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Huang Y, Mukherjee A, Schink S, Benites NC, Basan M. Evolution and stability of complex microbial communities driven by trade-offs. Mol Syst Biol 2024:10.1038/s44320-024-00051-8. [PMID: 38961275 DOI: 10.1038/s44320-024-00051-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024] Open
Abstract
Microbial communities are ubiquitous in nature and play an important role in ecology and human health. Cross-feeding is thought to be core to microbial communities, though it remains unclear precisely why it emerges. Why have multi-species microbial communities evolved in many contexts and what protects microbial consortia from invasion? Here, we review recent insights into the emergence and stability of coexistence in microbial communities. A particular focus is the long-term evolutionary stability of coexistence, as observed for microbial communities that spontaneously evolved in the E. coli long-term evolution experiment (LTEE). We analyze these findings in the context of recent work on trade-offs between competing microbial objectives, which can constitute a mechanistic basis for the emergence of coexistence. Coexisting communities, rather than monocultures of the 'fittest' single strain, can form stable endpoints of evolutionary trajectories. Hence, the emergence of coexistence might be an obligatory outcome in the evolution of microbial communities. This implies that rather than embodying fragile metastable configurations, some microbial communities can constitute formidable ecosystems that are difficult to disrupt.
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Affiliation(s)
- Yanqing Huang
- Harvard Medical School, Department of Systems Biology, Boston, USA
| | - Avik Mukherjee
- Harvard Medical School, Department of Systems Biology, Boston, USA
| | - Severin Schink
- Harvard Medical School, Department of Systems Biology, Boston, USA
| | | | - Markus Basan
- Harvard Medical School, Department of Systems Biology, Boston, USA.
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2
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Houpt NSB, Kassen R. On the De Novo Emergence of Ecological Interactions during Evolutionary Diversification: A Conceptual Framework and Experimental Test. Am Nat 2023; 202:800-817. [PMID: 38033179 DOI: 10.1086/726895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractEcological interactions are crucial to the structure and function of biological communities, but we lack a causal understanding of the forces shaping their emergence during evolutionary diversification. Here we provide a conceptual framework linking different modes of diversification (e.g., ecological diversification), which depend on environmental characteristics, to the evolution of different forms of ecological interactions (e.g., resource partitioning) in asexual lineages. We tested the framework by examining the net interactions in communities of Pseudomonas aeruginosa produced via experimental evolution in nutritionally simple (SIM) or complex (COM) environments by contrasting the productivity and competitive fitness of whole evolved communities relative to their component isolates. As expected, we found that nutritional complexity drove the evolution of communities with net positive interactions whereas SIM communities had similar performance as their component isolates. A follow-up experiment revealed that high fitness in two COM communities was driven by rare variants (frequency <0.1%) that antagonized PA14, the ancestral strain and common competitor used in fitness assays. Our study suggests that the evolution of de novo ecological interactions in asexual lineages is predictable at a broad scale from environmental conditions. Further, our work demonstrates that rare variants can disproportionately impact the function of relatively simple microbial communities.
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3
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Svet L, Parijs I, Isphording S, Lories B, Marchal K, Steenackers HP. Competitive interactions facilitate resistance development against antimicrobials. Appl Environ Microbiol 2023; 89:e0115523. [PMID: 37819078 PMCID: PMC10617502 DOI: 10.1128/aem.01155-23] [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: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 10/13/2023] Open
Abstract
While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.
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Affiliation(s)
- Luka Svet
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Simon Isphording
- Department of Plant Biotechnology and Bioinformatics, Data Integration and Biological Networks, UGent, Technologiepark 15, Gent, Belgium
| | - Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Data Integration and Biological Networks, UGent, Technologiepark 15, Gent, Belgium
| | - Hans P. Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
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4
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Kovács ÁT. Colony morphotype diversification as a signature of bacterial evolution. MICROLIFE 2023; 4:uqad041. [PMID: 37901115 PMCID: PMC10608940 DOI: 10.1093/femsml/uqad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/31/2023]
Abstract
The appearance of colony morphotypes is a signature of genetic diversification in evolving bacterial populations. Colony structure highly depends on the cell-cell interactions and polymer production that are adjusted during evolution in an environment that allows the development of spatial structures. Nucci and colleagues describe the emergence of a rough and dry morphotype of a noncapsulated Klebsiella variicola strain during a laboratory evolution study, resembling genetic changes observed in clinical isolates.
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Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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5
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Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [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: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
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Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
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Fitzgerald BA, Wadud A, Slimak Z, Slonczewski JL. Enterococcus faecalis OG1RF Evolution at Low pH Selects Fusidate-Sensitive Mutants in Elongation Factor G and at High pH Selects Defects in Phosphate Transport. Appl Environ Microbiol 2023; 89:e0046623. [PMID: 37272807 PMCID: PMC10304957 DOI: 10.1128/aem.00466-23] [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: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Enterococcus bacteria inhabit human and soil environments that show a wide range of pH values. Strains include commensals as well as antibiotic-resistant pathogens. We investigated the adaptation to pH stress in E. faecalis OG1RF by conducting experimental evolution under acidic (pH 4.8), neutral pH (pH 7.0), and basic (pH 9.0) conditions. A serial planktonic culture was performed for 500 generations and in a high-pH biofilm culture for 4 serial bead transfers. Nearly all of the mutations led to nonsynonomous codons, indicating adaptive selection. All of the acid-adapted clones from the planktonic culture showed a mutation in fusA (encoding elongation factor G). The acid-adapted fusA mutants had a trade-off of decreased resistance to fusidic acid (fusidate). All of the base-adapted clones from the planktonic cultures as well as some from the biofilm-adapted cultures showed mutations that affected the Pst phosphate ABC transporter (pstA, pstB, pstB2, pstC) and pyrR (pyrimidine biosynthesis regulator/uracil phosphoribosyltransferase). The biofilm cultures produced small-size colonies on brain heart infusion agar. These variants each contained a single mutation in pstB2, pstC, or pyrR. The pst and pyrR mutants outgrew the ancestral strain at pH 9.2, with a trade-off of lower growth at pH 4.8. Additional genes that had a mutation in multiple clones that evolved at high pH (but not at low pH) include opp1BCDF (oligopeptide ABC transporter), ccpA (catabolite control protein A), and ftsZ (septation protein). Overall, the experimental evolution of E. faecalis showed a strong pH dependence, favoring the fusidate-sensitive elongation factor G modification at low pH and the loss of phosphate transport genes at high pH. IMPORTANCE E. faecalis bacteria are found in dental biofilms, where they experience low pH as a result of fermentative metabolism. Thus, the effect of pH on antibiotic resistance has clinical importance. The loss of fusidate resistance is notable for OG1RF strains in which fusidate resistance is assumed to be a stable genetic marker. In endodontal infections, enterococci can resist calcium hydroxide therapy that generates extremely high pH values. In other environments, such as the soil and plant rhizosphere, enterococci experience acidification that is associated with climate change. Thus, the pH modulation of natural selection in enterococci is important for human health as well as for understanding soil environments.
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Affiliation(s)
| | - Ayman Wadud
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Zachary Slimak
- Department of Biology, Kenyon College, Gambier, Ohio, USA
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7
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Usui M, Yoshii Y, Thiriet-Rupert S, Ghigo JM, Beloin C. Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance. Commun Biol 2023; 6:275. [PMID: 36928386 PMCID: PMC10020551 DOI: 10.1038/s42003-023-04601-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial antibiotic resistance is a global health concern of increasing importance and intensive study. Although biofilms are a common source of infections in clinical settings, little is known about the development of antibiotic resistance within biofilms. Here, we use experimental evolution to compare selection of resistance mutations in planktonic and biofilm Escherichia coli populations exposed to clinically relevant cycles of lethal treatment with the aminoglycoside amikacin. Consistently, mutations in sbmA, encoding an inner membrane peptide transporter, and fusA, encoding the essential elongation factor G, are rapidly selected in biofilms, but not in planktonic cells. This is due to a combination of enhanced mutation rate, increased adhesion capacity and protective biofilm-associated tolerance. These results show that the biofilm environment favors rapid evolution of resistance and provide new insights into the dynamic evolution of antibiotic resistance in biofilms.
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Affiliation(s)
- Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan.
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Stanislas Thiriet-Rupert
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
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8
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Biofilms preserve the transmissibility of a multi-drug resistance plasmid. NPJ Biofilms Microbiomes 2022; 8:95. [PMID: 36481746 PMCID: PMC9732292 DOI: 10.1038/s41522-022-00357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolved Acinetobacter baumannii with an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection, biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations, plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizontal transfer of plasmids. In contrast, in biofilms, most plasmids retained their transfer genes, but on average, plasmid, persistence improved less over time. Our results showed that biofilms can act as refugia of MDR plasmids and favor the horizontal mode of plasmid transfer, which has important implications for the spread of MDR.
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9
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Biofilm antimicrobial susceptibility through an experimental evolutionary lens. NPJ Biofilms Microbiomes 2022; 8:82. [PMID: 36257971 PMCID: PMC9579162 DOI: 10.1038/s41522-022-00346-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
Experimental evolution experiments in which bacterial populations are repeatedly exposed to an antimicrobial treatment, and examination of the genotype and phenotype of the resulting evolved bacteria, can help shed light on mechanisms behind reduced susceptibility. In this review we present an overview of why it is important to include biofilms in experimental evolution, which approaches are available to study experimental evolution in biofilms and what experimental evolution has taught us about tolerance and resistance in biofilms. Finally, we present an emerging consensus view on biofilm antimicrobial susceptibility supported by data obtained during experimental evolution studies.
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10
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Tang PC, Eriksson O, Sjögren J, Fatsis-Kavalopoulos N, Kreuger J, Andersson DI. A Microfluidic Chip for Studies of the Dynamics of Antibiotic Resistance Selection in Bacterial Biofilms. Front Cell Infect Microbiol 2022; 12:896149. [PMID: 35619647 PMCID: PMC9128571 DOI: 10.3389/fcimb.2022.896149] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023] Open
Abstract
Biofilms are arguably the most important mode of growth of bacteria, but how antibiotic resistance emerges and is selected in biofilms remains poorly understood. Several models to study evolution of antibiotic resistance have been developed, however, their usability varies depending on the nature of the biological question. Here, we developed and validated a microfluidic chip (Brimor) for studying the dynamics of enrichment of antibiotic-resistant bacteria in biofilms using real-time monitoring with confocal microscopy. In situ extracellular cellulose staining and physical disruption of the biomass confirmed Escherichia coli growth as biofilms in the chip. We showed that seven generations of growth occur in 16 h when biofilms were established in the growth chambers of Brimor, and that bacterial death and growth rates could be estimated under these conditions using a plasmid with a conditional replication origin. Additionally, competition experiments between antibiotic-susceptible and -resistant bacteria at sub-inhibitory concentrations demonstrated that the antibiotic ciprofloxacin selected for antibiotic resistance in bacterial biofilms at concentrations 17-fold below the minimal inhibitory concentration of susceptible planktonic bacteria. Overall, the microfluidic chip is easy to use and a relevant model for studying the dynamics of selection of antibiotic resistance in bacterial biofilms and we anticipate that the Brimor chip will facilitate basic research in this area.
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Affiliation(s)
- Po-Cheng Tang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Olle Eriksson
- U-Print, Uppsala University 3D-Printing Facility, Uppsala University, Uppsala, Sweden
| | | | | | - Johan Kreuger
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
- *Correspondence: Dan I. Andersson, ; Johan Kreuger,
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- *Correspondence: Dan I. Andersson, ; Johan Kreuger,
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11
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Lin Y, Xu X, Maróti G, Strube ML, Kovács ÁT. Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes. NPJ Biofilms Microbiomes 2022; 8:27. [PMID: 35418164 PMCID: PMC9007996 DOI: 10.1038/s41522-022-00292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/19/2022] [Indexed: 11/12/2022] Open
Abstract
Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.
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Affiliation(s)
- Yicen Lin
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
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12
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Harris KB, Flynn KM, Cooper VS. Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations. Mol Biol Evol 2021; 38:5359-5375. [PMID: 34410431 PMCID: PMC8662654 DOI: 10.1093/molbev/msab248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How biodiversity arises and can be maintained in asexual microbial populations growing on a single resource remains unclear. Many models presume that beneficial genotypes will outgrow others and purge variation via selective sweeps. Environmental structure like that found in biofilms, which are associated with persistence during infection and other stressful conditions, may oppose this process and preserve variation. We tested this hypothesis by evolving Pseudomonas aeruginosa populations in biofilm-promoting arginine media for 3 months, using both a bead model of the biofilm life cycle and planktonic serial transfer. Surprisingly, adaptation and diversification were mostly uninterrupted by fixation events that eliminate diversity, with hundreds of mutations maintained at intermediate frequencies. The exceptions included genotypes with mutator alleles that also accelerated genetic diversification. Despite the rarity of hard sweeps, a remarkable 40 genes acquired parallel mutations in both treatments and often among competing genotypes within a population. These incomplete soft sweeps include several transporters (including pitA, pntB, nosD, and pchF) suggesting adaptation to the growth media that becomes highly alkaline during growth. Further, genes involved in signal transduction (including gacS, aer2, bdlA, and PA14_71750) reflect likely adaptations to biofilm-inducing conditions. Contrary to evolution experiments that select mutations in a few genes, these results suggest that some environments may expose a larger fraction of the genome and select for many adaptations at once. Thus, even growth on a sole carbon source can lead to persistent genetic and phenotypic variation despite strong selection that would normally purge diversity.
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Affiliation(s)
- Katrina B Harris
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kenneth M Flynn
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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13
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Tofalo R, Battistelli N, Perpetuini G, Valbonetti L, Rossetti AP, Perla C, Zulli C, Arfelli G. Oenococcus oeni Lifestyle Modulates Wine Volatilome and Malolactic Fermentation Outcome. Front Microbiol 2021; 12:736789. [PMID: 34650537 PMCID: PMC8506162 DOI: 10.3389/fmicb.2021.736789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022] Open
Abstract
In this study, nine Oenococcus oeni strains were tested for their ability to adhere to polystyrene using mMRS and wine as culture media. Moreover, planktonic and biofilm-detached cells were investigated for their influence on malic acid degradation kinetics and aroma compound production. Three strains were able to adhere on polystyrene plates in a strain-dependent way. In particular, MALOBACT-T1 and ISO359 strains mainly grew as planktonic cells, while the ISO360 strain was found prevalent in sessile state. The strain-dependent adhesion ability was confirmed by confocal laser scanning microscopy. Planktonic and biofilm detached cells showed a different metabolism. In fact, biofilm-detached cells had a better malic acid degradation kinetic and influenced the aroma composition of resulting wines, acting on the final concentration of esters, higher alcohols, and organic acids. Oenococcus oeni in biofilm lifestyle seems to be a suitable tool to improve malolactic fermentation outcome, and to contribute to wine aroma. The industrial-scale application of this strategy should be implemented to develop novel wine styles.
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Affiliation(s)
- Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Noemi Battistelli
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Giorgia Perpetuini
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Luca Valbonetti
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Alessio Pio Rossetti
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Carlo Perla
- Dalton Biotecnologie s.r.l., Spoltore, Italy
| | | | - Giuseppe Arfelli
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
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14
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Gryndler M, Gryndlerová H, Hujslová M, Bystrianský L, Malinská H, Šimsa D, Hršelová H. In vitro Evaluation of Biofilm Biomass Dynamics. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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González AS, Riego A, Vega V, García J, Galié S, Gutiérrez del Río I, Martínez de Yuso MDV, Villar CJ, Lombó F, De la Prida VM. Functional Antimicrobial Surface Coatings Deposited onto Nanostructured 316L Food-Grade Stainless Steel. NANOMATERIALS 2021; 11:nano11041055. [PMID: 33924070 PMCID: PMC8074267 DOI: 10.3390/nano11041055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/26/2022]
Abstract
In our study, we demonstrated the performance of antimicrobial coatings on properly functionalized and nanostructured 316L food-grade stainless steel pipelines. For the fabrication of these functional coatings, we employed facile and low-cost electrochemical techniques and surface modification processes. The development of a nanoporous structure on the 316L stainless steel surface was performed by following an electropolishing process in an electrolytic bath, at a constant anodic voltage of 40 V for 10 min, while the temperature was maintained between 0 and 10 °C. Subsequently, we incorporated on this nanostructure additional coatings with antimicrobial and bactericide properties, such as Ag nanoparticles, Ag films, or TiO2 thin layers. These functional coatings were grown on the nanostructured substrate by following electroless process, electrochemical deposition, and atomic layer deposition (ALD) techniques. Then, we analyzed the antimicrobial efficiency of these functionalized materials against different biofilms types (Candida parapsilosis, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis). The results of the present study demonstrate that the nanostructuring and surface functionalization processes constitute a promising route to fabricate novel functional materials exhibiting highly efficient antimicrobial features. In fact, we have shown that our use of an appropriated association of TiO2 layer and Ag nanoparticle coatings over the nanostructured 316L stainless steel exhibited an excellent antimicrobial behavior for all biofilms examined.
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Affiliation(s)
- A. Silvia González
- Departmano de Física, Facultad de Ciencias, Universidad de Oviedo, C/ Federico García Lorca nº 18, 33007 Oviedo, Spain; (V.V.); (J.G.); (V.M.D.l.P.)
- Correspondence:
| | - Angela Riego
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds—BIONUC”, Departmano de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Avda. Julián Clavería 7, 33006 Oviedo, Spain; (A.R.); (S.G.); (I.G.d.R.); (C.J.V.); (F.L.)
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33011 Oviedo, Spain
| | - Victor Vega
- Departmano de Física, Facultad de Ciencias, Universidad de Oviedo, C/ Federico García Lorca nº 18, 33007 Oviedo, Spain; (V.V.); (J.G.); (V.M.D.l.P.)
- Laboratorio de Membranas Nanoporosas, Edificio de Servicios Científico Técnicos “Severo Ochoa”, Universidad de Oviedo, C/ Fernando Bonguera s/n, 33006 Oviedo, Spain
| | - Javier García
- Departmano de Física, Facultad de Ciencias, Universidad de Oviedo, C/ Federico García Lorca nº 18, 33007 Oviedo, Spain; (V.V.); (J.G.); (V.M.D.l.P.)
| | - Serena Galié
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds—BIONUC”, Departmano de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Avda. Julián Clavería 7, 33006 Oviedo, Spain; (A.R.); (S.G.); (I.G.d.R.); (C.J.V.); (F.L.)
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33011 Oviedo, Spain
| | - Ignacio Gutiérrez del Río
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds—BIONUC”, Departmano de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Avda. Julián Clavería 7, 33006 Oviedo, Spain; (A.R.); (S.G.); (I.G.d.R.); (C.J.V.); (F.L.)
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33011 Oviedo, Spain
| | | | - Claudio Jesús Villar
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds—BIONUC”, Departmano de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Avda. Julián Clavería 7, 33006 Oviedo, Spain; (A.R.); (S.G.); (I.G.d.R.); (C.J.V.); (F.L.)
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33011 Oviedo, Spain
| | - Felipe Lombó
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds—BIONUC”, Departmano de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Avda. Julián Clavería 7, 33006 Oviedo, Spain; (A.R.); (S.G.); (I.G.d.R.); (C.J.V.); (F.L.)
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33011 Oviedo, Spain
| | - Victor Manuel De la Prida
- Departmano de Física, Facultad de Ciencias, Universidad de Oviedo, C/ Federico García Lorca nº 18, 33007 Oviedo, Spain; (V.V.); (J.G.); (V.M.D.l.P.)
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16
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Stalder T, Cornwell B, Lacroix J, Kohler B, Dixon S, Yano H, Kerr B, Forney LJ, Top EM. Evolving Populations in Biofilms Contain More Persistent Plasmids. Mol Biol Evol 2021; 37:1563-1576. [PMID: 32027370 PMCID: PMC7253198 DOI: 10.1093/molbev/msaa024] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid–bacteria coevolution is solely based on studies done in well-mixed liquid cultures, even though biofilms represent the main way of bacterial life on Earth and are responsible for most infections. The spatial structure and the heterogeneity provided by biofilms are known to lead to increased genetic diversity as compared with well-mixed liquids. Therefore, we expect that growth in this complex environment could affect the evolutionary trajectories of plasmid–host dyads. We experimentally evolved Shewanella oneidensis MR-1 with plasmid pBP136Gm in biofilms and chemostats and sequenced the genomes of clones and populations. Biofilm populations not only maintained a higher diversity of mutations than chemostat populations but contained a few clones with markedly more persistent plasmids that evolved via multiple distinct trajectories. These included the acquisition of a putative toxin–antitoxin transposon by the plasmid and chromosomal mutations. Some of these genetic changes resulted in loss of plasmid transferability or decrease in plasmid cost. Growth in chemostats led to a higher proportion of variants with decreased plasmid persistence, a phenomenon not detected in biofilms. We suggest that the presence of more stable plasmid–host dyads in biofilms reflects higher genetic diversity and possibly unknown selection pressures. Overall, this study underscores the importance of the mode of growth in the evolution of antibiotic-resistant bacteria.
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Affiliation(s)
- Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.,BEACON Center for the Study of Evolution in Action
| | - Brandon Cornwell
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Jared Lacroix
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Bethel Kohler
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Seth Dixon
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ben Kerr
- BEACON Center for the Study of Evolution in Action.,Department of Biology, University of Washington, Seattle, WA
| | - Larry J Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.,BEACON Center for the Study of Evolution in Action.,Department of Biology, University of Washington, Seattle, WA
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17
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Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs. NPJ Biofilms Microbiomes 2021; 7:3. [PMID: 33431848 PMCID: PMC7801651 DOI: 10.1038/s41522-020-00178-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Most bacteria in nature exist in biofilms, which are inherently tolerant to antibiotics. There is currently very limited understanding of how biofilms evolve in response to sub-lethal concentrations of antimicrobials. In this study, we use a biofilm evolution model to study the effects of sub-inhibitory concentrations of three antibiotics on Salmonella Typhimurium biofilms. We show that biofilms rapidly evolve resistance to each antibiotic they are exposed to, demonstrating a strong selective pressure on biofilms from low antibiotic concentrations. While all antibiotics tested select for clinical resistance, there is no common mechanism. Adaptation to antimicrobials, however, has a marked cost for other clinically important phenotypes, including biofilm formation and virulence. Cefotaxime selects mutants with the greatest deficit in biofilm formation followed by azithromycin and then ciprofloxacin. Understanding the impacts of exposure of biofilms to antibiotics will help understand evolutionary trajectories and may help guide how best to use antibiotics in a biofilm context. Experimental evolution in combination with whole-genome sequencing is a powerful tool for the prediction of evolution trajectories associated with antibiotic resistance in biofilms.
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18
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Connolly JPR, Roe AJ, O'Boyle N. Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria. Crit Rev Microbiol 2020; 47:126-140. [PMID: 33332206 DOI: 10.1080/1040841x.2020.1854172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
While evolution proceeds through the generation of random variant alleles, the application of selective pressures can select for subsets of mutations that confer fitness-improving physiological benefits. This, in essence, defines the process of adaptive evolution. The rapid replication rate of bacteria has allowed for the design of experiments to study these processes over a reasonable timeframe within a laboratory setting. This has been greatly assisted by advances in tractability of diverse microorganisms, next generation sequencing technologies and bioinformatic analysis pipelines. Examining the processes by which organisms adapt their genetic code to cope with sub-optimal growth conditions has yielded a wealth of molecular insight into diverse biological processes. Here we discuss how the study of adaptive evolutionary trajectories in bacteria has allowed for improved understanding of stress responses, revealed important insight into microbial physiology, allowed for the production of highly optimised strains for use in biotechnology and increased our knowledge of the role of genomic plasticity in chronic infections.
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Affiliation(s)
- James P R Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Nicky O'Boyle
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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19
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Kwak GY, Goo E, Jeong H, Hwang I. Adverse effects of adaptive mutation to survive static culture conditions on successful fitness of the rice pathogen Burkholderia glumae in a host. PLoS One 2020; 15:e0238151. [PMID: 32833990 PMCID: PMC7444824 DOI: 10.1371/journal.pone.0238151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria often possess relatively flexible genome structures and adaptive genetic variants that allow survival in unfavorable growth conditions. Bacterial survival tactics in disadvantageous microenvironments include mutations that are beneficial against threats in their niche. Here, we report that the aerobic rice bacterial pathogen Burkholderia glumae BGR1 changes a specific gene for improved survival in static culture conditions. Static culture triggered formation of colony variants with deletions or point mutations in the gene bspP (BGLU_RS28885), which putatively encodes a protein that contains PDC2, PAS-9, SpoIIE, and HATPase domains. The null mutant of bspP survived longer in static culture conditions and produced a higher level of bis-(3'-5')-cyclic dimeric guanosine monophosphate than the wild type. Expression of the bacterial cellulose synthase regulator (bcsB) gene was upregulated in the mutant, consistent with the observation that the mutant formed pellicles faster than the wild type. Mature pellicle formation was observed in the bspP mutant before pellicle formation in wild-type BGR1. However, the population density of the bspP null mutant decreased substantially when grown in Luria-Bertani medium with vigorous agitation due to failure of oxalate-mediated detoxification of the alkaline environment. The bspP null mutant was less virulent and exhibited less effective colonization of rice plants than the wild type. All phenotypes caused by mutations in bspP were recovered to those of the wild type by genetic complementation. Thus, although wild-type B. glumae BGR1 prolonged viability by spontaneous mutation under static culture conditions, such genetic changes negatively affected colonization in rice plants. These results suggest that adaptive gene sacrifice of B. glumae to survive unfavorable growth conditions is not always desirable as it can adversely affect adaptability in the host.
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Affiliation(s)
- Gi-Young Kwak
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Haeyoon Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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20
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Oleskin AV, Shenderov BA. Probiotics and Psychobiotics: the Role of Microbial Neurochemicals. Probiotics Antimicrob Proteins 2020; 11:1071-1085. [PMID: 31493127 DOI: 10.1007/s12602-019-09583-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In light of recent data, microorganisms should be construed as organisms that are capable of communication and collective behaviors. Microbial communication signals are involved both in interactions among microbial cells within microbial social systems, including the human body-inhabiting microconsortium, and the dialog between the microbiota and the host organism. The microbiota inhabits various niches of the host organism, especially the gastrointestinal (GI) tract. Microorganisms release diverse signal molecules and, in addition, specifically respond to host signals. This enables them to constantly interact with the nervous system including the brain and the immune system of the host organism. Evolutionarily conserved signals that are involved in the communication between microbiota and the host include neuroactive substances (neurochemicals) such as peptides, amino acids, biogenic amines, short-chain fatty acids, and gaseous substances. This ongoing dialog may either stabilize the host's physical and mental health state or, alternatively, cause serious health problems. Attempts are made to correct imbalances in the brain-gut-microbiota axis with probiotics including their subgroup called psychobiotics that release neuroactive substances directly influencing the human brain, psyche, and behavior. A number of recent review works address the microbiota-host system and its communication signals. Some of the publications focus on the involvement of neurochemicals in the bidirectional communication within the host-microbiota system. However, this work concentrates on the impact of bacterial cell components, metabolites, and signal molecules as promising alternatives to the currently widespread probiotics that have both advantages and disadvantages. Such biologically active agents of microbial origin are referred to as postbiotics or, alternatively, metabiotics (the term preferred in this work).
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Affiliation(s)
- Alexander V Oleskin
- General Ecology Department, School of Biology, Moscow State University, Vorobiev Hills, Moscow, Russia, 119991.
| | - Boris A Shenderov
- Laboratory of Bacteriology and Parasitology, Centre for Strategic Planning, Russian Ministry of Health; Moscow, Research Laboratory for Design & Implementation of Personalized Nutrition-Related Products & Diets, K. G. Razumovsky University of Technology & Management, Moscow, Russia
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21
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Bridier A, Piard JC, Briandet R, Bouchez T. Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms. MICROBIAL ECOLOGY 2020; 80:47-59. [PMID: 31844910 DOI: 10.1007/s00248-019-01470-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bacterial interactions in the diversification process. On the basis of colony morphology, three variants of P. putida KT2440 were obtained from co-culture after 168 h of growth whereas no variant was identified from the axenic KT2440 biofilm. The variants exhibited distinct phenotypes and produced biofilms with specific architecture in comparison with the ancestor. The variants better competed with the P. putida PCL1480 strain in the dual-strain biofilms after 24 h of co-culture in comparison with the ancestor. Moreover, the synergistic interaction of KT2440 ancestor and the variants led to an improved biofilm production and to higher competitive ability versus the PCL1480 strain, highlighting the key role of diversification in the adaptation of P. putida KT2440 in the mixed community. Whole genome sequencing revealed mutations in polysaccharides biosynthesis protein, membrane transporter, or lipoprotein signal peptidase genes in variants.
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Affiliation(s)
- Arnaud Bridier
- ANSES, Fougères Laboratory, AB2R, 10B rue Claude Bourgelat, 35300, Fougères, France.
- IRSTEA, UR PROSE, 1 rue Pierre-Gilles de Gennes, 92761, Antony Cedex, France.
| | - J C Piard
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - R Briandet
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - T Bouchez
- IRSTEA, UR PROSE, 1 rue Pierre-Gilles de Gennes, 92761, Antony Cedex, France
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22
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Niccum BA, Kastman EK, Kfoury N, Robbat A, Wolfe BE. Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function. mSystems 2020; 5:e00149-20. [PMID: 32546667 PMCID: PMC7300356 DOI: 10.1128/msystems.00149-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury).IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.
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Affiliation(s)
- Brittany A Niccum
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Erik K Kastman
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Nicole Kfoury
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Albert Robbat
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, Massachusetts, USA
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23
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Martin M, Dragoš A, Otto SB, Schäfer D, Brix S, Maróti G, Kovács ÁT. Cheaters shape the evolution of phenotypic heterogeneity in Bacillus subtilis biofilms. ISME JOURNAL 2020; 14:2302-2312. [PMID: 32483306 PMCID: PMC7608354 DOI: 10.1038/s41396-020-0685-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023]
Abstract
Biofilms are closely packed cells held and shielded by extracellular matrix composed of structural proteins and exopolysaccharides (EPS). As matrix components are costly to produce and shared within the population, EPS-deficient cells can act as cheaters by gaining benefits from the cooperative nature of EPS producers. Remarkably, genetically programmed EPS producers can also exhibit phenotypic heterogeneity at single-cell level. Previous studies have shown that spatial structure of biofilms limits the spread of cheaters, but the long-term influence of cheating on biofilm evolution is not well understood. Here, we examine the influence of EPS nonproducers on evolution of matrix production within the populations of EPS producers in a model biofilm-forming bacterium, Bacillus subtilis. We discovered that general adaptation to biofilm lifestyle leads to an increase in phenotypical heterogeneity of eps expression. However, prolonged exposure to EPS-deficient cheaters may result in different adaptive strategy, where eps expression increases uniformly within the population. We propose a molecular mechanism behind such adaptive strategy and demonstrate how it can benefit the EPS producers in the presence of cheaters. This study provides additional insights on how biofilms adapt and respond to stress caused by exploitation in long-term scenario.
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Affiliation(s)
- Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Simon B Otto
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel Schäfer
- Terrestrial Biofilms Group, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Susanne Brix
- Disease Systems Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark. .,Terrestrial Biofilms Group, Friedrich Schiller University Jena, 07743, Jena, Germany.
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24
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Dean Z, Maltas J, Wood KB. Antibiotic interactions shape short-term evolution of resistance in E. faecalis. PLoS Pathog 2020; 16:e1008278. [PMID: 32119717 PMCID: PMC7093004 DOI: 10.1371/journal.ppat.1008278] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 03/24/2020] [Accepted: 12/11/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic combinations are increasingly used to combat bacterial infections. Multidrug therapies are a particularly important treatment option for E. faecalis, an opportunistic pathogen that contributes to high-inoculum infections such as infective endocarditis. While numerous synergistic drug combinations for E. faecalis have been identified, much less is known about how different combinations impact the rate of resistance evolution. In this work, we use high-throughput laboratory evolution experiments to quantify adaptation in growth rate and drug resistance of E. faecalis exposed to drug combinations exhibiting different classes of interactions, ranging from synergistic to suppressive. We identify a wide range of evolutionary behavior, including both increased and decreased rates of growth adaptation, depending on the specific interplay between drug interaction and drug resistance profiles. For example, selection in a dual β-lactam combination leads to accelerated growth adaptation compared to selection with the individual drugs, even though the resulting resistance profiles are nearly identical. On the other hand, populations evolved in an aminoglycoside and β-lactam combination exhibit decreased growth adaptation and resistant profiles that depend on the specific drug concentrations. We show that the main qualitative features of these evolutionary trajectories can be explained by simple rescaling arguments that correspond to geometric transformations of the two-drug growth response surfaces measured in ancestral cells. The analysis also reveals multiple examples where resistance profiles selected by drug combinations are nearly growth-optimized along a contour connecting profiles selected by the component drugs. Our results highlight trade-offs between drug interactions and resistance profiles during the evolution of multi-drug resistance and emphasize evolutionary benefits and disadvantages of particular drug pairs targeting enterococci.
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Affiliation(s)
- Ziah Dean
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
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25
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Eberly AR, Beebout CJ, Carmen Tong CM, Van Horn GT, Green HD, Fitzgerald MJ, De S, Apple EK, Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA, Clayton DB, Stratton CW, Schmitz JE, Hadjifrangiskou M. Defining a Molecular Signature for Uropathogenic versus Urocolonizing Escherichia coli: The Status of the Field and New Clinical Opportunities. J Mol Biol 2019; 432:786-804. [PMID: 31794727 DOI: 10.1016/j.jmb.2019.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 01/05/2023]
Abstract
Urinary tract infections (UTIs) represent a major burden across the population, although key facets of their pathophysiology and host interaction remain unclear. Escherichia coli epitomizes these obstacles: this gram-negative bacterial species is the most prevalent agent of UTIs worldwide and can also colonize the urogenital tract in a phenomenon known as asymptomatic bacteriuria (ASB). Unfortunately, at the level of the individual E. coli strains, the relationship between UTI and ASB is poorly defined, confounding our understanding of microbial pathogenesis and strategies for clinical management. Unlike diarrheagenic pathotypes of E. coli, the definition of uropathogenic E. coli (UPEC) remains phenomenologic, without conserved phenotypes and known genetic determinants that rigorously distinguish UTI- and ASB-associated strains. This article provides a cross-disciplinary review of the current issues from interrelated mechanistic and diagnostic perspectives and describes new opportunities by which clinical resources can be leveraged to overcome molecular challenges. Specifically, we present our work harnessing a large collection of patient-derived isolates to identify features that do (and do not) distinguish UTI- from ASB-associated E. coli strains. Analyses of biofilm formation, previously reported to be higher in ASB strains, revealed extensive phenotypic heterogeneity that did not correlate with symptomatology. However, metabolomic experiments revealed distinct signatures between ASB and cystitis isolates, including in the purine pathway (previously shown to be critical for intracellular survival during acute infection). Together, these studies demonstrate how large-scale, wild-type approaches can help dissect the physiology of colonization versus infection, suggesting that the molecular definition of UPEC may rest at the level of global bacterial metabolism.
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Affiliation(s)
- Allison R Eberly
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Connor J Beebout
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ching Man Carmen Tong
- Division of Pediatric Urology, Department of Urology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gerald T Van Horn
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hamilton D Green
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madison J Fitzgerald
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shuvro De
- Division of Pediatric Urology, Department of Urology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Emily K Apple
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Simona G Codreanu
- Center for Innovative Technologies, Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Stacy D Sherrod
- Center for Innovative Technologies, Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - John A McLean
- Center for Innovative Technologies, Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Douglass B Clayton
- Division of Pediatric Urology, Department of Urology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles W Stratton
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Division of Laboratory Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology & Inflammation (VI4), Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan E Schmitz
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Division of Laboratory Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology & Inflammation (VI4), Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology & Inflammation (VI4), Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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26
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Maltas J, Wood KB. Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance. PLoS Biol 2019; 17:e3000515. [PMID: 31652256 PMCID: PMC6834293 DOI: 10.1371/journal.pbio.3000515] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 11/06/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Evolved resistance to one antibiotic may be associated with "collateral" sensitivity to other drugs. Here, we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict because independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. Although phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in a four-drug uniform cycle.
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Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
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27
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Li C, Chng KR, Kwah JS, Av-Shalom TV, Tucker-Kellogg L, Nagarajan N. An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data. MICROBIOME 2019; 7:118. [PMID: 31439018 PMCID: PMC6706891 DOI: 10.1186/s40168-019-0729-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/13/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND The dynamics of microbial communities is driven by a range of interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood. With the increasing availability of high-throughput microbiome taxonomic profiling data, it is now conceivable to directly learn the ecological models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is severely limited by the lack of accurate absolute cell density measurements (biomass). METHODS We present a new computational approach that resolves this key limitation in the inference of generalized Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference with an expectation-maximization algorithm (BEEM). RESULTS BEEM outperforms the state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM's application to previously inaccessible public datasets (due to the lack of biomass data) allowed us to construct ecological models of microbial communities in the human gut on a per-individual basis, revealing personalized dynamics and keystone species. CONCLUSIONS BEEM addresses a key bottleneck in "systems analysis" of microbiomes by enabling accurate inference of ecological models from high throughput sequencing data without the need for experimental biomass measurements.
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Affiliation(s)
- Chenhao Li
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore
- School of Computing, National University of Singapore, Singapore, 117543 Singapore
| | - Kern Rei Chng
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore
| | - Junmei Samantha Kwah
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore
| | - Tamar V. Av-Shalom
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3 Canada
- Department of Computer Science, University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Lisa Tucker-Kellogg
- Centre for Computational Biology, Duke–NUS Graduate Medical School, Singapore, 169857 Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore
- School of Computing, National University of Singapore, Singapore, 117543 Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
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28
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Remigi P, Masson-Boivin C, Rocha EP. Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions. Trends Microbiol 2019; 27:623-634. [DOI: 10.1016/j.tim.2019.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
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29
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Grinberg M, Orevi T, Kashtan N. Bacterial surface colonization, preferential attachment and fitness under periodic stress. PLoS Comput Biol 2019; 15:e1006815. [PMID: 30835727 PMCID: PMC6420035 DOI: 10.1371/journal.pcbi.1006815] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/15/2019] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Early bacterial surface colonization is not a random process wherein cells arbitrarily attach to surfaces and grow; but rather, attachment events, movement and cellular interactions induce non-random spatial organization. We have only begun to understand how the apparent self-organization affects the fitness of the population. A key factor contributing to fitness is the tradeoff between solitary-planktonic and aggregated surface-attached biofilm lifestyles. Though planktonic cells typically grow faster, bacteria in aggregates are more resistant to stress such as desiccation, antibiotics and predation. Here we ask if and to what extent informed surface-attachments improve fitness during early surface colonization under periodic stress conditions. We use an individual-based modeling approach to simulate foraging planktonic cells colonizing a surface under alternating wet-dry cycles. Such cycles are common in the largest terrestrial microbial habitats–soil, roots, and leaf surfaces–that are not constantly saturated with water and experience daily periods of desiccation stress. We compared different surface-attachment strategies, and analyzed the emerging spatio-temporal dynamics of surface colonization and population yield as a measure of fitness. We demonstrate that a simple strategy of preferential attachment (PA), biased to dense sites, carries a large fitness advantage over any random attachment across a broad range of environmental conditions–particularly under periodic stress. A vast portion of bacterial life on Earth takes place on surfaces. In many of these surfaces cells collectively organize into biofilms that are known to provide them protection from various environmental stresses. Early bacterial colonization of surfaces, prior to the development of mature biofilm, is a critical stage during which cells attempt to establish a sustainable population. It is not a random process wherein cells arbitrarily attach to surfaces and grow to form micro-colonies. Rather, surface-attachments, movement and cellular interactions take place to yield non-random organization. Using computer simulations, based on individual-based modeling, we demonstrate that simple attachment strategies, where planktonic cells preferentially attach to existing surface-attached aggregates, may confer fitness advantage over random attachment. The advantage of preferential attachment is particularly substantial under periodic stress–a common characteristic of many natural microbial habitats. This is due to a more efficient recruitment of planktonic cells that accelerates the formation of stress-protected aggregates.
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Affiliation(s)
- Maor Grinberg
- The department of Plant Pathology and Microbiology, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tomer Orevi
- The department of Plant Pathology and Microbiology, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nadav Kashtan
- The department of Plant Pathology and Microbiology, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail:
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30
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Kovács ÁT, Dragoš A. Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles. J Mol Biol 2019; 431:4749-4759. [PMID: 30769118 DOI: 10.1016/j.jmb.2019.02.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/21/2019] [Accepted: 02/04/2019] [Indexed: 12/25/2022]
Abstract
For several decades, laboratory evolution has served as a powerful method to manipulate microorganisms and to explore long-term dynamics in microbial populations. Next to canonical Escherichia coli planktonic cultures, experimental evolution has expanded into alternative cultivation methods and species, opening the doors to new research questions. Bacillus subtilis, the spore-forming and root-colonizing bacterium, can easily develop in the laboratory as a liquid-air interface colonizing pellicle biofilm. Here, we summarize recent findings derived from this tractable experimental model. Clonal pellicle biofilms of B. subtilis can rapidly undergo morphological and genetic diversification creating new ecological interactions, for example, exploitation by biofilm non-producers. Moreover, long-term exposure to such matrix non-producers can modulate cooperation in biofilms, leading to different phenotypic heterogeneity pattern of matrix production with larger subpopulation of "ON" cells. Alternatively, complementary variants of biofilm non-producers, each lacking a distinct matrix component, can engage in a genetic division of labor, resulting in superior biofilm productivity compared to the "generalist" wild type. Nevertheless, inter-genetic cooperation appears to be evanescent and rapidly vanquished by individual biofilm formation strategies altering the amount or the properties of the remaining matrix component. Finally, fast-evolving mobile genetic elements can unpredictably shift intra-species interactions in B. subtilis biofilms. Understanding evolution in clonal biofilm populations will facilitate future studies in complex multispecies biofilms that are more representative of nature.
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Affiliation(s)
- Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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31
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Cooper VS, Warren TM, Matela AM, Handwork M, Scarponi S. EvolvingSTEM: a microbial evolution-in-action curriculum that enhances learning of evolutionary biology and biotechnology. Evolution 2019; 12:12. [PMID: 32647555 PMCID: PMC7328067 DOI: 10.1186/s12052-019-0103-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/29/2019] [Indexed: 12/02/2022]
Abstract
Evolution is a central, unifying theory for all of life science, yet the subject is poorly represented in most secondary-school biology courses, especially in the United States. One challenge to learning evolution is that it is taught as a conceptual, retrospective subject with few tangible outcomes for students. These typical passive learning strategies lead to student disengagement with the material and misunderstanding of evolutionary concepts. To promote greater investment and comprehension, we developed EvolvingSTEM, an inquiry-based laboratory curriculum that demonstrates concepts of natural selection, heredity, and ecological diversity through experimental evolution of a benign bacterium. Students transfer populations of Pseudomonas fluorescens growing on plastic beads, which selects for biofilm formation and mutants with new, conspicuous phenotypes. We introduced our curriculum to four introductory high school biology classes alongside their standard curriculum materials and found that students who learned evolution through EvolvingSTEM scored significantly better on a common assessment targeted to Next Generation Science Standards than students taught only the standard curriculum. This latter group subsequently achieved similar scores once they too completed our curriculum. Our work demonstrates that inquiry-based, hands-on experiences with evolving bacterial populations can greatly enhance student learning of evolutionary concepts.
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Affiliation(s)
- Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA.,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH USA
| | - Taylor M Warren
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH USA
| | - Abigail M Matela
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA USA
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32
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Dragoš A, Lakshmanan N, Martin M, Horváth B, Maróti G, Falcón García C, Lieleg O, Kovács ÁT. Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms. FEMS Microbiol Ecol 2018; 93:4604779. [PMID: 29126191 DOI: 10.1093/femsec/fix155] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discovered that-similarly to other species-B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Nivedha Lakshmanan
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Balázs Horváth
- Seqomics Biotechnology Ltd, Vállalkozók útja 7, Mórahalom 6782, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
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33
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Richter A, Hölscher T, Pausch P, Sehrt T, Brockhaus F, Bange G, Kovács ÁT. Hampered motility promotes the evolution of wrinkly phenotype in Bacillus subtilis. BMC Evol Biol 2018; 18:155. [PMID: 30326845 PMCID: PMC6192195 DOI: 10.1186/s12862-018-1266-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/26/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Selection for a certain trait in microbes depends on the genetic background of the strain and the selection pressure of the environmental conditions acting on the cells. In contrast to the sessile state in the biofilm, various bacterial cells employ flagellum-dependent motility under planktonic conditions suggesting that the two phenotypes are mutually exclusive. However, flagellum dependent motility facilitates the prompt establishment of floating biofilms on the air-medium interface, called pellicles. Previously, pellicles of B. subtilis were shown to be preferably established by motile cells, causing a reduced fitness of non-motile derivatives in the presence of the wild type strain. RESULTS Here, we show that lack of active flagella promotes the evolution of matrix overproducers that can be distinguished by the characteristic wrinkled colony morphotype. The wrinkly phenotype is associated with amino acid substitutions in the master repressor of biofilm-related genes, SinR. By analyzing one of the mutations, we show that it alters the tetramerization and DNA binding properties of SinR, allowing an increased expression of the operon responsible for exopolysaccharide production. Finally, we demonstrate that the wrinkly phenotype is advantageous when cells lack flagella, but not in the wild type background. CONCLUSIONS Our experiments suggest that loss of function phenotypes could expose rapid evolutionary adaptation in bacterial biofilms that is otherwise not evident in the wild type strains.
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Affiliation(s)
- Anne Richter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 221, 2800, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology, Department of Chemistry, Philipps University Marburg, 35043, Marburg, Germany
| | - Tim Sehrt
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Franziska Brockhaus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, Department of Chemistry, Philipps University Marburg, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 221, 2800, Kongens Lyngby, Denmark. .,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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34
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Volke DC, Nikel PI. Getting Bacteria in Shape: Synthetic Morphology Approaches for the Design of Efficient Microbial Cell Factories. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800111] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
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35
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Noirot-Gros MF, Shinde S, Larsen PE, Zerbs S, Korajczyk PJ, Kemner KM, Noirot PH. Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation. Front Microbiol 2018; 9:853. [PMID: 29774013 PMCID: PMC5943511 DOI: 10.3389/fmicb.2018.00853] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/13/2018] [Indexed: 12/20/2022] Open
Abstract
Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots.
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Affiliation(s)
| | - Shalaka Shinde
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter J Korajczyk
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Philippe H Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
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36
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Abstract
Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving populations are influenced by all population genetic forces, including selection, mutation, drift, and recombination, and the relative contributions of these forces may be seen as mysterious. Here, I describe why the outcomes of experimental evolution should be viewed with greater certainty because the force of selection typically dominates. Importantly, any mutant rising rapidly to high frequency in large populations must have acquired adaptive traits in the selective environment. Sequencing the genomes of these mutants can identify genes or pathways that contribute to an adaptation. I review the logic and simple mathematics why this evolve-and-resequence approach is a powerful way to find the mutations or mutation combinations that best increase fitness in any new environment.
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Affiliation(s)
- Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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37
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Bikker FJ, Hoogenkamp MA, Malhaoui A, Nazmi K, Neilands J, Krom BP. Phytosphingosine Prevents the Formation of Young Salivary Biofilms in vitro. Caries Res 2017; 52:7-13. [DOI: 10.1159/000480712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/28/2017] [Indexed: 12/28/2022] Open
Abstract
Dental biofilms are formed in a multistep process that is initiated by the adhesion of oral bacteria to the dental hard surface. As dental biofilms are associated with oral diseases their control is necessary in order to maintain oral health. Recently, it was revealed that phytosphingosine (PHS)-treated hydroxyapatite discs showed anti-adhesive activity in a static in vitro biofilm model against Streptococcus mutans. The goal of the present study was to further unravel the anti-adhesive and anti-biofilm properties of PHS in both static and dynamic in vitro biofilm models against a full salivary inoculum. After 3 h under static conditions, bacterial adherence on PHS-treated cover glass slides was reduced by 60% compared to the untreated surface. After 6 and 24 h under static conditions, no significant differences in bacterial adherence were observed between PHS-treated and untreated cover glass slides. However, under dynamic conditions, i.e., the presence of shear forces, virtually no bacterial adherence was observed for up to 16 h on PHS-coated surfaces. Besides, PHS showed a strong bactericidal activity on salivary biofilms. Treatment of a 3- and 6-h statically grown biofilm resulted in a 99 and 94% reduction of viable cells, respectively, which was effectuated within minutes. In principle, these anti-adherence and anti-biofilm properties make PHS a promising candidate ingredient for use in oral care products aimed at oral microbial control.
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Gutiérrez D, Fernández L, Martínez B, Ruas-Madiedo P, García P, Rodríguez A. Real-Time Assessment of Staphylococcus aureus Biofilm Disruption by Phage-Derived Proteins. Front Microbiol 2017; 8:1632. [PMID: 28883818 PMCID: PMC5573737 DOI: 10.3389/fmicb.2017.01632] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/11/2017] [Indexed: 01/03/2023] Open
Abstract
A current focus of research is the development of new tools for removing bacterial biofilms in industrial settings. Bacteriophage-encoded proteins, such as endolysins, virion-associated peptidoglycan hydrolases, and exopolysaccharide depolymerases, have been shown to be efficient against these structures. However, the current screening techniques for the identification of antibiofilm properties of phage-derived proteins have important shortcomings. The aim of this work was to use the rapid, reproducible and accurate technology "real-time cell analyzer" for screening and comparing the antibiofilm ability of four phage-derived compounds, three lytic proteins (LysH5, CHAP-SH3b, and HydH5-SH3b) and one exopolysaccharide depolymerase (Dpo7) against Staphylococcus aureus biofilms, which have been associated with recurrent contamination of food products. The data generated after biofilm treatment allowed for the calculation of different antibiofilm parameters: (1) the minimum biofilm eradicating concentration that removes 50% of the biofilm (ranging from 3.5 ± 1.1 to 6.6 ± 0.5 μM), (2) the lowest concentration needed to observe an antibiofilm effect (∼1.5 μM for all the proteins), and (3) the specific antibiofilm activity and the percentage of biofilm removal that revealed LysH5 as the best antibiofilm compound. Overall, this technology might be used to quickly assess and compare by standardized parameters the disaggregating activity of phage antibiofilm proteins.
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Affiliation(s)
- Diana Gutiérrez
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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Bridier A, Piard JC, Pandin C, Labarthe S, Dubois-Brissonnet F, Briandet R. Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities. Front Microbiol 2017; 8:1364. [PMID: 28775718 PMCID: PMC5517491 DOI: 10.3389/fmicb.2017.01364] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Biofilms are dynamic habitats which constantly evolve in response to environmental fluctuations and thereby constitute remarkable survival strategies for microorganisms. The modulation of biofilm functional properties is largely governed by the active remodeling of their three-dimensional structure and involves an arsenal of microbial self-produced components and interconnected mechanisms. The production of matrix components, the spatial reorganization of ecological interactions, the generation of physiological heterogeneity, the regulation of motility, the production of actives enzymes are for instance some of the processes enabling such spatial organization plasticity. In this contribution, we discussed the foundations of architectural plasticity as an adaptive driver of biofilms through the review of the different microbial strategies involved. Moreover, the possibility to harness such characteristics to sculpt biofilm structure as an attractive approach to control their functional properties, whether beneficial or deleterious, is also discussed.
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Affiliation(s)
- Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, ANSESFougères, France
| | - Jean-Christophe Piard
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Caroline Pandin
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Simon Labarthe
- MaIAGE, INRA, Université Paris-SaclayJouy-en-Josas, France
| | | | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
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Hölscher T, Kovács ÁT. Sliding on the surface: bacterial spreading without an active motor. Environ Microbiol 2017; 19:2537-2545. [PMID: 28370801 DOI: 10.1111/1462-2920.13741] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/20/2017] [Accepted: 03/23/2017] [Indexed: 11/28/2022]
Abstract
Bacteria are able to translocate over surfaces using different types of active and passive motility mechanisms. Sliding is one of the passive types of movement since it is powered by the pushing force of dividing cells and additional factors facilitating the expansion over surfaces. In this review, we describe the sliding proficient bacteria that were previously investigated in details highlighting the sliding facilitating compounds and the regulation of sliding motility. Besides surfactants that reduce the friction between cells and substratum, other compounds including exopolysaccharides, hydrophobic proteins, or glycopeptidolipids where discovered to promote sliding. Therefore, we present the sliding bacteria in three groups depending on the additional compound required for sliding. Despite recent accomplishments in sliding research there are still many open questions about the mechanisms underlying sliding motility and its regulation in diverse bacterial species.
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Affiliation(s)
- Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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41
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De novo evolved interference competition promotes the spread of biofilm defectors. Nat Commun 2017; 8:15127. [PMID: 28462927 PMCID: PMC5418572 DOI: 10.1038/ncomms15127] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/02/2017] [Indexed: 11/16/2022] Open
Abstract
Biofilms are social entities where bacteria live in tightly packed agglomerations, surrounded by self-secreted exopolymers. Since production of exopolymers is costly and potentially exploitable by non-producers, mechanisms that prevent invasion of non-producing mutants are hypothesized. Here we study long-term dynamics and evolution in Bacillus subtilis biofilm populations consisting of wild-type (WT) matrix producers and mutant non-producers. We show that non-producers initially fail to incorporate into biofilms formed by the WT cells, resulting in 100-fold lower final frequency compared to the WT. However, this is modulated in a long-term scenario, as non-producers evolve the ability to better incorporate into biofilms, thereby slightly decreasing the productivity of the whole population. Detailed molecular analysis reveals that the unexpected shift in the initially stable biofilm is coupled with newly evolved phage-mediated interference competition. Our work therefore demonstrates how collective behaviour can be disrupted as a result of rapid adaptation through mobile genetic elements. The production of secreted polymers in bacterial biofilms is costly, and therefore mechanisms preventing invasion of non-producing mutants are hypothesized. Here, the authors show that non-producers can evolve the ability to better incorporate into biofilms via phage-mediated interference.
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Lind PA, Farr AD, Rainey PB. Evolutionary convergence in experimental Pseudomonas populations. ISME JOURNAL 2016; 11:589-600. [PMID: 27911438 DOI: 10.1038/ismej.2016.157] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/05/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022]
Abstract
Model microbial systems provide opportunity to understand the genetic bases of ecological traits, their evolution, regulation and fitness contributions. Experimental populations of Pseudomonas fluorescens rapidly diverge in spatially structured microcosms producing a range of surface-colonising forms. Despite divergent molecular routes, wrinkly spreader (WS) niche specialist types overproduce a cellulosic polymer allowing mat formation at the air-liquid interface and access to oxygen. Given the range of ways by which cells can form mats, such phenotypic parallelism is unexpected. We deleted the cellulose-encoding genes from the ancestral genotype and asked whether this mutant could converge on an alternate phenotypic solution. Two new traits were discovered. The first involved an exopolysaccharide encoded by pgaABCD that functions as cell-cell glue similar to cellulose. The second involved an activator of an amidase (nlpD) that when defective causes cell chaining. Both types form mats, but were less fit in competition with cellulose-based WS types. Surprisingly, diguanylate cyclases linked to cellulose overexpression underpinned evolution of poly-beta-1,6-N-acetyl-d-glucosamine (PGA)-based mats. This prompted genetic analyses of the relationships between the diguanylate cyclases WspR, AwsR and MwsR, and both cellulose and PGA. Our results suggest that c-di-GMP regulatory networks may have been shaped by evolution to accommodate loss and gain of exopolysaccharide modules facilitating adaptation to new environments.
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Affiliation(s)
- Peter A Lind
- New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University at Albany, Auckland, New Zealand.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Andrew D Farr
- New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University at Albany, Auckland, New Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University at Albany, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris-Tech), PSL Research University, Paris, France
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Hölscher T, Dragoš A, Gallegos-Monterrosa R, Martin M, Mhatre E, Richter A, Kovács ÁT. Monitoring Spatial Segregation in Surface Colonizing Microbial Populations. J Vis Exp 2016. [PMID: 27842347 PMCID: PMC5226080 DOI: 10.3791/54752] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Microbes provide an intriguing system to study social interaction among individuals within a population. The short generation times and relatively simple genetic modification procedures of microbes facilitate the development of the sociomicrobiology field. To assess the fitness of certain microbial species, selected strains or their genetically modified derivatives within one population, can be fluorescently labelled and tracked using microscopy adapted with appropriate fluorescence filters. Expanding colonies of diverse microbial species on agar media can be used to monitor the spatial distribution of cells producing distinctive fluorescent proteins. Here, we present a detailed protocol for the use of green- and red-fluorescent protein producing bacterial strains to follow spatial arrangement during surface colonization, including flagellum-driven community movement (swarming), exopolysaccharide- and hydrophobin-dependent growth mediated spreading (sliding), and complex colony biofilm formation. Non-domesticated isolates of the Gram-positive bacterium, Bacillus subtilis can be utilized to scrutinize certain surface spreading traits and their effect on two-dimensional distribution on the agar-solidified medium. By altering the number of cells used to initiate colony biofilms, the assortment levels can be varied on a continuous scale. Time-lapse fluorescent microscopy can be used to witness the interaction between different phenotypes and genotypes at a certain assortment level and to determine the relative success of either.
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Affiliation(s)
- Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Anna Dragoš
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | | | - Marivic Martin
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Anne Richter
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena;
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Berlanga M, Guerrero R. Living together in biofilms: the microbial cell factory and its biotechnological implications. Microb Cell Fact 2016; 15:165. [PMID: 27716327 PMCID: PMC5045575 DOI: 10.1186/s12934-016-0569-5] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023] Open
Abstract
In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.
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Affiliation(s)
- Mercedes Berlanga
- Section Microbiology, Department of Biology, Health and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, s/n, 08028 Barcelona, Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona-IDIBELL, Barcelona, Spain
- Barcelona Knowledge Hub, Academia Europaea, Barcelona, Spain
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