201
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Conditional privatization of a public siderophore enables Pseudomonas aeruginosa to resist cheater invasion. Nat Commun 2018; 9:1383. [PMID: 29643375 PMCID: PMC5895777 DOI: 10.1038/s41467-018-03791-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 01/06/2023] Open
Abstract
Understanding the mechanisms that promote cooperative behaviors of bacteria in their hosts is of great significance to clinical therapies. Environmental stress is generally believed to increase competition and reduce cooperation in bacteria. Here, we show that bacterial cooperation can in fact be maintained because of environmental stress. We show that Pseudomonas aeruginosa regulates the secretion of iron-scavenging siderophores in the presence of different environmental stresses, reserving this public good for private use in protection against reactive oxygen species when under stress. We term this strategy "conditional privatization". Using a combination of experimental evolution and theoretical modeling, we demonstrate that in the presence of environmental stress the conditional privatization strategy is resistant to invasion by non-producing cheaters. These findings show how the regulation of public goods secretion under stress affects the evolutionary stability of cooperation in a pathogenic population, which may assist in the rational development of novel therapies.
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202
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Vurukonda SSKP, Giovanardi D, Stefani E. Plant Growth Promoting and Biocontrol Activity of Streptomyces spp. as Endophytes. Int J Mol Sci 2018; 19:E952. [PMID: 29565834 PMCID: PMC5979581 DOI: 10.3390/ijms19040952] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 01/12/2023] Open
Abstract
There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often lead to resistance in plant pathogens. In agriculture, plant growth-promoting and biocontrol microorganisms have emerged as safe alternatives to chemical pesticides. Streptomyces spp. and their metabolites may have great potential as excellent agents for controlling various fungal and bacterial phytopathogens. Streptomycetes belong to the rhizosoil microbial communities and are efficient colonizers of plant tissues, from roots to the aerial parts. They are active producers of antibiotics and volatile organic compounds, both in soil and in planta, and this feature is helpful for identifying active antagonists of plant pathogens and can be used in several cropping systems as biocontrol agents. Additionally, their ability to promote plant growth has been demonstrated in a number of crops, thus inspiring the wide application of streptomycetes as biofertilizers to increase plant productivity. The present review highlights Streptomyces spp.-mediated functional traits, such as enhancement of plant growth and biocontrol of phytopathogens.
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Affiliation(s)
| | - Davide Giovanardi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy.
| | - Emilio Stefani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy.
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203
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Antibiotic Stimulation of a Bacillus subtilis Migratory Response. mSphere 2018; 3:mSphere00586-17. [PMID: 29507890 PMCID: PMC5821984 DOI: 10.1128/msphere.00586-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/31/2018] [Indexed: 11/20/2022] Open
Abstract
Competitive interactions between bacteria reveal physiological adaptations that benefit fitness. Bacillus subtilis is a Gram-positive species with several adaptive mechanisms for competition and environmental stress. Biofilm formation, sporulation, and motility are the outcomes of widespread changes in a population of B. subtilis. These changes emerge from complex, regulated pathways for adapting to external stresses, including competition from other species. To identify competition-specific functions, we cultured B. subtilis with multiple species of Streptomyces and observed altered patterns of growth for each organism. In particular, when plated on agar medium near Streptomyces venezuelae, B. subtilis initiates a robust and reproducible mobile response. To investigate the mechanistic basis for the interaction, we determined the type of motility used by B. subtilis and isolated inducing metabolites produced by S. venezuelae. Bacillus subtilis has three defined forms of motility: swimming, swarming, and sliding. Streptomyces venezuelae induced sliding motility specifically in our experiments. The inducing agents produced by S. venezuelae were identified as chloramphenicol and a brominated derivative at subinhibitory concentrations. Upon further characterization of the mobile response, our results demonstrated that subinhibitory concentrations of chloramphenicol, erythromycin, tetracycline, and spectinomycin all activate a sliding motility response by B. subtilis. Our data are consistent with sliding motility initiating under conditions of protein translation stress. This report underscores the importance of hormesis as an early warning system for potential bacterial competitors and antibiotic exposure. IMPORTANCE Antibiotic resistance is a major challenge for the effective treatment of infectious diseases. Identifying adaptive mechanisms that bacteria use to survive low levels of antibiotic stress is important for understanding pathways to antibiotic resistance. Furthermore, little is known about the effects of individual bacterial interactions on multispecies communities. This work demonstrates that subinhibitory amounts of some antibiotics produced by streptomycetes induce active motility in B. subtilis, which may alter species interaction dynamics among species-diverse bacterial communities in natural environments. The use of antibiotics at subinhibitory concentrations results in many changes in bacteria, including changes in biofilm formation, small-colony variants, formation of persisters, and motility. Identifying the mechanistic bases of these adaptations is crucial for understanding how bacterial communities are impacted by antibiotics.
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204
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Flanagan L, Steen RR, Saxby K, Klatter M, Aucott BJ, Winstanley C, Fairlamb IJS, Lynam JM, Parkin A, Friman VP. The Antimicrobial Activity of a Carbon Monoxide Releasing Molecule (EBOR-CORM-1) Is Shaped by Intraspecific Variation within Pseudomonas aeruginosa Populations. Front Microbiol 2018; 9:195. [PMID: 29472912 PMCID: PMC5809400 DOI: 10.3389/fmicb.2018.00195] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
Carbon monoxide releasing molecules (CORMs) have been suggested as a new synthetic class of antimicrobials to treat bacterial infections. Here we utilized a novel EBOR-CORM-1 ([NEt4][MnBr2(CO)4]) capable of water-triggered CO-release, and tested its efficacy against a collection of clinical Pseudomonas aeruginosa strains that differ in infection-related virulence traits. We found that while EBOR-CORM-1 was effective in clearing planktonic and biofilm cells of P. aeruginosa strain PAO1 in a concentration dependent manner, this effect was less clear and varied considerably between different P. aeruginosa cystic fibrosis (CF) lung isolates. While a reduction in cell growth was observed after 8 h of CORM application, either no effect or even a slight increase in cell densities and the amount of biofilm was observed after 24 h. This variation could be partly explained by differences in bacterial virulence traits: while CF isolates showed attenuated in vivo virulence and growth compared to strain PAO1, they formed much more biofilm, which could have potentially protected them from the CORM. Even though no clear therapeutic benefits against a subset of isolates was observed in an in vivo wax moth acute infection model, EBOR-CORM-1 was more efficient at reducing the growth of CF isolate co-culture populations harboring intraspecific variation, in comparison with efficacy against more uniform single isolate culture populations. Together these results suggest that CORMs could be effective at controlling genetically diverse P. aeruginosa populations typical for natural chronic CF infections and that the potential benefits of some antibiotics might not be observed if tested only against clonal bacterial populations.
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Affiliation(s)
- Lindsey Flanagan
- Department of Biology, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
| | - Rachel R. Steen
- Department of Chemistry, University of York, York, United Kingdom
| | - Karinna Saxby
- Department of Biology, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
| | - Mirre Klatter
- Department of Biology, University of York, York, United Kingdom
| | | | - Craig Winstanley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - Jason M. Lynam
- Department of Chemistry, University of York, York, United Kingdom
| | - Alison Parkin
- Department of Chemistry, University of York, York, United Kingdom
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205
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Quorum-sensing control of antibiotic resistance stabilizes cooperation in Chromobacterium violaceum. ISME JOURNAL 2018; 12:1263-1272. [PMID: 29374267 DOI: 10.1038/s41396-018-0047-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/08/2017] [Accepted: 12/21/2017] [Indexed: 01/10/2023]
Abstract
Many Proteobacteria use quorum sensing to regulate production of public goods, such as antimicrobials and proteases, that are shared among members of a community. Public goods are vulnerable to exploitation by cheaters, such as quorum sensing-defective mutants. Quorum sensing- regulated private goods, goods that benefit only producing cells, can prevent the emergence of cheaters under certain growth conditions. Previously, we developed a laboratory co-culture model to investigate the importance of quorum-regulated antimicrobials during interspecies competition. In our model, Burkholderia thailandensis and Chromobacterium violaceum each use quorum sensing-controlled antimicrobials to inhibit the other species' growth. Here, we show that C. violaceum uses quorum sensing to increase resistance to bactobolin, a B. thailandensis antibiotic, by increasing transcription of a putative antibiotic efflux pump. We demonstrate conditions where C. violaceum quorum-defective cheaters emerge and show that in these conditions, bactobolin restrains cheaters. We also demonstrate that bactobolin restrains quorum-defective mutants in our co-culture model, and the increase in antimicrobial-producing cooperators drives the C. violaceum population to become more competitive. Our results describe a mechanism of cheater restraint involving quorum control of efflux pumps and demonstrate that interspecies competition can reinforce cooperative behaviors by placing constraints on quorum sensing-defective mutants.
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206
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Mavridou DAI, Gonzalez D, Kim W, West SA, Foster KR. Bacteria Use Collective Behavior to Generate Diverse Combat Strategies. Curr Biol 2018; 28:345-355.e4. [PMID: 29395918 DOI: 10.1016/j.cub.2017.12.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/06/2017] [Accepted: 12/14/2017] [Indexed: 01/06/2023]
Abstract
Animals have evolved a wide diversity of aggressive behavior often based upon the careful monitoring of other individuals. Bacteria are also capable of aggression, with many species using toxins to kill or inhibit their competitors. Like animals, bacteria also have systems to monitor others during antagonistic encounters, but how this translates into behavior remains poorly understood. Here, we use colonies of Escherichia coli carrying colicin-encoding plasmids as a model for studying antagonistic behavior. We show that in the absence of threat, dispersed cells with low reproductive value produce colicin toxins spontaneously, generating efficient pre-emptive attacks. Cells can also respond conditionally to toxins released by clonemates via autoinduction or other genotypes via competition sensing. The strength of both pre-emptive and responsive attacks varies widely between strains. We demonstrate that this variability occurs easily through mutation by rationally engineering strains to recapitulate the diversity in naturally occurring strategies. Finally, we discover that strains that can detect both competitors and clonemates are capable of massive coordinated attacks on competing colonies. This collective behavior protects established colonies from competitors, mirroring the evolution of alarm calling in the animal world.
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Affiliation(s)
- Despoina A I Mavridou
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK; MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, London SW7 2DD, UK
| | - Diego Gonzalez
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK
| | - Wook Kim
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK.
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207
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Quinto EJ, Marín JM, Caro I, Mateo J, Schaffner DW. Bayesian modeling of two- and three-species bacterial competition in milk. Food Res Int 2017; 105:952-961. [PMID: 29433294 DOI: 10.1016/j.foodres.2017.12.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022]
Abstract
Listeria monocytogenes is a well-known food-borne pathogen and is among the bacteria best adapted to grow at low temperatures. Psychrotrophic spoilage microorganisms present in milk and milk products are primarily in the genus Pseudomonas, and their numbers increase during cold storage leading to deterioration and/or spoilage. The nature of the competition in two- or three-species bacterial systems with L. monocytogenes, L. innocua, and P. fluorescens in skimmed milk at 7 or 14°C was studied. The Baranyi growth model was used to estimate the growth rate and the maximum population density of the three microorganisms for each strain in single cultures or in two- or three-strains co-cultures. The highest Listeria populations were achieved by pure cultures, decreasing in co-culture with P. fluorescens at both temperatures. A modified deterministic logistic model was applied which includes inhibition functions for single cultures, and two- or three-species cultures. A subsequent Bayesian approach was applied for modelling the bacterial interactions. There was not a direct correlation between the growth rate of P. fluorescens and its inhibitory effect on Listeria species. The use of some species from the natural food microflora to inhibit pathogen growth may be an important tool to enhance the safety of refrigerated foods such as milk and dairy products.
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Affiliation(s)
- E J Quinto
- Department of Food Science and Nutrition, College of Medicine, University of Valladolid, 47005 Valladolid, Spain.
| | - J M Marín
- Department of Statistics, University Carlos III de Madrid, 28903 Getafe, Madrid, Spain.
| | - I Caro
- Department of Food Science and Nutrition, College of Medicine, University of Valladolid, 47005 Valladolid, Spain; Department of Food Hygiene and Food Technology, University of León, Campus de Vegazana s/n, 24071 León, Spain.
| | - J Mateo
- Department of Food Hygiene and Food Technology, University of León, Campus de Vegazana s/n, 24071 León, Spain.
| | - D W Schaffner
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA.
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208
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A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites. mSystems 2017; 2:mSystems00129-17. [PMID: 29152587 PMCID: PMC5686522 DOI: 10.1128/msystems.00129-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/24/2017] [Indexed: 11/25/2022] Open
Abstract
Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript analysis, and measurements of member productivity and population size. It can also facilitate discovery of natural products that are only produced within microbial consortia. Thus, this synthetic community system has utility to address fundamental questions about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir. Exometabolites, including small molecules, extracellular enzymes, and antibiotics, are assayed from the reservoir using sensitive mass spectrometry. Community member outcomes, such as growth, productivity, and gene regulation, can be determined using flow cytometry, biomass measurements, and transcript analyses, respectively. The synthetic community design allows for determination of the consequences of microbiome diversity for emergent community properties and for functional changes over time or after perturbation. Because it is versatile, scalable, and accessible, this synthetic community system has the potential to practically advance knowledge of microbial interactions that occur within both natural and artificial communities. IMPORTANCE Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript analysis, and measurements of member productivity and population size. It can also facilitate discovery of natural products that are only produced within microbial consortia. Thus, this synthetic community system has utility to address fundamental questions about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Author Video: An author video summary of this article is available.
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209
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Quorum-Sensing Systems as Targets for Antivirulence Therapy. Trends Microbiol 2017; 26:313-328. [PMID: 29132819 DOI: 10.1016/j.tim.2017.10.005] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/26/2017] [Accepted: 10/20/2017] [Indexed: 02/08/2023]
Abstract
The development of novel therapies to control diseases caused by antibiotic-resistant pathogens is one of the major challenges we are currently facing. Many important plant, animal, and human pathogens regulate virulence by quorum sensing, bacterial cell-to-cell communication with small signal molecules. Consequently, a significant research effort is being undertaken to identify and use quorum-sensing-interfering agents in order to control diseases caused by these pathogens. In this review, an overview of our current knowledge of quorum-sensing systems of Gram-negative model pathogens is presented as well as the link with virulence of these pathogens, and recent advances and challenges in the development of quorum-sensing-interfering therapies are discussed.
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210
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Sexton DJ, Schuster M. Nutrient limitation determines the fitness of cheaters in bacterial siderophore cooperation. Nat Commun 2017; 8:230. [PMID: 28794499 PMCID: PMC5550491 DOI: 10.1038/s41467-017-00222-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/09/2017] [Indexed: 11/28/2022] Open
Abstract
Cooperative behaviors provide a collective benefit, but are considered costly for the individual. Here, we report that these costs vary dramatically in different contexts and have opposing effects on the selection for non-cooperating cheaters. We investigate a prominent example of bacterial cooperation, the secretion of the peptide siderophore pyoverdine by Pseudomonas aeruginosa, under different nutrient-limiting conditions. Using metabolic modeling, we show that pyoverdine incurs a fitness cost only when its building blocks carbon or nitrogen are growth-limiting and are diverted from cellular biomass production. We confirm this result experimentally with a continuous-culture approach. We show that pyoverdine non-producers (cheaters) enjoy a large fitness advantage in co-culture with producers (cooperators) and spread to high frequency when limited by carbon, but not when limited by phosphorus. The principle of nutrient-dependent fitness costs has implications for the stability of cooperation in pathogenic and non-pathogenic environments, in biotechnological applications, and beyond the microbial realm. Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.
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Affiliation(s)
- D Joseph Sexton
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA.
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211
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McAdams D. Resistance diagnosis and the changing epidemiology of antibiotic resistance. Ann N Y Acad Sci 2017; 1388:5-17. [PMID: 28134444 DOI: 10.1111/nyas.13300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/27/2016] [Indexed: 11/29/2022]
Abstract
Widespread adoption of point-of-care resistance diagnostics (POCRD) reduces ineffective antibiotic use but could increase overall antibiotic use. Indeed, in the context of a standard susceptible-infected epidemiological model with a single antibiotic, POCRD accelerates the rise of resistance in the disease-causing bacterial population. When multiple antibiotics are available, however, POCRD may slow the rise of resistance even as more patients receive antibiotic treatment, belying the conventional wisdom that antibiotics are "exhaustible resources" whose increased use necessarily promotes the rise of resistance.
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Affiliation(s)
- David McAdams
- Fuqua School of Business and Economics Department, Duke University, Durham, North Carolina
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212
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Wang B, Liu W, Liu X, Franks AE, Teng Y, Luo Y. Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 590-591:297-303. [PMID: 28274604 DOI: 10.1016/j.scitotenv.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Microcosms for enrichment of DDT degrading microorganisms were monitored using culture-dependent and -independent methods. Culture dependent methods isolated several strains with DDT degradation potential, Pseudomonas species being the most frequent. One isolate, Streptomyces sp. strain D3, had a degradation rate of 77% with 20mgL-1 of DDT after 7days incubation, D3 also had degradation rates of 75% and 30% for PCB77 (3,3',4,4'-tetrachloro biphenyl) and PCNB (pentachloronitrobenzene) respectively. Culture-independent high-throughput sequencing identified a different subset of the microbial community within the enrichment microcosms to the culture dependent method. Pseudomonas, the most frequently isolated strain, only represented the 12th most abundant operational taxonomic unit in the sequencing dataset (relative abundance 0.9%). The most frequently observed bacterial genus in the culture-independent analysis did not correspond with those recovered by culture-dependent methods. These results suggested that deep sequencing followed by a targeted isolation approach might provide an advantageous route to bioremediation studies.
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Affiliation(s)
- Beibei Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaoyan Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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213
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Abstract
Bacterial type VI secretion systems (T6SSs) function as contractile nanomachines to puncture target cells and deliver lethal effectors. In the 10 years since the discovery of the T6SS, much has been learned about the structure and function of this versatile protein secretion apparatus. Most of the conserved protein components that comprise the T6SS apparatus itself have been identified and ascribed specific functions. In addition, numerous effector proteins that are translocated by the T6SS have been identified and characterized. These protein effectors usually represent toxic cargoes that are delivered by the attacker cell to a target cell. Researchers in the field are beginning to better understand the lifestyle or physiology that dictates when bacteria normally express their T6SS. In this article, we consider what is known about the structure and regulation of the T6SS, the numerous classes of antibacterial effector T6SS substrates, and how the action of the T6SS relates to a given lifestyle or behavior in certain bacteria.
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214
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Jones SE, Elliot MA. Streptomyces Exploration: Competition, Volatile Communication and New Bacterial Behaviours. Trends Microbiol 2017; 25:522-531. [DOI: 10.1016/j.tim.2017.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 10/20/2022]
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215
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Tripathi BM, Moroenyane I, Sherman C, Lee YK, Adams JM, Steinberger Y. Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel. MICROBIAL ECOLOGY 2017; 74:168-176. [PMID: 28074247 DOI: 10.1007/s00248-017-0931-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the soil microbiome.
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Affiliation(s)
- Binu M Tripathi
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Itumeleng Moroenyane
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, 531 boulevard de Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Chen Sherman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 529002, Ramat-Gan, Israel
| | - Yoo Kyung Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Jonathan M Adams
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Republic of Korea.
| | - Yosef Steinberger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 529002, Ramat-Gan, Israel.
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216
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Pseudomonas aeruginosa-Derived Rhamnolipids and Other Detergents Modulate Colony Morphotype and Motility in the Burkholderia cepacia Complex. J Bacteriol 2017; 199:JB.00171-17. [PMID: 28439038 DOI: 10.1128/jb.00171-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/16/2017] [Indexed: 12/16/2022] Open
Abstract
Competitive interactions mediated by released chemicals (e.g., toxins) are prominent in multispecies communities, but the effects of these chemicals at subinhibitory concentrations on susceptible bacteria are poorly understood. Although Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc) can exist together as a coinfection in cystic fibrosis airways, P. aeruginosa toxins can kill Bcc species in vitro Consequently, these bacteria become an ideal in vitro model system to study the impact of sublethal levels of toxins on the biology of typical susceptible bacteria, such as the Bcc, when exposed to P. aeruginosa toxins. Using P. aeruginosa spent medium as a source of toxins, we showed that a small window of subinhibitory concentrations modulated the colony morphotype and swarming motility of some but not all tested Bcc strains, for which rhamnolipids were identified as the active molecule. Using a random transposon mutagenesis approach, we identified several genes required by the Bcc to respond to low concentrations of rhamnolipids and consequently affect the ability of this microbe to change its morphotype and swarm over surfaces. Among those genes identified were those coding for type IVb-Tad pili, which are often required for virulence in various bacterial pathogens. Our study demonstrates that manipulating chemical gradients in vitro can lead to the identification of bacterial behaviors relevant to polymicrobial infections.IMPORTANCE Interspecies interactions can have profound effects on the development and outcomes of polymicrobial infections. Consequently, improving the molecular understanding of these interactions could provide us with new insights on the possible long-term consequences of these chronic infections. In this study, we show that P. aeruginosa-derived rhamnolipids, which participate in Bcc killing at high concentrations, can also trigger biological responses in Burkholderia spp. at low concentrations. The modulation of potential virulence phenotypes in the Bcc by P. aeruginosa suggests that these interactions contribute to pathogenesis and disease severity in the context of polymicrobial infections.
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217
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Schuster M, Sexton DJ, Hense BA. Why Quorum Sensing Controls Private Goods. Front Microbiol 2017; 8:885. [PMID: 28579979 PMCID: PMC5437708 DOI: 10.3389/fmicb.2017.00885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022] Open
Abstract
Cell-cell communication, also termed quorum sensing (QS), is a widespread process that coordinates gene expression in bacterial populations. The generally accepted view is that QS optimizes the cell density-dependent benefit attained from cooperative behaviors, often in the form of secreted products referred to as "public goods." This view is challenged by an increasing number of cell-associated products or "private goods" reported to be under QS-control for which a collective benefit is not apparent. A prominent example is nucleoside hydrolase from Pseudomonas aeruginosa, a periplasmic enzyme that catabolizes adenosine. Several recent studies have shown that private goods can function to stabilize cooperation by co-regulated public goods, seemingly explaining their control by QS. Here we argue that this property is a by-product of selection for other benefits rather than an adaptation. Emphasizing ecophysiological context, we propose alternative explanations for the QS control of private goods. We suggest that the benefit attained from private goods is associated with high cell density, either because a relevant ecological condition correlates with density, or because the private good is, directly or indirectly, involved in cooperative behavior. Our analysis helps guide a systems approach to QS, with implications for antivirulence drug design and synthetic biology.
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Affiliation(s)
- Martin Schuster
- Department of Microbiology, Oregon State UniversityCorvallis, OR, United States
| | - D Joseph Sexton
- Department of Microbiology, Oregon State UniversityCorvallis, OR, United States
| | - Burkhard A Hense
- Institute of Computational Biology, Helmholtz Zentrum MünchenNeuherberg, Germany
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218
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de Boer W. Upscaling of fungal-bacterial interactions: from the lab to the field. Curr Opin Microbiol 2017; 37:35-41. [PMID: 28437664 DOI: 10.1016/j.mib.2017.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
Abstract
Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.
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Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Soil Quality, Wageningen University, Wageningen, The Netherlands.
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219
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Niehus R, Picot A, Oliveira NM, Mitri S, Foster KR. The evolution of siderophore production as a competitive trait. Evolution 2017; 71:1443-1455. [DOI: 10.1111/evo.13230] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/03/2017] [Accepted: 03/12/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Rene Niehus
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit (MORU); 10400 Bangkok Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine; University of Oxford; Oxford United Kingdom
| | - Aurore Picot
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Sorbonne Universités, UPMC Univ Paris 6, UPEC, Univ Paris Diderot, Univ Paris-Est Créteil, CNRS, INRA, IRD; Institute of Ecology and Environmental Sciences-Paris (iEES Paris); 7 quai Saint-Bernard 75 252 Paris France
| | - Nuno M. Oliveira
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Department of Applied Mathematics and Theoretical Physics (DAMTP); Centre for Mathematical Sciences; Wilberforce Road Cambridge CB3 0WA United Kingdom
| | - Sara Mitri
- Department of Fundamental Microbiology; University of Lausanne; CH-1015 Lausanne Switzerland
| | - Kevin R. Foster
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Oxford Centre for Integrative Systems Biology; University of Oxford; South Parks Road Oxford OX1 3QU United Kingdom
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220
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Ashrafi R, Bruneaux M, Sundberg LR, Pulkkinen K, Ketola T. Application of high resolution melting assay (HRM) to study temperature-dependent intraspecific competition in a pathogenic bacterium. Sci Rep 2017; 7:980. [PMID: 28428555 PMCID: PMC5430548 DOI: 10.1038/s41598-017-01074-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/22/2017] [Indexed: 01/18/2023] Open
Abstract
Studies on species’ responses to climate change have focused largely on the direct effect of abiotic factors and in particular temperature, neglecting the effects of biotic interactions in determining the outcome of climate change projections. Many microbes rely on strong interference competition; hence the fitness of many pathogenic bacteria could be a function of both their growth properties and intraspecific competition. However, due to technical challenges in distinguishing and tracking individual strains, experimental evidence on intraspecific competition has been limited so far. Here, we developed a robust application of the high-resolution melting (HRM) assay to study head-to-head competition between mixed genotype co-cultures of a waterborne bacterial pathogen of fish, Flavobacterium columnare, at two different temperatures. We found that competition outcome in liquid cultures seemed to be well predicted by growth yield of isolated strains, but was mostly inconsistent with interference competition results measured in inhibition tests on solid agar, especially as no growth inhibition between strain pairs was detected at the higher temperature. These results suggest that, for a given temperature, the factors driving competition outcome differ between liquid and solid environments.
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Affiliation(s)
- Roghaieh Ashrafi
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland.
| | - Matthieu Bruneaux
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland
| | - Katja Pulkkinen
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyvaskyla, Finland
| | - Tarmo Ketola
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland
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221
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The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria. Trends Microbiol 2017; 25:280-292. [DOI: 10.1016/j.tim.2016.12.002] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 01/11/2023]
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222
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Lombardi L, Zoppo M, Rizzato C, Egan CG, Scarpato R, Tavanti A. Use of Amplification Fragment Length Polymorphism to Genotype Pseudomonas stutzeri Strains Following Exposure to Ultraviolet Light A. Pol J Microbiol 2017; 66:107-111. [PMID: 29359695 DOI: 10.5604/17331331.1234998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Changes in ultraviolet light radiation can act as a selective force on the genetic and physiological traits of a microbial community. Two strains of the common soil bacterium Pseudomonas stutzeri, isolated from aquifer cores and from human spinal fluid were exposed to ultraviolet light. Amplification length polymorphism analysis (AFLP) was used to genotype this bacterial species and evaluate the effect of UVA-exposure on genomic DNA extracted from 18 survival colonies of the two strains compared to unexposed controls. AFLP showed a high discriminatory power, confirming the existence of different genotypes within the species and presence of DNA polymorphisms in UVA-exposed colonies.
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Affiliation(s)
- Lisa Lombardi
- Department of Biology, Genetic Unit, University of Pisa, Italy
| | - Marina Zoppo
- Department of Biology, Genetic Unit, University of Pisa, Italy
| | - Cosmeri Rizzato
- Department of Biology, Genetic Unit, University of Pisa, Italy
| | | | | | - Arianna Tavanti
- Department of Biology, Genetic Unit, University of Pisa, Italy
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223
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García-Bayona L, Guo MS, Laub MT. Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins. eLife 2017; 6:e24869. [PMID: 28323618 PMCID: PMC5380434 DOI: 10.7554/elife.24869] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/20/2017] [Indexed: 12/18/2022] Open
Abstract
Most bacteria are in fierce competition with other species for limited nutrients. Some bacteria can kill nearby cells by secreting bacteriocins, a diverse group of proteinaceous antimicrobials. However, bacteriocins are typically freely diffusible, and so of little value to planktonic cells in aqueous environments. Here, we identify an atypical two-protein bacteriocin in the α-proteobacterium Caulobacter crescentus that is retained on the surface of producer cells where it mediates cell contact-dependent killing. The bacteriocin-like proteins CdzC and CdzD harbor glycine-zipper motifs, often found in amyloids, and CdzC forms large, insoluble aggregates on the surface of producer cells. These aggregates can drive contact-dependent killing of other organisms, or Caulobacter cells not producing the CdzI immunity protein. The Cdz system uses a type I secretion system and is unrelated to previously described contact-dependent inhibition systems. However, Cdz-like systems are found in many bacteria, suggesting that this form of contact-dependent inhibition is common.
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Affiliation(s)
- Leonor García-Bayona
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, United States
| | - Monica S Guo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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224
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Westhoff S, van Wezel GP, Rozen DE. Distance-dependent danger responses in bacteria. Curr Opin Microbiol 2017; 36:95-101. [PMID: 28258981 DOI: 10.1016/j.mib.2017.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 12/23/2022]
Abstract
The last decade has seen a resurgence in our understanding of the diverse mechanisms that bacteria use to kill one another. We are also beginning to uncover the responses and countermeasures that bacteria use when faced with specific threats or general cues of potential danger from bacterial competitors. In this Perspective, we propose that diverse offensive and defensive responses in bacteria have evolved to offset dangers detected at different distances. Thus, while volatile organic compounds provide bacterial cells with a warning at the greatest distance, diffusible compounds like antibiotics or contact mediated killing systems, indicate a more pressing danger warranting highly-specific responses. In the competitive environments in which bacteria live, it is crucial that cells are able to detect real or potential dangers from other cells. By utilizing mechanisms of detection that can infer the distance from danger, bacteria can fine-tune aggressive interactions so that they can optimally respond to threats occurring with distinct levels of risk.
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Affiliation(s)
- Sanne Westhoff
- Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300 BE Leiden, The Netherlands.
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300 BE Leiden, The Netherlands
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300 BE Leiden, The Netherlands
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225
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Chen F, Chen G, Liu Y, Jin Y, Cheng Z, Liu Y, Yang L, Jin S, Wu W. Pseudomonas aeruginosa Oligoribonuclease Contributes to Tolerance to Ciprofloxacin by Regulating Pyocin Biosynthesis. Antimicrob Agents Chemother 2017; 61:e02256-16. [PMID: 28052848 PMCID: PMC5328516 DOI: 10.1128/aac.02256-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023] Open
Abstract
Bacterial oligoribonuclease (Orn) is a conserved 3'-to-5' exonuclease. In Pseudomonas aeruginosa, it has been demonstrated that Orn plays a major role in the hydrolysis of pGpG, which is required for cyclic-di-GMP homeostasis. Meanwhile, Orn is involved in the degradation of nanoRNAs, which can alter global gene expression by serving as transcription initiation primers. Previously, we found that Orn is required for the type III secretion system and pathogenesis of P. aeruginosa, indicating a role of Orn in the bacterial response to environmental stimuli. Here we report that Orn is required for the tolerance of P. aeruginosa to ciprofloxacin. Transcriptome analysis of an orn mutant revealed the upregulation of pyocin biosynthesis genes. Mutation of genes involved in pyocin biosynthesis in the background of an orn mutant restored bacterial tolerance to ciprofloxacin. We further demonstrate that the upregulation of pyocin biosynthesis genes is due to RecA-mediated autoproteolysis of PrtR, which is the major negative regulator of pyocin biosynthesis genes. In addition, the SOS response genes were upregulated in the orn mutant, indicating a DNA damage stress. Therefore, our results revealed a novel role of Orn in bacterial tolerance to ciprofloxacin.
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Affiliation(s)
- Fei Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Gukui Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yiwei Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yang Liu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, Singapore, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, Singapore, Singapore
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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226
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Ketola T, Mikonranta L, Laakso J, Mappes J. Different food sources elicit fast changes to bacterial virulence. Biol Lett 2017; 12:20150660. [PMID: 26763215 DOI: 10.1098/rsbl.2015.0660] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmentally transmitted, opportunistic bacterial pathogens have a life cycle that alternates between hosts and environmental reservoirs. Resources are often scarce and fluctuating in the outside-host environment, whereas overcoming the host immune system could allow pathogens to establish a new, resource abundant and stable niche within the host. We tested if short-term exposure to different outside-host resource types and concentrations affect Serratia marcescens-(bacterium)'s virulence in Galleria mellonella (moth). As expected, virulence was mostly dictated by the bacterial dose, but we also found a clear increase in virulence when the bacterium had inhabited a low (versus high) resource concentration, or animal-based (versus plant-based) resources for 48 h prior to injection. The results suggest that temporal changes in pathogen's resource environment can induce very rapid changes in virulence and affect infection severity. Such changes could also play an important role in shifts from environmental lifestyle to pathogenicity or switches in host range and have implications for the management of opportunistic pathogens and disease outbreaks.
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Affiliation(s)
- T Ketola
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä 40014, Finland
| | - L Mikonranta
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä 40014, Finland
| | - J Laakso
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä 40014, Finland Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - J Mappes
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä 40014, Finland
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227
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Behie SW, Bonet B, Zacharia VM, McClung DJ, Traxler MF. Molecules to Ecosystems: Actinomycete Natural Products In situ. Front Microbiol 2017; 7:2149. [PMID: 28144233 PMCID: PMC5239776 DOI: 10.3389/fmicb.2016.02149] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/20/2016] [Indexed: 11/13/2022] Open
Abstract
Actinomycetes, filamentous actinobacteria found in numerous ecosystems around the globe, produce a wide range of clinically useful natural products (NP). In natural environments, actinomycetes live in dynamic communities where environmental cues and ecological interactions likely influence NP biosynthesis. Our current understating of these cues, and the ecological roles of NP, is in its infancy. We postulate that understanding the ecological context in which actinomycete metabolites are made is fundamental to advancing the discovery of novel NP. In this review we explore the ecological relevance of actinomycetes and their secondary metabolites from varying ecosystems, and suggest that investigating the ecology of actinomycete interactions warrants particular attention with respect to metabolite discovery. Furthermore, we focus on the chemical ecology and in situ analysis of actinomycete NP and consider the implications for NP biosynthesis at ecosystem scales.
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Affiliation(s)
- Scott W Behie
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Bailey Bonet
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Vineetha M Zacharia
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Dylan J McClung
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
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228
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Bruce JB, West SA, Griffin AS. Bacteriocins and the assembly of natural Pseudomonas fluorescens populations. J Evol Biol 2016; 30:352-360. [PMID: 28000957 PMCID: PMC6849615 DOI: 10.1111/jeb.13010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/31/2016] [Indexed: 12/28/2022]
Abstract
When competing for space and resources, bacteria produce toxins known as bacteriocins to gain an advantage over competitors. Recent studies in the laboratory have confirmed theoretical predictions that bacteriocin production can determine coexistence, by eradicating sensitive competitors or driving the emergence of resistant genotypes. However, there is currently limited evidence that bacteriocin‐mediated competition influences the coexistence and distribution of genotypes in natural environments, and what factors drive interactions towards inhibition remain unclear. Using natural soil populations of Pseudomonas fluorescens, we assessed the ability of the isolates to inhibit one another with respect to spatial proximity in the field, genetic similarity and niche overlap. The majority of isolates were found to produce bacteriocins; however, widespread resistance between coexisting isolates meant relatively few interactions resulted in inhibition. When inhibition did occur, it occurred more frequently between ecologically similar isolates. However, in contrast with results from other natural populations, we found no relationship between the frequency of inhibition and the genetic similarity of competitors. Our results suggest that bacteriocin production plays an important role in mediating competition over resources in natural settings and, by selecting for isolates resistant to local bacteriocin production, can influence the assembly of natural populations of P. fluorescens.
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Affiliation(s)
- J B Bruce
- Department of Zoology, University of Oxford, Oxford, UK
| | - S A West
- Department of Zoology, University of Oxford, Oxford, UK
| | - A S Griffin
- Department of Zoology, University of Oxford, Oxford, UK
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229
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Sundberg LR, Ketola T, Laanto E, Kinnula H, Bamford JKH, Penttinen R, Mappes J. Intensive aquaculture selects for increased virulence and interference competition in bacteria. Proc Biol Sci 2016; 283:20153069. [PMID: 26936249 DOI: 10.1098/rspb.2015.3069] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although increased disease severity driven by intensive farming practices is problematic in food production, the role of evolutionary change in disease is not well understood in these environments. Experiments on parasite evolution are traditionally conducted using laboratory models, often unrelated to economically important systems. We compared how the virulence, growth and competitive ability of a globally important fish pathogen, Flavobacterium columnare, change under intensive aquaculture. We characterized bacterial isolates from disease outbreaks at fish farms during 2003-2010, and compared F. columnare populations in inlet water and outlet water of a fish farm during the 2010 outbreak. Our data suggest that the farming environment may select for bacterial strains that have high virulence at both long and short time scales, and it seems that these strains have also evolved increased ability for interference competition. Our results are consistent with the suggestion that selection pressures at fish farms can cause rapid changes in pathogen populations, which are likely to have long-lasting evolutionary effects on pathogen virulence. A better understanding of these evolutionary effects will be vital in prevention and control of disease outbreaks to secure food production.
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Affiliation(s)
- Lotta-Riina Sundberg
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
| | - Tarmo Ketola
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
| | - Elina Laanto
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
| | - Hanna Kinnula
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
| | - Jaana K H Bamford
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
| | - Reetta Penttinen
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
| | - Johanna Mappes
- University of Jyvaskyla, Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science (and Nanoscience Centre), PO Box 35, Jyvaskyla 40014, Finland
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230
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Growth differences and competition between Listeria monocytogenes strains determine their predominance on ham slices and lead to bias during selective enrichment with the ISO protocol. Int J Food Microbiol 2016; 235:60-70. [DOI: 10.1016/j.ijfoodmicro.2016.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/20/2016] [Accepted: 07/11/2016] [Indexed: 12/21/2022]
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231
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Ghoul M, Mitri S. The Ecology and Evolution of Microbial Competition. Trends Microbiol 2016; 24:833-845. [DOI: 10.1016/j.tim.2016.06.011] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/15/2016] [Accepted: 06/28/2016] [Indexed: 01/23/2023]
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232
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Rendueles O, Velicer GJ. Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes. ISME JOURNAL 2016; 11:555-568. [PMID: 27662568 PMCID: PMC5270557 DOI: 10.1038/ismej.2016.115] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/19/2016] [Accepted: 07/03/2016] [Indexed: 01/16/2023]
Abstract
Evolutionary adaptation can be achieved by mechanisms accessible to all organisms, including faster growth and interference competition, but self-generated motility offers additional possibilities. We tested whether 55 populations of the bacterium Myxococcus xanthus that underwent selection for increased fitness at the leading edge of swarming colonies adapted by swarming faster toward unused resources or by other means. Populations adapted greatly but diversified markedly in both swarming phenotypes and apparent mechanisms of adaptation. Intriguingly, although many adapted populations swarm intrinsically faster than their ancestors, numerous others do not. Some populations evolved interference competition toward their ancestors, whereas others gained the ability to facultatively increase swarming rate specifically upon direct interaction with ancestral competitors. Our results both highlight the diverse range of mechanisms by which actively motile organisms can adapt evolutionarily and help to explain the high levels of swarming-phenotype diversity found in local soil populations of M. xanthus.
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Affiliation(s)
- Olaya Rendueles
- Institute for Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich, Switzerland
| | - Gregory J Velicer
- Institute for Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich, Switzerland
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233
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Janek D, Zipperer A, Kulik A, Krismer B, Peschel A. High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors. PLoS Pathog 2016; 12:e1005812. [PMID: 27490492 PMCID: PMC4973975 DOI: 10.1371/journal.ppat.1005812] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023] Open
Abstract
The human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as Staphylococcus aureus. The potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied. Of 89 nasal Staphylococcus isolates, unexpectedly, the vast majority (84%) was found to produce antimicrobial substances in particular under habitat-specific stress conditions, such as iron limitation or exposure to hydrogen peroxide. Activity spectra were generally narrow but highly variable with activities against certain nasal members of the Actinobacteria, Proteobacteria, Firmicutes, or several groups of bacteria. Staphylococcus species and many other Firmicutes were insusceptible to most of the compounds. A representative bacteriocin was identified as a nukacin-related peptide whose inactivation reduced the capacity of the producer Staphylococcus epidermidis IVK45 to limit growth of other nasal bacteria. Of note, the bacteriocin genes were found on mobile genetic elements exhibiting signs of extensive horizontal gene transfer and rearrangements. Thus, continuously evolving bacteriocins appear to govern bacterial competition in the human nose and specific bacteriocins may become important agents for eradication of notorious opportunistic pathogens from human microbiota. The complex and dynamic microbial communities of human body surfaces are of utmost importance for human body functions in health and diseases. Human microbiomes contribute to metabolic processes, instruct the immune system, and often include antibiotic-resistant pathogens, responsible for the majority of severe bacterial infections. It is generally accepted that microbiota composition is strongly affected by mechanisms of microbial interference, but how specific bacteria may achieve fitness benefits and outcompete other microbes has remained largely unknown. We demonstrate that production of antimicrobial bacteriocins is not an occasional trait but a dominant and highly variable strategy among human nasal bacteria for limiting the growth of competing microbes. We found that more than 80% of nasal Staphylococcus isolates produce bacteriocins with highly diverse activity spectra, in particular under habitat-specific stress conditions such as iron limitation and exposure to hydrogen peroxide. Inactivation of a representative bacteriocin diminished the producer’s competitive capability indicating that bacteriocins may be a major driving force for the dynamics of microbiomes in nutrient-poor habitats such as the human nose. The identification of bacteriocin genes on mobile genetic elements with composite structure suggests that they are subject to highly dynamic co-evolutionary processes.
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Affiliation(s)
- Daniela Janek
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
- German Center for Infection Research, Partner site Tübingen, Tübingen, Germany
| | - Alexander Zipperer
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
- German Center for Infection Research, Partner site Tübingen, Tübingen, Germany
| | - Andreas Kulik
- German Center for Infection Research, Partner site Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
- German Center for Infection Research, Partner site Tübingen, Tübingen, Germany
- * E-mail:
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
- German Center for Infection Research, Partner site Tübingen, Tübingen, Germany
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234
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Nice or nasty: Protein translocation between bacteria and the different forms of response. Proc Natl Acad Sci U S A 2016; 113:8559-61. [PMID: 27422548 DOI: 10.1073/pnas.1609443113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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235
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236
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Jagmann N, Bleicher V, Busche T, Kalinowski J, Philipp B. The guanidinobutyrase GbuA is essential for the alkylquinolone-regulated pyocyanin production during parasitic growth of Pseudomonas aeruginosa in co-culture with Aeromonas hydrophila. Environ Microbiol 2016; 18:3550-3564. [PMID: 27322205 DOI: 10.1111/1462-2920.13419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa controls the production of virulence factors by quorum sensing (QS). Besides cell density, QS in P. aeruginosa is co-regulated by metabolic influences, especially nutrient limitation. Previously, a co-culture model system was established consisting of P. aeruginosa and the chitinolytic bacterium Aeromonas hydrophila, in which parasitic growth of P. aeruginosa is strictly dependent on the QS-controlled production of pyocyanin in response to nutrient limitation (Jagmann et al., ). In this study, the co-culture was employed to identify novel genes involved in the regulation of pyocyanin production. Via transposon mutagenesis, the gene gbuA encoding a guanidinobutyrase was identified, deletion of which led to a loss of pyocyanin production in co-cultures and to a reduced pyocyanin production in single cultures. Addition of the natural substrate of GbuA to the mutant strain enhanced the negative effect on pyocyanin production in single cultures. The gbuA mutant showed a reduced transcription of the pqsABCDE operon and could be complemented by PqsE overexpression and addition of alkylquinolone signal molecules. The strong effect of gbuA deletion on the QS-controlled pyocyanin production in co-cultures showed the value of this approach for the discovery of novel gene functions linking metabolism and QS in P. aeruginosa.
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Affiliation(s)
- Nina Jagmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität (WWU) Münster, Corrensstr. 3, Münster, 48149, Germany
| | - Vera Bleicher
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität (WWU) Münster, Corrensstr. 3, Münster, 48149, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Universitätsstr. 25, Bielefeld, 33615, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Universitätsstr. 25, Bielefeld, 33615, Germany
| | - Bodo Philipp
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität (WWU) Münster, Corrensstr. 3, Münster, 48149, Germany.
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237
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Interbacterial signaling via Burkholderia contact-dependent growth inhibition system proteins. Proc Natl Acad Sci U S A 2016; 113:8296-301. [PMID: 27335458 DOI: 10.1073/pnas.1606323113] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In prokaryotes and eukaryotes, cell-cell communication and recognition of self are critical to coordinate multicellular functions. Although kin and kind discrimination are increasingly appreciated to shape naturally occurring microbe populations, the underlying mechanisms that govern these interbacterial interactions are insufficiently understood. Here, we identify a mechanism of interbacterial signal transduction that is mediated by contact-dependent growth inhibition (CDI) system proteins. CDI systems have been characterized by their ability to deliver a polymorphic protein toxin into the cytoplasm of a neighboring bacterium, resulting in growth inhibition or death unless the recipient bacterium produces a corresponding immunity protein. Using the model organism Burkholderia thailandensis, we show that delivery of a catalytically active CDI system toxin to immune (self) bacteria results in gene expression and phenotypic changes within the recipient cells. Termed contact-dependent signaling (CDS), this response promotes biofilm formation and other community-associated behaviors. Engineered strains that are isogenic with B. thailandensis, except the DNA region encoding the toxin and immunity proteins, did not display CDS, whereas a strain of Burkholderia dolosa producing a nearly identical toxin-immunity pair induced signaling in B. thailandensis Our data indicate that bcpAIOB loci confer dual benefits; they direct antagonism toward non-self bacteria and promote cooperation between self bacteria, with self being defined by the bcpAIOB allele and not by genealogic relatedness.
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238
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Abstract
The ability of bacteria to recognize kin provides a means to form social groups. In turn these groups can lead to cooperative behaviors that surpass the ability of the individual. Kin recognition involves specific biochemical interactions between a receptor(s) and an identification molecule(s). Recognition specificity, ensuring that nonkin are excluded and kin are included, is critical and depends on the number of loci and polymorphisms involved. After recognition and biochemical perception, the common ensuing cooperative behaviors include biofilm formation, quorum responses, development, and swarming motility. Although kin recognition is a fundamental mechanism through which cells might interact, microbiologists are only beginning to explore the topic. This review considers both molecular and theoretical aspects of bacterial kin recognition. Consideration is also given to bacterial diversity, genetic relatedness, kin selection theory, and mechanisms of recognition.
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Affiliation(s)
- Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071;
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239
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Krezalek MA, Skowron KB, Guyton KL, Shakhsheer B, Hyoju S, Alverdy JC. The intestinal microbiome and surgical disease. Curr Probl Surg 2016; 53:257-93. [PMID: 27497246 DOI: 10.1067/j.cpsurg.2016.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/07/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Monika A Krezalek
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Kinga B Skowron
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Kristina L Guyton
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Baddr Shakhsheer
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Sanjiv Hyoju
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - John C Alverdy
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL.
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240
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241
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Aussel L, Beuzón CR, Cascales E. Meeting report: Adaptation and communication of bacterial pathogens. Virulence 2016; 7:481-90. [PMID: 26890494 DOI: 10.1080/21505594.2016.1152441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteria usually live in complex environments, sharing niche and resources with other bacterial species, unicellular eukaryotic cells or complex organisms. Thus, they have evolved mechanisms to communicate, to compete and to adapt to changing environment as diverse as human tissues, animals or plants. Understanding the molecular mechanisms underlying these adaptation processes is therefore of primary importance for epidemiology and human health protection, and was the focus of a Current Trends in Biomedicine workshop organized by the International University of Andalucia in late October 2015 in Baeza (Spain). The topic was covered by complementary sessions: (i) interbacterial communication and competition that enable a better access to nutrients or a more efficient colonization of the ecological niche, (ii) adaptation of intracellular pathogens to their host, focusing on metabolic pathways, adaptive mechanisms and populational heterogeneity, and (iii) adaptation of animal and plant pathogens as well as plant-associated bacteria to a plant niche. This workshop emphasized the broad repertoire of mechanisms and factors bacteria have evolved to become efficient pathogens.
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Affiliation(s)
- Laurent Aussel
- a Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université , CNRS - UMR 7257, Marseille Cedex , France
| | - Carmen R Beuzón
- b Departamento de Biología Celular , Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC) , Málaga , Spain
| | - Eric Cascales
- c Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université , CNRS - UMR 7255, Marseille Cedex , France
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242
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Bacterial tweets and podcasts #signaling#eavesdropping#microbialfightclub. Mol Biochem Parasitol 2016; 208:41-8. [PMID: 27208877 DOI: 10.1016/j.molbiopara.2016.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/16/2016] [Indexed: 11/22/2022]
Abstract
Once thought to live independently, bacteria are now known to be highly social organisms. Their behaviors ranges from cooperatively forming complex multispecies communities to fiercely competing for resources. Work over the past fifty years has shown that bacteria communicate through diverse mechanisms, such as exchanging diffusible molecules, exporting molecules in membrane vesicles, and interacting through direct cell-cell contact. These methods allow bacteria to sense and respond to other cells around them and coordinate group behavior. In this review, we share the discoveries and lessons learned in the field of bacterial communication with the aim of providing insights to parasitologists and other researchers working on related questions.
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243
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Effect of the competitive growth of Lactobacillus sakei MN on the growth kinetics of Listeria monocytogenes Scott A in model meat gravy. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.11.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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244
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Schluter J, Schoech AP, Foster KR, Mitri S. The Evolution of Quorum Sensing as a Mechanism to Infer Kinship. PLoS Comput Biol 2016; 12:e1004848. [PMID: 27120081 PMCID: PMC4847791 DOI: 10.1371/journal.pcbi.1004848] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/04/2016] [Indexed: 01/30/2023] Open
Abstract
Bacteria regulate many phenotypes via quorum sensing systems. Quorum sensing is typically thought to evolve because the regulated cooperative phenotypes are only beneficial at certain cell densities. However, quorum sensing systems are also threatened by non-cooperative "cheaters" that may exploit quorum-sensing regulated cooperation, which begs the question of how quorum sensing systems are maintained in nature. Here we study the evolution of quorum sensing using an individual-based model that captures the natural ecology and population structuring of microbial communities. We first recapitulate the two existing observations on quorum sensing evolution: density-dependent benefits favor quorum sensing but competition and cheating will destabilize it. We then model quorum sensing in a dense community like a biofilm, which reveals a novel benefit to quorum sensing that is intrinsically evolutionarily stable. In these communities, competing microbial genotypes gradually segregate over time leading to positive correlation between density and genetic similarity between neighboring cells (relatedness). This enables quorum sensing to track genetic relatedness and ensures that costly cooperative traits are only activated once a cell is safely surrounded by clonemates. We hypothesize that under similar natural conditions, the benefits of quorum sensing will not result from an assessment of density but from the ability to infer kinship.
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Affiliation(s)
- Jonas Schluter
- Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Armin P. Schoech
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (KRF); (SM)
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- * E-mail: (KRF); (SM)
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245
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Abstract
Bacterial biofilms are dense and often mixed-species surface-attached communities in which bacteria coexist and compete for limited space and nutrients. Here we present the different antagonistic interactions described in biofilm environments and their underlying molecular mechanisms, along with ecological and evolutionary insights as to how competitive interactions arise and are maintained within biofilms.
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246
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Zhu X, Jiang L, Ye M, Sun L, Gragnoli C, Wu R. Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping. Trends Genet 2016; 32:256-268. [PMID: 27017185 DOI: 10.1016/j.tig.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/12/2016] [Accepted: 02/19/2016] [Indexed: 12/27/2022]
Abstract
Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation.
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Affiliation(s)
- Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lidan Sun
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Claudia Gragnoli
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; Molecular Biology Laboratory, Bios Biotech Multi-Diagnostic Health Center, Rome, Italy
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, Pennsylvania State University, Hershey, PA 17033, USA; Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA.
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247
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Burcham ZM, Hood JA, Pechal JL, Krausz KL, Bose JL, Schmidt CJ, Benbow ME, Jordan HR. Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration. Forensic Sci Int 2016; 264:63-9. [PMID: 27032615 DOI: 10.1016/j.forsciint.2016.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 02/24/2016] [Accepted: 03/10/2016] [Indexed: 01/08/2023]
Abstract
Microbially mediated mechanisms of human decomposition begin immediately after death, and are a driving force for the conversion of a once living organism to a resource of energy and nutrients. Little is known about post-mortem microbiology in cadavers, particularly the community structure of microflora residing within the cadaver and the dynamics of these communities during decomposition. Recent work suggests these bacterial communities undergo taxa turnover and shifts in community composition throughout the post-mortem interval. In this paper we describe how the microbiome of a living host changes and transmigrates within the body after death thus linking the microbiome of a living individual to post-mortem microbiome changes. These differences in the human post-mortem from the ante-mortem microbiome have demonstrated promise as evidence in death investigations. We investigated the post-mortem structure and function dynamics of Staphylococcus aureus and Clostridium perfringens after intranasal inoculation in the animal model Mus musculus L. (mouse) to identify how transmigration of bacterial species can potentially aid in post-mortem interval estimations. S. aureus was tracked using in vivo and in vitro imaging to determine colonization routes associated with different physiological events of host decomposition, while C. perfringens was tracked using culture-based techniques. Samples were collected at discrete time intervals associated with various physiological events and host decomposition beginning at 1h and ending at 60 days post-mortem. Results suggest that S. aureus reaches its highest concentration at 5-7 days post-mortem then begins to rapidly decrease and is undetectable by culture on day 30. The ability to track these organisms as they move in to once considered sterile space may be useful for sampling during autopsy to aid in determining post-mortem interval range estimations, cause of death, and origins associated with the geographic location of human remains during death investigations.
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Affiliation(s)
- Z M Burcham
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.
| | - J A Hood
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.
| | - J L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, USA.
| | - K L Krausz
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - J L Bose
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - C J Schmidt
- Department of Pathology, University of Michigan, MI, USA.
| | - M E Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA; Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA.
| | - H R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.
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248
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Phaeobacter sp. strain Y4I utilizes two separate cell-to-cell communication systems to regulate production of the antimicrobial indigoidine. Appl Environ Microbiol 2016; 81:1417-25. [PMID: 25527537 DOI: 10.1128/aem.02551-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The marine roseobacter Phaeobacter sp. strain Y4I synthesizes the blue antimicrobial secondary metabolite indigoidine when grown in a biofilm or on agar plates. Prior studies suggested that indigoidine production may be, in part, regulated by cell-to-cell communication systems. Phaeobacter sp. strain Y4I possesses two luxR and luxI homologous N-acyl-L-homoserine lactone (AHL)-mediated cell-to-cell communication systems, designated pgaRI and phaRI. We show here that Y4I produces two dominantAHLs, the novel monounsaturated N-(3-hydroxydodecenoyl)-L-homoserine lactone (3OHC(12:1)-HSL) and the relatively common N-octanoyl-L-homoserine lactone (C8-HSL), and provide evidence that they are synthesized by PhaI and PgaI, respectively.A Tn5 insertional mutation in either genetic locus results in the abolishment (pgaR::Tn5) or reduction (phaR::Tn5) of pigment production. Motility defects and denser biofilms were also observed in these mutant backgrounds, suggesting an overlap in the functional roles of these systems. Production of the AHLs occurs at distinct points during growth on an agar surface and was determined by isotope dilution high-performance liquid chromatography–tandem mass spectrometry (ID-HPLC-MS/MS) analysis.Within 2 h of surface inoculation, only 3OHC(12:1)-HSL was detected in agar extracts. As surface-attached cells became established (at approximately 10 h), the concentration of 3OHC(12:1)-HSL decreased, and the concentration of C8-HSL increased rapidly over 14 h.After longer (>24-h) establishment periods, the concentrations of the two AHLs increased to and stabilized at approximately 15 nM and approximately 600 nM for 3OHC12:1-HSL and C8-HSL, respectively. In contrast, the total amount of indigoidine increased steadily from undetectable to 642 Mby 48 h. Gene expression profiles of the AHL and indigoidine synthases (pgaI, phaI, and igiD) were consistent with their metabolite profiles. These data provide evidence that pgaRI and phaRI play overlapping roles in the regulation of indigoidine biosynthesis, and it is postulated that this allows Phaeobacter sp. strain Y4I to coordinate production of indigoidine with different growth-phase-dependent physiologies.
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249
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 488] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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250
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Tyc O, Zweers H, de Boer W, Garbeva P. Volatiles in Inter-Specific Bacterial Interactions. Front Microbiol 2015; 6:1412. [PMID: 26733959 PMCID: PMC4683202 DOI: 10.3389/fmicb.2015.01412] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/27/2015] [Indexed: 01/08/2023] Open
Abstract
The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Hans Zweers
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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