performed RNA-seq experiments comparing the knock-out mutant with the wild-type. More than 160 genes were found differentially expressed in the knock-out mutant. Parts of these genes, important for biofilm formation and motility regulation, are known to belong also to the AmrZ transcriptional regulator regulon. Here, we show that ErsA binds in vitro and positively regulates amrZ mRNA at post-transcriptional level in vivo suggesting an interesting contribution of the ErsA-amrZ mRNA interaction in biofilm development at several regulatory levels.
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Affiliation(s)
- Marilena Falcone
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Elio Rossi
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Helle K Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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20
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A broad range quorum sensing inhibitor working through sRNA inhibition. Sci Rep 2017; 7:9857. [PMID: 28851971 PMCID: PMC5575346 DOI: 10.1038/s41598-017-09886-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/21/2017] [Indexed: 11/15/2022] Open
Abstract
For the last decade, chemical control of bacterial virulence has received considerable attention. Ajoene, a sulfur-rich molecule from garlic has been shown to reduce expression of key quorum sensing regulated virulence factors in the opportunistic pathogen Pseudomonas aeruginosa. Here we show that the repressing effect of ajoene on quorum sensing occurs by inhibition of small regulatory RNAs (sRNA) in P. aeruginosa as well as in Staphylococcus aureus, another important human pathogen that employs quorum sensing to control virulence gene expression. Using various reporter constructs, we found that ajoene lowered expression of the sRNAs RsmY and RsmZ in P. aeruginosa and the small dual-function regulatory RNA, RNAIII in S. aureus, that controls expression of key virulence factors. We confirmed the modulation of RNAIII by RNA sequencing and found that the expression of many QS regulated genes encoding virulence factors such as hemolysins and proteases were lowered in the presence of ajoene in S. aureus. Importantly, our findings show that sRNAs across bacterial species potentially may qualify as targets of anti-virulence therapy and that ajoene could be a lead structure in search of broad-spectrum compounds transcending the Gram negative-positive borderline.
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21
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Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity. J Microbiol Methods 2017; 140:47-57. [PMID: 28679111 DOI: 10.1016/j.mimet.2017.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 01/08/2023]
Abstract
Confocal laser scanning microscopy (CLSM) is one of the most relevant technologies for studying biofilms in situ. Several tools have been developed to investigate and quantify the architecture of biofilms. However, an approach to quantify correctly the evolution of intensity of a fluorescent signal as a function of the structural parameters of a biofilm is still lacking. Here we present a tool developed in the ImageJ open source software that can be used to extract both structural and fluorescence intensity from CLSM data: BIAM (Biofilm Intensity and Architecture Measurement). This is of utmost significance when studying the fundamental mechanisms of biofilm growth, differentiation and development or when aiming to understand the effect of external molecules on biofilm phenotypes. In order to provide an example of the potential of such a tool in this study we focused on biofilm dispersion. cis-2-Decenoic acid (CDA) is a molecule known to induce biofilm dispersion of multiple bacterial species. The mechanisms by which CDA induces dispersion are still poorly understood. To investigate the effects of CDA on biofilms, we used a reporter strain of Escherichia coli (E. coli) that expresses the GFPmut2 protein under control of the rrnBP1 promoter. Experiments were done in flow cells and image acquisition was made with CLSM. Analysis carried out using the new tool, BIAM, indicates that CDA affects the fluorescence intensity of the biofilm structures as well as biofilm architectures. Indeed, our results demonstrate that CDA removes more than 35% of biofilm biovolume and suggest that it results in an increase of the biofilm's mean fluorescence intensity (MFI) by more than 26% compared to the control biofilm in the absence of CDA.
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22
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Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions. GENOME ANNOUNCEMENTS 2017; 5:5/16/e00155-17. [PMID: 28428290 PMCID: PMC5399249 DOI: 10.1128/genomea.00155-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Acinetobacter johnsonii C6 originates from creosote-polluted groundwater and performs ecological and evolutionary interactions with Pseudomonas putida in biofilms. The draft genome of A. johnsonii C6 is 3.7 Mbp and was shaped by mobile genetic elements. It reveals genes facilitating the biodegradation of aromatic hydrocarbons and resistance to antimicrobials and metals.
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23
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Model-based quantification of metabolic interactions from dynamic microbial-community data. PLoS One 2017; 12:e0173183. [PMID: 28278266 PMCID: PMC5344373 DOI: 10.1371/journal.pone.0173183] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/16/2017] [Indexed: 02/01/2023] Open
Abstract
An important challenge in microbial ecology is to infer metabolic-exchange fluxes between growing microbial species from community-level data, concerning species abundances and metabolite concentrations. Here we apply a model-based approach to integrate such experimental data and thereby infer metabolic-exchange fluxes. We designed a synthetic anaerobic co-culture of Clostridium acetobutylicum and Wolinella succinogenes that interact via interspecies hydrogen transfer and applied different environmental conditions for which we expected the metabolic-exchange rates to change. We used stoichiometric models of the metabolism of the two microorganisms that represents our current physiological understanding and found that this understanding - the model - is sufficient to infer the identity and magnitude of the metabolic-exchange fluxes and it suggested unexpected interactions. Where the model could not fit all experimental data, it indicates specific requirement for further physiological studies. We show that the nitrogen source influences the rate of interspecies hydrogen transfer in the co-culture. Additionally, the model can predict the intracellular fluxes and optimal metabolic exchange rates, which can point to engineering strategies. This study therefore offers a realistic illustration of the strengths and weaknesses of model-based integration of heterogenous data that makes inference of metabolic-exchange fluxes possible from community-level experimental data.
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24
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Microbial competition in porous environments can select against rapid biofilm growth. Proc Natl Acad Sci U S A 2016; 114:E161-E170. [PMID: 28007984 DOI: 10.1073/pnas.1525228113] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow-biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live.
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25
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Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kačániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C. Critical review on biofilm methods. Crit Rev Microbiol 2016; 43:313-351. [PMID: 27868469 DOI: 10.1080/1040841x.2016.1208146] [Citation(s) in RCA: 598] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.
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Affiliation(s)
- Joana Azeredo
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Nuno F Azevedo
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Romain Briandet
- c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Nuno Cerca
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Tom Coenye
- d Laboratory of Pharmaceutical Microbiology , Ghent University , Ghent , Belgium
| | - Ana Rita Costa
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Mickaël Desvaux
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Giovanni Di Bonaventura
- f Department of Medical, Oral, and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT) , "G. d'Annunzio" University of Chieti-Pescara , Chieti , Italy
| | - Michel Hébraud
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Zoran Jaglic
- g Department of Food and Feed Safety, Laboratory of Food Bacteriology , Veterinary Research Institute , Brno , Czech Republic
| | - Miroslava Kačániová
- h Department of Microbiology, Faculty of Biotechnology and Food Sciences , Slovak University of Agriculture in Nitra , Nitra , Slovakia
| | - Susanne Knøchel
- i Department of Food Science (FOOD) , University of Copenhagen , Frederiksberg C , Denmark
| | - Anália Lourenço
- j Department of Computer Science , University of Vigo , Ourense , Spain
| | - Filipe Mergulhão
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Rikke Louise Meyer
- k Aarhus University, Interdisciplinary Nanoscience Center (iNANO) , Aarhus , Denmark
| | - George Nychas
- l Agricultural University of Athens, Lab of Microbiology and Biotechnology of Foods , Athens , Greece
| | - Manuel Simões
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Odile Tresse
- m LUNAM Université, Oniris, SECALIM UMR1024 INRA , Université de Nantes , Nantes , France
| | - Claus Sternberg
- n Department of Biotechnology and Biomedicine , Technical University of Denmark , Lyngby, Denmark
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Bianco MI, Toum L, Yaryura PM, Mielnichuk N, Gudesblat GE, Roeschlin R, Marano MR, Ielpi L, Vojnov AA. Xanthan Pyruvilation Is Essential for the Virulence of Xanthomonas campestris pv. campestris. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:688-699. [PMID: 27464764 DOI: 10.1094/mpmi-06-16-0106-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Xanthan, the main exopolysaccharide (EPS) synthesized by Xanthomonas spp., contributes to bacterial stress tolerance and enhances attachment to plant surfaces by helping in biofilm formation. Therefore, xanthan is essential for successful colonization and growth in planta and has also been proposed to be involved in the promotion of pathogenesis by calcium ion chelation and, hence, in the suppression of the plant defense responses in which this cation acts as a signal. The aim of this work was to study the relationship between xanthan structure and its role as a virulence factor. We analyzed four Xanthomonas campestris pv. campestris mutants that synthesize structural variants of xanthan. We found that the lack of acetyl groups that decorate the internal mannose residues, ketal-pyruvate groups, and external mannose residues affects bacterial adhesion and biofilm architecture. In addition, the mutants that synthesized EPS without pyruvilation or without the external mannose residues did not develop disease symptoms in Arabidopsis thaliana. We also observed that the presence of the external mannose residues and, hence, pyruvilation is required for xanthan to suppress callose deposition as well as to interfere with stomatal defense. In conclusion, pyruvilation of xanthan seems to be essential for Xanthomonas campestris pv. campestris virulence.
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Affiliation(s)
- María Isabel Bianco
- 1 Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
| | - Laila Toum
- 1 Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
| | - Pablo Marcelo Yaryura
- 2 Centro de Investigaciones y Transferencia (CIT Villa María), CONICET-Instituto de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María. Av. Arturo Jauretche 1555, (5900), Villa María, Córdoba, Argentina
| | - Natalia Mielnichuk
- 1 Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
| | - Gustavo Eduardo Gudesblat
- 1 Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
- 3 Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Departamento de Biodiversidad y Biología Experimental (DBBE), CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Buenos Aires (C1428EGA), Argentina
| | - Roxana Roeschlin
- 4 Instituto de Biología Molecular y Celular de Rosario (IBR)-CONICET, Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda s/n, (S2000FHN) Rosario, Argentina; and
| | - María Rosa Marano
- 4 Instituto de Biología Molecular y Celular de Rosario (IBR)-CONICET, Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda s/n, (S2000FHN) Rosario, Argentina; and
| | - Luis Ielpi
- 5 Laboratorio de Genética Bacteriana, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA)-CONICET, Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Adrián A Vojnov
- 1 Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468 (C1440FFX), Ciudad de Buenos Aires, Argentina
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Liu W, Røder HL, Madsen JS, Bjarnsholt T, Sørensen SJ, Burmølle M. Interspecific Bacterial Interactions are Reflected in Multispecies Biofilm Spatial Organization. Front Microbiol 2016; 7:1366. [PMID: 27630624 PMCID: PMC5005372 DOI: 10.3389/fmicb.2016.01366] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/18/2016] [Indexed: 12/31/2022] Open
Abstract
Interspecies interactions are essential for the persistence and development of any kind of complex community, and microbial biofilms are no exception. Multispecies biofilms are structured and spatially defined communities that have received much attention due to their omnipresence in natural environments. Species residing in these complex bacterial communities usually interact both intra- and interspecifically. Such interactions are considered to not only be fundamental in shaping overall biomass and the spatial distribution of cells residing in multispecies biofilms, but also to result in coordinated regulation of gene expression in the different species present. These communal interactions often lead to emergent properties in biofilms, such as enhanced tolerance against antibiotics, host immune responses, and other stresses, which have been shown to provide benefits to all biofilm members not only the enabling sub-populations. However, the specific molecular mechanisms of cellular processes affecting spatial organization, and vice versa, are poorly understood and very complex to unravel. Therefore, detailed description of the spatial organization of individual bacterial cells in multispecies communities can be an alternative strategy to reveal the nature of interspecies interactions of constituent species. Closing the gap between visual observation and biological processes may become crucial for resolving biofilm related problems, which is of utmost importance to environmental, industrial, and clinical implications. This review briefly presents the state of the art of studying interspecies interactions and spatial organization of multispecies communities, aiming to support theoretical and practical arguments for further advancement of this field.
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Affiliation(s)
- Wenzheng Liu
- Molecular Microbial Ecology Group, Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Henriette L Røder
- Molecular Microbial Ecology Group, Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Jonas S Madsen
- Molecular Microbial Ecology Group, Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Faculty of Health Sciences, University of CopenhagenCopenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University HospitalCopenhagen, Denmark
| | - Søren J Sørensen
- Molecular Microbial Ecology Group, Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Mette Burmølle
- Molecular Microbial Ecology Group, Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
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Plotnikova EG, Shumkova ES, Shumkov MS. Whole-cell bacterial biosensors for the detection of aromatic hydrocarbons and their chlorinated derivatives (Review). APPL BIOCHEM MICRO+ 2016. [DOI: 10.1134/s0003683816040128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mangwani N, Kumari S, Das S. Bacterial biofilms and quorum sensing: fidelity in bioremediation technology. Biotechnol Genet Eng Rev 2016; 32:43-73. [DOI: 10.1080/02648725.2016.1196554] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha 769 008, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha 769 008, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha 769 008, India
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Røder HL, Sørensen SJ, Burmølle M. Studying Bacterial Multispecies Biofilms: Where to Start? Trends Microbiol 2016; 24:503-513. [DOI: 10.1016/j.tim.2016.02.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 11/26/2022]
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Lutz C, Thomas T, Steinberg P, Kjelleberg S, Egan S. Effect of interspecific competition on trait variation inPhaeobacter inhibensbiofilms. Environ Microbiol 2016; 18:1635-45. [DOI: 10.1111/1462-2920.13253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/26/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Carla Lutz
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
| | - Torsten Thomas
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
| | - Peter Steinberg
- Centre for Marine Bio-Innovation
- School of Biological, Earth and Environmental Science; University of New South Wales; Sydney Australia
- Singapore Centre for Environmental Life Sciences Engineering; Nanyang Technological University; Singapore
- Sydney Institute of Marine Science; Mosman New South Wales Australia
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
- Singapore Centre for Environmental Life Sciences Engineering; Nanyang Technological University; Singapore
| | - Suhelen Egan
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
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Wigneswaran V, Amador CI, Jelsbak L, Sternberg C, Jelsbak L. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories. F1000Res 2016; 5. [PMID: 27092245 PMCID: PMC4821285 DOI: 10.12688/f1000research.7876.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/24/2016] [Indexed: 11/20/2022] Open
Abstract
Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.
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Affiliation(s)
- Vinoth Wigneswaran
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Lotte Jelsbak
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Claus Sternberg
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Engineering microbial consortia for controllable outputs. ISME JOURNAL 2016; 10:2077-84. [PMID: 26967105 PMCID: PMC4989317 DOI: 10.1038/ismej.2016.26] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 11/29/2015] [Accepted: 12/30/2015] [Indexed: 01/06/2023]
Abstract
Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.
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34
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Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates. ISME JOURNAL 2016; 10:1568-78. [PMID: 26771930 DOI: 10.1038/ismej.2015.243] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/08/2022]
Abstract
Different microbial cell types typically specialize at performing different metabolic processes. A canonical example is substrate cross-feeding, where one cell type consumes a primary substrate into an intermediate and another cell type consumes the intermediate. While substrate cross-feeding is widely observed, its consequences on ecosystem processes is often unclear. How does substrate cross-feeding affect the rate or extent of substrate consumption? We hypothesized that substrate cross-feeding eliminates competition between different enzymes and reduces the accumulation of growth-inhibiting intermediates, thus accelerating substrate consumption. We tested this hypothesis using isogenic mutants of the bacterium Pseudomonas stutzeri that either completely consume nitrate to dinitrogen gas or cross-feed the intermediate nitrite. We demonstrate that nitrite cross-feeding eliminates inter-enzyme competition and, in turn, reduces nitrite accumulation. We further demonstrate that nitrite cross-feeding accelerates substrate consumption, but only when nitrite has growth-inhibiting effects. Knowledge about inter-enzyme competition and the inhibitory effects of intermediates could therefore be important for deciding how to best segregate different metabolic processes into different microbial cell types to optimize a desired biotransformation.
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35
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Commault AS, Lear G, Weld RJ. Maintenance of Geobacter -dominated biofilms in microbial fuel cells treating synthetic wastewater. Bioelectrochemistry 2015; 106:150-8. [DOI: 10.1016/j.bioelechem.2015.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 04/19/2015] [Accepted: 04/22/2015] [Indexed: 11/24/2022]
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36
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Giaouris E, Heir E, Desvaux M, Hébraud M, Møretrø T, Langsrud S, Doulgeraki A, Nychas GJ, Kačániová M, Czaczyk K, Ölmez H, Simões M. Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens. Front Microbiol 2015; 6:841. [PMID: 26347727 PMCID: PMC4542319 DOI: 10.3389/fmicb.2015.00841] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/31/2015] [Indexed: 12/15/2022] Open
Abstract
A community-based sessile life style is the normal mode of growth and survival for many bacterial species. Under such conditions, cell-to-cell interactions are inevitable and ultimately lead to the establishment of dense, complex and highly structured biofilm populations encapsulated in a self-produced extracellular matrix and capable of coordinated and collective behavior. Remarkably, in food processing environments, a variety of different bacteria may attach to surfaces, survive, grow, and form biofilms. Salmonella enterica, Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus are important bacterial pathogens commonly implicated in outbreaks of foodborne diseases, while all are known to be able to create biofilms on both abiotic and biotic surfaces. Particularly challenging is the attempt to understand the complexity of inter-bacterial interactions that can be encountered in such unwanted consortia, such as competitive and cooperative ones, together with their impact on the final outcome of these communities (e.g., maturation, physiology, antimicrobial resistance, virulence, dispersal). In this review, up-to-date data on both the intra- and inter-species interactions encountered in biofilms of these pathogens are presented. A better understanding of these interactions, both at molecular and biophysical levels, could lead to novel intervention strategies for controlling pathogenic biofilm formation in food processing environments and thus improve food safety.
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Affiliation(s)
- Efstathios Giaouris
- Department of Food Science and Nutrition, Faculty of the Environment, University of the Aegean, Myrina, Lemnos Island, Greece
| | - Even Heir
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Mickaël Desvaux
- INRA, UR454 Microbiologie, Centre Auvergne-Rhône-Alpes, Saint-Genès-Champanelle, France
| | - Michel Hébraud
- INRA, UR454 Microbiologie, Centre Auvergne-Rhône-Alpes, Saint-Genès-Champanelle, France
| | - Trond Møretrø
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Solveig Langsrud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Agapi Doulgeraki
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Faculty of Foods, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - George-John Nychas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Faculty of Foods, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Miroslava Kačániová
- Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Katarzyna Czaczyk
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznań, Poland
| | - Hülya Ölmez
- TÜBİTAK Marmara Research Center, Food Institute, Gebze, Kocaeli, Turkey
| | - Manuel Simões
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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Oliveira NM, Martinez-Garcia E, Xavier J, Durham WM, Kolter R, Kim W, Foster KR. Biofilm Formation As a Response to Ecological Competition. PLoS Biol 2015; 13:e1002191. [PMID: 26158271 PMCID: PMC4497666 DOI: 10.1371/journal.pbio.1002191] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/29/2015] [Indexed: 12/28/2022] Open
Abstract
Bacteria form dense surface-associated communities known as biofilms that are central to their persistence and how they affect us. Biofilm formation is commonly viewed as a cooperative enterprise, where strains and species work together for a common goal. Here we explore an alternative model: biofilm formation is a response to ecological competition. We co-cultured a diverse collection of natural isolates of the opportunistic pathogen Pseudomonas aeruginosa and studied the effect on biofilm formation. We show that strain mixing reliably increases biofilm formation compared to unmixed conditions. Importantly, strain mixing leads to strong competition: one strain dominates and largely excludes the other from the biofilm. Furthermore, we show that pyocins, narrow-spectrum antibiotics made by other P. aeruginosa strains, can stimulate biofilm formation by increasing the attachment of cells. Side-by-side comparisons using microfluidic assays suggest that the increase in biofilm occurs due to a general response to cellular damage: a comparable biofilm response occurs for pyocins that disrupt membranes as for commercial antibiotics that damage DNA, inhibit protein synthesis or transcription. Our data show that bacteria increase biofilm formation in response to ecological competition that is detected by antibiotic stress. This is inconsistent with the idea that sub-lethal concentrations of antibiotics are cooperative signals that coordinate microbial communities, as is often concluded. Instead, our work is consistent with competition sensing where low-levels of antibiotics are used to detect and respond to the competing genotypes that produce them. Mixing natural isolates of the pathogenic bacterium Pseudomonas aeruginosa shows that the formation of biofilm is a response to antibiotic stress from competing genotypes. Bacteria often attach to each other and to surfaces and make biofilms. These dense communities occur everywhere, including on us and inside us, where they are central to both health and disease. Biofilm formation is often viewed as the coordinated action of multiple strains that work together in order to prosper and protect each other. In this study, we provide evidence for a very different view: biofilms are formed when bacterial strains compete with one another. We mixed together different strains of the widespread pathogen Pseudomonas aeruginosa and found that pairs often make bigger biofilms than either one alone. Rather than working together, however, we show that one strain normally kills the other off and that biofilm formation is actually a response to the damage of antibiotic warfare. Our work helps to explain the widespread observation that treating bacteria with clinical antibiotics can stimulate biofilm formation. When we treat bacteria, they respond as if the attack is coming from a foreign strain that must be outnumbered and outcompeted in a biofilm.
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Affiliation(s)
- Nuno M. Oliveira
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
| | - Esteban Martinez-Garcia
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Joao Xavier
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- Memorial Sloan-Kettering Cancer Center, Computational Biology Program, New York, New York, United States of America
| | | | - Roberto Kolter
- Harvard Medical School, Department of Microbiology and Immunobiology, Boston, Massachusetts, United States of America
| | - Wook Kim
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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Development of Spatial Distribution Patterns by Biofilm Cells. Appl Environ Microbiol 2015; 81:6120-8. [PMID: 26116674 DOI: 10.1128/aem.01614-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/19/2015] [Indexed: 01/14/2023] Open
Abstract
Confined spatial patterns of microbial distribution are prevalent in nature, such as in microbial mats, soil communities, and water stream biofilms. The symbiotic two-species consortium of Pseudomonas putida and Acinetobacter sp. strain C6, originally isolated from a creosote-polluted aquifer, has evolved a distinct spatial organization in the laboratory that is characterized by an increased fitness and productivity. In this consortium, P. putida is reliant on microcolonies formed by Acinetobacter sp. C6, to which it attaches. Here we describe the processes that lead to the microcolony pattern by Acinetobacter sp. C6. Ecological spatial pattern analyses revealed that the microcolonies were not entirely randomly distributed and instead were arranged in a uniform pattern. Detailed time-lapse confocal microscopy at the single-cell level demonstrated that the spatial pattern was the result of an intriguing self-organization: small multicellular clusters moved along the surface to fuse with one another to form microcolonies. This active distribution capability was dependent on environmental factors (carbon source and oxygen) and historical contingency (formation of phenotypic variants). The findings of this study are discussed in the context of species distribution patterns observed in macroecology, and we summarize observations about the processes involved in coadaptation between P. putida and Acinetobacter sp. C6. Our results contribute to an understanding of spatial species distribution patterns as they are observed in nature, as well as the ecology of engineered communities that have the potential for enhanced and sustainable bioprocessing capacity.
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Kürsten D, Möller F, Gross GA, Lenk C, Visaveliya N, Schüler T, Köhler JM. Identification of response classes from heavy metal‐tolerant soil microbial communities by highly resolved concentration‐dependent screenings in a microfluidic system. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Dana Kürsten
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Frances Möller
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Gregor Alexander Gross
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Claudia Lenk
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Nikunjkumar Visaveliya
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Tim Schüler
- TLDA Weimar Humboldtstr. 11 D‐99423 Weimar Germany
| | - Johann Michael Köhler
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
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NewIn VitroModel To Study the Effect of Human Simulated Antibiotic Concentrations on Bacterial Biofilms. Antimicrob Agents Chemother 2015; 59:4074-81. [DOI: 10.1128/aac.05037-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/20/2015] [Indexed: 11/20/2022] Open
Abstract
ABSTRACTA newin vitropharmacokinetic/pharmacodynamic simulator for bacterial biofilms utilizing flow cell technology and confocal laser scanning microscopy is described. The device has the ability to simulate the changing antibiotic concentrations in humans associated with intravenous dosing on bacterial biofilms grown under continuous culture conditions. The free drug concentrations of a single 2-g meropenem intravenous bolus dose and first-order elimination utilizing a half-life of 0.895 h (elimination rate constant, 0.776 h−1) were simulated. The antibacterial activity of meropenem against biofilms ofPseudomonas aeruginosaPAO1 and three clinical strains isolated from patients with cystic fibrosis was investigated. Additionally, the effect of meropenem on PAO1 biofilms cultured for 24 h versus that on biofilms cultured for 72 h was examined. Using confocal laser scanning microscopy, rapid biofilm killing was observed in the first hour of the dosing interval for all biofilms. However, for PAO1 biofilms cultured for 72 h, only bacterial subpopulations at the periphery of the biofilm were affected, with subpopulations at the substratum remaining viable, even at the conclusion of the dosing interval. The described model is a novel method to investigate antimicrobial killing of bacterial biofilms using human simulated concentrations.
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Quorum sensing-regulated chitin metabolism provides grazing resistance to Vibrio cholerae biofilms. ISME JOURNAL 2015; 9:1812-20. [PMID: 25615438 PMCID: PMC4511936 DOI: 10.1038/ismej.2014.265] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/08/2014] [Indexed: 12/28/2022]
Abstract
Association of Vibrio cholerae with chitinous surfaces of zooplankton is important for its persistence in marine environments, as it provides accessibility to nutrients and resistance to stresses. Predation by heterotrophic protists has a major impact on the survival of V. cholerae. V. cholerae forms biofilms as its main defensive strategy, and quorum sensing (QS) additionally regulates the production of antiprotozoal factors. The role of chitin and QS regulation in V. cholerae grazing resistance was investigated by exposing V. cholerae wild-type (WT) and QS mutant biofilms grown on chitin flakes to the bacteriotrophic, surface-feeding flagellate Rhynchomonas nasuta. V. cholerae formed more biofilm biomass on chitin flakes compared with nonchitinous surfaces. The growth of R. nasuta was inhibited by WT biofilms grown on chitin flakes, whereas the inhibition was attenuated in QS mutant biofilms. The chitin-dependent toxicity was also observed when the V. cholerae biofilms were developed under continuous flow or grown on a natural chitin source, the exoskeleton of Artemia. In addition, the antiprotozoal activity and ammonium concentration of V. cholerae biofilm supernatants were quantified. The ammonium levels (3.5 mM) detected in the supernatants of V. cholerae WT biofilms grown on chitin flakes were estimated to reduce the number of R. nasuta by >80% in add-back experiments, and the supernatant of QS mutant biofilms was less toxic owing to a decrease in ammonium production. Transcriptomic analysis revealed that the majority of genes involved in chitin metabolism and chemotaxis were significantly downregulated in QS mutant biofilms when grown on chitin compared with the WT biofilms.
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Brileya KA, Camilleri LB, Zane GM, Wall JD, Fields MW. Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy. Front Microbiol 2014; 5:693. [PMID: 25566209 PMCID: PMC4266047 DOI: 10.3389/fmicb.2014.00693] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/22/2014] [Indexed: 12/03/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) can interact syntrophically with other community members in the absence of sulfate, and interactions with hydrogen-consuming methanogens are beneficial when these archaea consume potentially inhibitory H2 produced by the SRB. A dual continuous culture approach was used to characterize population structure within a syntrophic biofilm formed by the SRB Desulfovibrio vulgaris Hildenborough and the methanogenic archaeum Methanococcus maripaludis. Under the tested conditions, monocultures of D. vulgaris formed thin, stable biofilms, but monoculture M. maripaludis did not. Microscopy of intact syntrophic biofilm confirmed that D. vulgaris formed a scaffold for the biofilm, while intermediate and steady-state images revealed that M. maripaludis joined the biofilm later, likely in response to H2 produced by the SRB. Close interactions in structured biofilm allowed efficient transfer of H2 to M. maripaludis, and H2 was only detected in cocultures with a mutant SRB that was deficient in biofilm formation (ΔpilA). M. maripaludis produced more carbohydrate (uronic acid, hexose, and pentose) as a monoculture compared to total coculture biofilm, and this suggested an altered carbon flux during syntrophy. The syntrophic biofilm was structured into ridges (∼300 × 50 μm) and models predicted lactate limitation at ∼50 μm biofilm depth. The biofilm had structure that likely facilitated mass transfer of H2 and lactate, yet maximized biomass with a more even population composition (number of each organism) when compared to the bulk-phase community. Total biomass protein was equivalent in lactate-limited and lactate-excess conditions when a biofilm was present, but in the absence of biofilm, total biomass protein was significantly reduced. The results suggest that multispecies biofilms create an environment conducive to resource sharing, resulting in increased biomass retention, or carrying capacity, for cooperative populations.
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Affiliation(s)
- Kristen A Brileya
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA ; Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | - Laura B Camilleri
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA ; Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | - Grant M Zane
- Division of Biochemistry, University of Missouri Columbia, MO, USA
| | - Judy D Wall
- Division of Biochemistry, University of Missouri Columbia, MO, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA ; Center for Biofilm Engineering, Montana State University Bozeman, MT, USA ; Thermal Biology Institute, Montana State University Bozeman, MT, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; National Center for Genome Resources Santa Fe, NM, USA
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Wilkins M, Hall-Stoodley L, Allan RN, Faust SN. New approaches to the treatment of biofilm-related infections. J Infect 2014; 69 Suppl 1:S47-52. [DOI: 10.1016/j.jinf.2014.07.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
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Jahid IK, Ha SD. The Paradox of Mixed-Species Biofilms in the Context of Food Safety. Compr Rev Food Sci Food Saf 2014. [DOI: 10.1111/1541-4337.12087] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iqbal Kabir Jahid
- School of Food Science and Technology; Chung-Ang Univ; 72-1 Nae-Ri, Daedeok-Myun Anseong-Si Gyeonggi-do 456-756 South Korea
- Dept. of Microbiology; Jessore Univ. of Science and Technology; Jessore-7408 Bangladesh
| | - Sang-Do Ha
- School of Food Science and Technology; Chung-Ang Univ; 72-1 Nae-Ri, Daedeok-Myun Anseong-Si Gyeonggi-do 456-756 South Korea
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Dispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles. Nat Commun 2014; 5:4462. [PMID: 25042103 DOI: 10.1038/ncomms5462] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/20/2014] [Indexed: 01/21/2023] Open
Abstract
Bacteria assume distinct lifestyles during the planktonic and biofilm modes of growth. Increased levels of the intracellular messenger c-di-GMP determine the transition from planktonic to biofilm growth, while a reduction causes biofilm dispersal. It is generally assumed that cells dispersed from biofilms immediately go into the planktonic growth phase. Here we use single-nucleotide resolution transcriptomic analysis to show that the physiology of dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells. In dispersed cells, the expression of the small regulatory RNAs RsmY and RsmZ is downregulated, whereas secretion genes are induced. Dispersed cells are highly virulent against macrophages and Caenorhabditis elegans compared with planktonic cells. In addition, they are highly sensitive towards iron stress, and the combination of a biofilm-dispersing agent, an iron chelator and tobramycin efficiently reduces the survival of the dispersed cells.
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Seth EC, Taga ME. Nutrient cross-feeding in the microbial world. Front Microbiol 2014; 5:350. [PMID: 25071756 PMCID: PMC4086397 DOI: 10.3389/fmicb.2014.00350] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/23/2014] [Indexed: 12/25/2022] Open
Abstract
The stability and function of a microbial community depends on nutritional interactions among community members such as the cross-feeding of essential small molecules synthesized by a subset of the population. In this review, we describe examples of microbe–microbe and microbe–host cofactor cross-feeding, a type of interaction that influences the forms of metabolism carried out within a community. Cofactor cross-feeding can contribute to both the health and nutrition of a host organism, the virulence and persistence of pathogens, and the composition and function of environmental communities. By examining the impact of shared cofactors on microbes from pure culture to natural communities, we stand to gain a better understanding of the interactions that link microbes together, which may ultimately be a key to developing strategies for manipulating microbial communities with human health, agricultural, and environmental implications.
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Affiliation(s)
- Erica C Seth
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
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Ren D, Madsen JS, Sørensen SJ, Burmølle M. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation. ISME JOURNAL 2014; 9:81-9. [PMID: 24936766 DOI: 10.1038/ismej.2014.96] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 05/08/2014] [Accepted: 05/10/2014] [Indexed: 01/11/2023]
Abstract
Biofilms that form on roots, litter and soil particles typically contain multiple bacterial species. Currently, little is known about multispecies biofilm interactions and few studies have been based on environmental isolates. Here, the prevalence of synergistic effects in biofilm formation among seven different soil isolates, cocultured in combinations of four species, was investigated. We observed greater biofilm biomass production in 63% of the four-species culture combinations tested than in biofilm formed by single-species cultures, demonstrating a high prevalence of synergism in multispecies biofilm formation. One four-species consortium, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, exhibited strong synergy in biofilm formation and was selected for further study. Of the four strains, X. retroflexus was the only one capable of forming abundant biofilm in isolation, under the in vitro conditions investigated. In accordance, strain-specific quantitative PCR revealed that X. retroflexus was predominant within the four-species consortium (>97% of total biofilm cell number). Despite low relative abundance of all the remaining strains, all were indispensable for the strong synergistic effect to occur within the four-species biofilm. Moreover, absolute individual strain cell numbers were significantly enhanced when compared with those of single-species biofilms, indicating that all the individual strains benefit from inclusion in the multispecies community. Our results show a high prevalence of synergy in biofilm formation in multispecies consortia isolated from a natural bacterial habitat and suggest that interspecific cooperation occurs.
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Affiliation(s)
- Dawei Ren
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas S Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Panova A, Dimkov R. Depth Distribution of Freshwater Microorganisms and Physicochemical Characteristics in Iskar Reservoir. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Growth of Myxococcus xanthus in continuous-flow-cell bioreactors as a method for studying development. Appl Environ Microbiol 2014; 80:2461-7. [PMID: 24509931 DOI: 10.1128/aem.03369-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nutrient sensors and developmental timers are two classes of genes vital to the establishment of early development in the social soil bacterium Myxococcus xanthus. The products of these genes trigger and regulate the earliest events that drive the colony from a vegetative state to aggregates, which ultimately leads to the formation of fruiting bodies and the cellular differentiation of the individual cells. In order to more accurately identify the genes and pathways involved in the initiation of this multicellular developmental program in M. xanthus, we adapted a method of growing vegetative populations within a constant controllable environment by using flow cell bioreactors, or flow cells. By establishing an M. xanthus community within a flow cell, we are able to test developmental responses to changes in the environment with fewer concerns for effects due to nutrient depletion or bacterial waste production. This approach allows for greater sensitivity in investigating communal environmental responses, such as nutrient sensing. To demonstrate the versatility of our growth environment, we carried out time-lapse confocal laser scanning microscopy to visualize M. xanthus biofilm growth and fruiting body development, as well as fluorescence staining of exopolysaccharides deposited by biofilms. We also employed the flow cells in a nutrient titration to determine the minimum concentration required to sustain vegetative growth. Our data show that by using a flow cell, M. xanthus can be held in a vegetative growth state at low nutrient concentrations for long periods, and then, by slightly decreasing the nutrient concentration, cells can be allowed to initiate the developmental program.
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In vitro activities of dermaseptins K4S4 and K4K20S4 against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa planktonic growth and biofilm formation. Antimicrob Agents Chemother 2014; 58:2221-8. [PMID: 24492362 DOI: 10.1128/aac.02142-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The rising number of infections caused by biofilm formation and the difficulties associated with their treatment by conventional antimicrobial therapies have led to an intensive search for novel antibiofilm agents. Dermaseptins are antimicrobial peptides with a number of attractive properties that might offer alternative therapies against resistant microorganisms. In this study, we synthesized a set of dermaseptin-derived peptides and evaluated their activities against Gram-positive and Gram-negative bacterial biofilm formation. All dermaseptin-derived peptides demonstrated concentration-dependent antibiofilm activities at microgram concentrations, and their activities were dependent on the nature of the peptides, with the highest levels of activity being exhibited by highly charged molecules. Fluorescent binding and confocal microscopy demonstrated that dermaseptin K4S4, a substituted derivative of the native molecule S4, significantly decreased the viability of planktonic and surface-attached bacteria and stopped biofilm formation under dynamic flow conditions. Cytotoxicity assays with HeLa cells showed that some of the tested peptides were less cytotoxic than current antibiotics. Overall, these findings indicate that dermaseptin derivatives might constitute new lead structures for the development of potent antibiofilm agents.
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