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Gtari M, Beauchemin NJ, Sarker I, Sen A, Ghodhbane-Gtari F, Tisa LS. An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia. Appl Environ Microbiol 2024; 90:e0028824. [PMID: 38651928 PMCID: PMC11107149 DOI: 10.1128/aem.00288-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems. IMPORTANCE While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.
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Affiliation(s)
- Maher Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
| | - Nicholas J. Beauchemin
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Indrani Sarker
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Faten Ghodhbane-Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of La Manouba, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Guillén S, Domínguez L, Mañas P, Álvarez I, Carrasco E, Cebrián G. Modelling the low temperature growth boundaries of Salmonella Enteritidis in raw and pasteurized egg yolk, egg white and liquid whole egg: Influence of the initial concentration. Int J Food Microbiol 2024; 414:110619. [PMID: 38367341 DOI: 10.1016/j.ijfoodmicro.2024.110619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 12/27/2023] [Accepted: 02/04/2024] [Indexed: 02/19/2024]
Abstract
Salmonella is the most frequently reported cause of foodborne outbreaks with known origin in Europe, with eggs and egg products standing out as the most frequent food source (when it was known). The growth and survival of Salmonella in eggs and egg products have been extensively studied and, recently, it has been reported that factors such as the initial concentration and thermal history of the egg product can also influence its growth capability. Therefore, the objective of this study was to define the boundary zones of the growth/no growth domain of Salmonella Enteritidis (4 strains) as a function of temperature (low temperature boundary) and the initial concentration in different egg products. A series of polynomial logistic regression equations were successfully adjusted, allowing the study of these factors and their interaction on the probability of growth of S. Enteritidis in these products. Results obtained indicate that the minimum growth temperatures of Salmonella Enteritidis are higher in egg white (9.5-18.3 °C) than in egg yolk (7.1-7.8 °C) or liquid whole egg (7.2-7.9 °C). Results also demonstrate that in raw liquid whole egg and raw and pasteurized egg white, the minimum growth temperature of Salmonella Enteritidis does depend on the initial concentration. Similarly, the previous thermal history of the egg product only influenced the minimum growth temperature in some of them. On the other hand, large differences in the minimum growth temperatures among strains were observed in some products (up to approx. 6 °C in egg white). Finally, it should be noted that none of the strains grew at 5 °C under any of the conditions assayed. Therefore, storage of egg products (particularly whole liquid egg and egg yolk) below this temperature might be regarded/proposed as a good management approach. Our experimental approach has allowed us to provide a more accurate prediction of S. Enteritidis minimum growth temperatures in egg products by taking into account additional factors (initial concentration and thermal history) while also providing a quantification of the intra-specie variability. This would be of high relevance for improving the safety of egg products.
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Affiliation(s)
- Silvia Guillén
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Lara Domínguez
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Pilar Mañas
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Ignacio Álvarez
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Elena Carrasco
- Departamento de Bromatología y Tecnología de los Alimentos, Campus de Excelencia Internacional Agroalimentario CeiA3, UIC ENZOEM, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
| | - Guillermo Cebrián
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain.
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3
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Moreno-Fenoll C, Ardré M, Rainey PB. Polar accumulation of pyoverdin and exit from stationary phase. MICROLIFE 2024; 5:uqae001. [PMID: 38370141 PMCID: PMC10873284 DOI: 10.1093/femsml/uqae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Pyoverdin is a water-soluble metal-chelator synthesized by members of the genus Pseudomonas and used for the acquisition of insoluble ferric iron. Although freely diffusible in aqueous environments, preferential dissemination of pyoverdin among adjacent cells, fine-tuning of intracellular siderophore concentrations, and fitness advantages to pyoverdin-producing versus nonproducing cells, indicate control of location and release. Here, using time-lapse fluorescence microscopy to track single cells in growing microcolonies of Pseudomonas fluorescens SBW25, we show accumulation of pyoverdin at cell poles. Accumulation occurs on cessation of cell growth, is achieved by cross-feeding in pyoverdin-nonproducing mutants and is reversible. Moreover, accumulation coincides with localization of a fluorescent periplasmic reporter, suggesting that pyoverdin accumulation at cell poles is part of the general cellular response to starvation. Compatible with this conclusion is absence of non-accumulating phenotypes in a range of pyoverdin mutants. Analysis of the performance of pyoverdin-producing and nonproducing cells under conditions promoting polar accumulation shows an advantage to accumulation on resumption of growth after stress. Examination of pyoverdin polar accumulation in a multispecies community and in a range of laboratory and natural species of Pseudomonas, including P. aeruginosa PAO1 and P. putida KT2440, confirms that the phenotype is characteristic of Pseudomonas.
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Affiliation(s)
- Clara Moreno-Fenoll
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Maxime Ardré
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
| | - Paul B Rainey
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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4
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Heffernan JR, Wildenthal JA, Tran H, Katumba GL, McCoy WH, Henderson JP. Yersiniabactin is a quorum-sensing autoinducer and siderophore in uropathogenic Escherichia coli. mBio 2024; 15:e0027723. [PMID: 38236035 PMCID: PMC10865836 DOI: 10.1128/mbio.00277-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024] Open
Abstract
Siderophores are secreted ferric ion chelators used to obtain iron in nutrient-limited environmental niches, including human hosts. While all Escherichia coli express the enterobactin (Ent) siderophore system, isolates from patients with urinary tract infections additionally express the genetically distinct yersiniabactin (Ybt) siderophore system. To determine whether the Ent and Ybt systems are functionally redundant for iron uptake, we compared the growth of different isogenic siderophore biosynthetic mutants in the presence of transferrin, a human iron-binding protein. We observed that Ybt expression does not compensate for deficient Ent expression following low-density inoculation. Using transcriptional and product analysis, we found this non-redundancy to be attributable to a density-dependent transcriptional stimulation cycle in which Ybt functions as an autoinducer. These results distinguish the Ybt system as a combined quorum-sensing and siderophore system. These functions may reflect Ybt as a public good within bacterial communities or as an adaptation to confined, subcellular compartments in infected hosts. This combined functionality may contribute to the extraintestinal pathogenic potential of E. coli and related Enterobacterales.IMPORTANCEPatients with urinary tract infections are often infected with Escherichia coli strains carrying adaptations that increase their pathogenic potential. One of these adaptations is the accumulation of multiple siderophore systems, which scavenge iron for nutritional use. While iron uptake is important for bacterial growth, the increased metabolic costs of siderophore production could diminish bacterial fitness during infections. In a siderophore-dependent growth condition, we show that the virulence-associated yersiniabactin siderophore system in uropathogenic E. coli is not redundant with the ubiquitous E. coli enterobactin system. This arises not from differences in iron-scavenging activity but because yersiniabactin is preferentially expressed during bacterial crowding, leaving bacteria dependent upon enterobactin for growth at low cell density. Notably, this regulatory mode arises because yersiniabactin stimulates its own expression, acting as an autoinducer in a previously unappreciated quorum-sensing system. This unexpected result connects quorum-sensing with pathogenic potential in E. coli and related Enterobacterales.
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Affiliation(s)
- James R. Heffernan
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John A. Wildenthal
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Hung Tran
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - George L. Katumba
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William H. McCoy
- Division of Dermatology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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5
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Lin H, Wang D, Wang Q, Mao J, Bai Y, Qu J. Interspecific competition prevents the proliferation of social cheaters in an unstructured environment. THE ISME JOURNAL 2024; 18:wrad038. [PMID: 38365247 PMCID: PMC10939377 DOI: 10.1093/ismejo/wrad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 02/18/2024]
Abstract
Bacterial communities are intricate ecosystems in which various members interact, compete for resources, and influence each other's growth. Antibiotics intensify this complexity, posing challenges in maintaining biodiversity. In this study, we delved into the behavior of kin bacterial communities when subjected to antibiotic perturbations, with a particular focus on how interspecific interactions shape these responses. We hypothesized that social cheating-where resistant strains shield both themselves and neighboring cheaters-obstructed coexistence, especially when kin bacteria exhibited varied growth rates and antibiotic sensitivities. To explore potential pathways to coexistence, we incorporated a third bacterial member, anticipating a shift in the dynamics of community coexistence. Simulations and experimental bacterial communities confirmed our predictions, emphasizing the pivotal role of interspecific competition in promoting coexistence under antibiotic interference. These insights are crucial for understanding bacterial ecosystem stability, interpreting drug-microbiome interactions, and predicting bacterial community adaptations to environmental changes.
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Affiliation(s)
- Hui Lin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qiaojuan Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Jie Mao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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6
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. J Biol Chem 2024; 300:105554. [PMID: 38072063 PMCID: PMC10788543 DOI: 10.1016/j.jbc.2023.105554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here, we find the siderophore enterobactin (Ent) and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined Ent biosynthesis and import mutants, we identify lower molecular weight dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-Ent complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed Ent, we find that Ent and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - John I Robinson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Lindsey K Steinberg
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA.
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7
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Souza LS, Folmar J, Salle A, Eda S. Partial privatization and cooperation in biofilms. AN ACAD BRAS CIENC 2023; 95:e20220985. [PMID: 38126521 DOI: 10.1590/0001-3765202320220985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/24/2023] [Indexed: 12/23/2023] Open
Abstract
The evolution of cooperation in microbes is a challenge to explain because microbes producing costly goods for the benefit of any strain types (cooperators) often withstand the threat of elimination by interacting with individuals that exploit these benefits without contributing (defectors). Here we developed an individual-based model to investigate whether partial privatization via the partial secretion of goods can favor cooperation in structured, surface-attaching microbial populations, biofilms. Whether partial secretion can favor cooperation in biofilms is unclear for two reasons. First, while partial privatization has been shown to foster cooperation in unstructured populations, little is known about the role of partial privatization in biofilms. Second, while limited diffusion of goods favors cooperation in biofilms because molecules are more likely to be shared with genetically-related individuals, partial secretion reduces goods that could have been directed towards genetically related individuals. Our results show that although partial secretion weakens the role that limited diffusion has on fostering cooperation, partial secretion favors cooperation in biofilms. Overall, our results provide predictions that future experiments could test to reveal contributions of relatedness and partial secretion to the social evolution of biofilms.
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Affiliation(s)
- Lucas S Souza
- University of Tennessee, Department of Ecology and Evolutionary Biology, 1416 Circle Dr, 37996, Knoxville, Tennessee, USA
| | - Jackie Folmar
- Yale University, Yale University Office of Undergraduate Admissions, 38 Hillhouse Ave, 06520-8234, New Haven, Connecticut, USA
| | - Abby Salle
- Lincoln Memorial University, College of Osteopathic Medicine, 6965 Cumberland Gap Pkwy, 37752, Harrogate, Tennessee, USA
| | - Shigetoshi Eda
- University of Tennessee, Department of Forestry, Wildlife and Fisheries, 2505 E.J. Chapman Drive, 37996-4563, Knoxville, Tennessee, USA
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8
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Shao J, Rong N, Wu Z, Gu S, Liu B, Shen N, Li Z. Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters. iScience 2023; 26:107396. [PMID: 37701813 PMCID: PMC10494312 DOI: 10.1016/j.isci.2023.107396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/26/2023] [Accepted: 07/11/2023] [Indexed: 09/14/2023] Open
Abstract
Microbes shape their habitats by consuming resources and producing a diverse array of chemicals that can serve as public goods. Despite the risk of exploitation by cheaters, genes encoding sharable molecules like siderophores are widely found in nature, prompting investigations into the mechanisms that allow producers to resist invasion by cheaters. In this work, we presented the chemostat-typed "resource partition model" to demonstrate that dividing the iron resource between private and public siderophores can promote stable or dynamic coexistence between producers and cheaters in a well-mixed environment. Moreover, our analysis shows that when microbes not only consume but also produce resources, chemical innovation leads to stability criteria that differ from those of classical consumer resource models, resulting in more complex dynamics. Our work sheds light on the role of chemical innovations in microbial communities and the potential for resource partition to facilitate dynamical coexistence between cooperative and cheating organisms.
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Affiliation(s)
- Jiqi Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhenchao Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Beibei Liu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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9
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550588. [PMID: 37546885 PMCID: PMC10402112 DOI: 10.1101/2023.07.25.550588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Uropathogenic E. coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here we find the siderophore enterobactin and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined enterobactin biosynthesis and import mutants, we identify lower molecular weight, dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-enterobactin complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed enterobactin, we find that enterobactin and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John I. Robinson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsey K. Steinberg
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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10
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Anne F, Gwenaëlle G, Isabelle S, Pierre F. Improved engineering of Pseudomonas aeruginosa to study the adaptation of pyoverdine production under intra- or inter- specific bacterial competition. J Microbiol Methods 2023; 210:106753. [PMID: 37271375 DOI: 10.1016/j.mimet.2023.106753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/27/2023] [Accepted: 05/28/2023] [Indexed: 06/06/2023]
Abstract
Pseudomonas aeruginosa (PA) is a common cause of chronic infections, particularly feared by cystic fibrosis patients. PA colonizes the lung where it adapts to the local environment, and/or to treatments by drugs. This genotypic and phenotypic adaptation, in turns, influences its interaction with its environment, like bacteria from the microbiota. As an example, to access iron, PA produces and secretes two siderophores, pyoverdine and pyochelin that are iron chelators scavenging iron from the environment and bringing it back into the bacterial cells. Siderophores production depends on the level of iron starvation, on the presence of other bacteria, etc. this latter component being less well investigated. Even if studies on bacterial interactions, and their evolution, have been increasing since several years, we are still facing a lack of tools, for example, to specifically follow the growth of PA isolates in such competitive environments. We thus improved a cloning method to gain time in the cloning steps, to lower the polar effects, and to accurately follow the interactions of any PA isolate with other bacteria. For that, a fluorescent reporter gene was inserted between two genes, the glutamine-fructose-6-phosphate transaminase (glmS) and PA5548. This reporter was efficiently produced either from an inducible or a house-keeping promoter, and its expression did not lead to polar effects. We used this strain to study intra and inter-specific bacterial competitions for iron between different lung pathogens. We thus grew wild-type PA together either with an isogenic PA ΔpvdS variant, that does not produce the most efficient siderophore pyoverdine, or with Klebsiella pneumoniae or Acinetobacter baumanii, two other lung pathogens. We finally monitored the effect of the loss of pvdS on the competition between PA and the other bacterial species. These studies enabled us to differentiate intra from inter specific competitions, both arising in the lung environment, and pinpoint the importance of the bacterial specie for the adaptation of pyoverdine production.
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Affiliation(s)
- Forster Anne
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Graulier Gwenaëlle
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Schalk Isabelle
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Fechter Pierre
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France.
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11
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Pezzotti G, Ofuji S, Imamura H, Adachi T, Yamamoto T, Kanamura N, Ohgitani E, Marin E, Zhu W, Mazda O, Togo A, Kimura S, Iwata T, Shiba H, Ouhara K, Aoki T, Kawai T. In Situ Raman Analysis of Biofilm Exopolysaccharides Formed in Streptococcus mutans and Streptococcus sanguinis Commensal Cultures. Int J Mol Sci 2023; 24:ijms24076694. [PMID: 37047667 PMCID: PMC10095091 DOI: 10.3390/ijms24076694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
This study probed in vitro the mechanisms of competition/coexistence between Streptococcus sanguinis (known for being correlated with health in the oral cavity) and Streptococcus mutans (responsible for aciduric oral environment and formation of caries) by means of quantitative Raman spectroscopy and imaging. In situ Raman assessments of live bacterial culture/coculture focusing on biofilm exopolysaccharides supported the hypothesis that both species engaged in antagonistic interactions. Experiments of simultaneous colonization always resulted in coexistence, but they also revealed fundamental alterations of the biofilm with respect to their water-insoluble glucan structure. Raman spectra (collected at fixed time but different bacterial ratios) showed clear changes in chemical bonds in glucans, which pointed to an action by Streptococcus sanguinis to discontinue the impermeability of the biofilm constructed by Streptococcus mutans. The concurrent effects of glycosidic bond cleavage in water-insoluble α - 1,3-glucan and oxidation at various sites in glucans' molecular chains supported the hypothesis that secretion of oxygen radicals was the main "chemical weapon" used by Streptococcus sanguinis in coculture.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Department of Molecular Science and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Satomi Ofuji
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Azusa Togo
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kimura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tadahisa Iwata
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Kazuhisa Ouhara
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Takashi Aoki
- Faculty of Fiber Science and Engineering, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, FL 33314, USA
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12
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Heffernan JR, Katumba GL, McCoy WH, Henderson JP. Yersiniabactin is a quorum sensing autoinducer and siderophore in uropathogenic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527953. [PMID: 36798367 PMCID: PMC9934619 DOI: 10.1101/2023.02.09.527953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Siderophores are secreted ferric ion chelators used to obtain iron in nutrient-limited environmental niches, including human hosts. While all E. coli encode the enterobactin (Ent) siderophore system, isolates from patients with urinary tract infections additionally encode the genetically distinct yersiniabactin (Ybt) siderophore system. To determine whether the Ent and Ybt systems are functionally redundant for iron uptake, we compared growth of different isogenic siderophore biosynthesis mutants in the presence of transferrin, a human iron-binding protein. We observed that the Ybt system does not compensate for loss of the Ent system during siderophore-dependent, low density growth. Using transcriptional and product analysis, we found that this non-redundancy is attributable to a density-dependent transcriptional stimulation cycle in which Ybt assume an additional autoinducer function. These results distinguish the Ybt system as a combined quorum-sensing and siderophore system. These functions may reflect Ybt as a public good within bacterial communities or as an adaptation to confined, subcellular compartments in infected hosts. The efficiency of this arrangement may contribute to the extraintestinal pathogenic potential of E. coli and related Enterobacterales. IMPORTANCE Urinary tract infections (UTIs) are one of the most common human bacterial infections encountered by physicians. Adaptations that increase the pathogenic potential of commensal microbes such as E.coli are of great interest. One potential adaptation observed in clinical isolates is accumulation of multiple siderophore systems, which scavenge iron for nutritional use. While iron uptake is important for bacterial growth, the increased metabolic costs of siderophore production could diminish bacterial fitness during infections. In a siderophore-dependent growth conditions, we show that the virulence-associated yersiniabactin siderophore system in uropathogenic E. coli is not redundant with the ubiquitous E. coli enterobactin system. This arises not from differences in iron scavenging activity but because yersiniabactin is preferentially expressed during bacterial crowding, leaving bacteria dependent upon enterobactin for growth at low cell density. Notably, this regulatory mode arises because yersiniabactin stimulates its own expression, acting as an autoinducer in a previously unappreciated quorum-sensing system. This unexpected result connects quorum-sensing with pathogenic potential in E. coli and related Enterobacterales.
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13
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Souza LS, Irie Y, Eda S. Black Queen Hypothesis, partial privatization, and quorum sensing evolution. PLoS One 2022; 17:e0278449. [PMID: 36449503 PMCID: PMC9710793 DOI: 10.1371/journal.pone.0278449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Microorganisms produce costly cooperative goods whose benefit is partially shared with nonproducers, called 'mixed' goods. The Black Queen Hypothesis predicts that partial privatization has two major evolutionary implications. First, to favor strains producing several types of mixed goods over nonproducing strains. Second, to favor the maintenance of cooperative traits through different strains instead of having all cooperative traits present in a single strain (metabolic specialization). Despite the importance of quorum sensing regulation of mixed goods, it is unclear how partial privatization affects quorum sensing evolution. Here, we studied the influence of partial privatization on the evolution of quorum sensing. We developed a mathematical population genetics model of an unstructured microbial population considering four strains that differ in their ability to produce an autoinducer (quorum sensing signaling molecule) and a mixed good. Our model assumes that the production of the autoinducers and the mixed goods is constitutive and/or depends on quorum sensing. Our results suggest that, unless autoinducers are costless, partial privatization cannot favor quorum sensing. This result occurs because with costly autoinducers: (1) a strain that produces both autoinducer and goods (fully producing strain) cannot persist in the population; (2) the strain only producing the autoinducer and the strain producing mixed goods in response to the autoinducers cannot coexist, i.e., metabolic specialization cannot be favored. Together, partial privatization might have been crucial to favor a primordial form of quorum sensing-where autoinducers were thought to be a metabolic byproduct (costless)-but not the transition to nowadays costly autoinducers.
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Affiliation(s)
- Lucas Santana Souza
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Yasuhiko Irie
- Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden
| | - Shigetoshi Eda
- Department of Forestry, Wildlife and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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14
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Lerch BA, Smith DA, Koffel T, Bagby SC, Abbott KC. How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods. PLoS Comput Biol 2022; 18:e1010666. [PMID: 36318525 PMCID: PMC9651594 DOI: 10.1371/journal.pcbi.1010666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/11/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
The production of costly public goods (as distinct from metabolic byproducts) has largely been understood through the realization that spatial structure can minimize losses to non-producing "cheaters" by allowing for the positive assortment of producers. In well-mixed systems, where positive assortment is not possible, the stable production of public goods has been proposed to depend on lineages that become indispensable as the sole producers of those goods while their neighbors lose production capacity through genome streamlining (the Black Queen Hypothesis). Here, we develop consumer-resource models motivated by nitrogen-fixing, siderophore-producing bacteria that consider the role of colimitation in shaping eco-evolutionary dynamics. Our models demonstrate that in well-mixed environments, single "public goods" can only be ecologically and evolutionarily stable if they are partially privatized (i.e., if producers reserve a portion of the product pool for private use). Colimitation introduces the possibility of subsidy: strains producing a fully public good can exclude non-producing strains so long as the producing strain derives sufficient benefit from the production of a second partially private good. We derive a lower bound for the degree of privatization necessary for production to be advantageous, which depends on external resource concentrations. Highly privatized, low-investment goods, in environments where the good is limiting, are especially likely to be stably produced. Coexistence emerges more rarely in our mechanistic model of the external environment than in past phenomenological approaches. Broadly, we show that the viability of production depends critically on the environmental context (i.e., external resource concentrations), with production of shared resources favored in environments where a partially-privatized resource is scarce.
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Affiliation(s)
- Brian A. Lerch
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Derek A. Smith
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas Koffel
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
| | - Sarah C. Bagby
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen C. Abbott
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
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15
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Lissens M, Joos M, Lories B, Steenackers HP. Evolution-proof inhibitors of public good cooperation: a screening strategy inspired by social evolution theory. FEMS Microbiol Rev 2022; 46:6604382. [PMID: 35675280 PMCID: PMC9616471 DOI: 10.1093/femsre/fuac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/22/2022] [Indexed: 01/07/2023] Open
Abstract
Interference with public good cooperation provides a promising novel antimicrobial strategy since social evolution theory predicts that resistant mutants will be counter-selected if they share the public benefits of their resistance with sensitive cells in the population. Although this hypothesis is supported by a limited number of pioneering studies, an extensive body of more fundamental work on social evolution describes a multitude of mechanisms and conditions that can stabilize public behaviour, thus potentially allowing resistant mutants to thrive. In this paper we theorize on how these different mechanisms can influence the evolution of resistance against public good inhibitors. Based hereon, we propose an innovative 5-step screening strategy to identify novel evolution-proof public good inhibitors, which involves a systematic evaluation of the exploitability of public goods under the most relevant experimental conditions, as well as a careful assessment of the most optimal way to interfere with their action. Overall, this opinion paper is aimed to contribute to long-term solutions to fight bacterial infections.
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Affiliation(s)
- Maries Lissens
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven, Leuven, B-3001, Belgium
| | - Mathieu Joos
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven, Leuven, B-3001, Belgium
| | - Bram Lories
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven, Leuven, B-3001, Belgium
| | - Hans P Steenackers
- Corresponding author: Centre of Microbial and Plant Genetics (CMPG), Kasteelpark Arenberg 20 – Box 2460, B-3001 Leuven, Belgium. E-mail:
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16
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Guillén S, Cebrián G. Relationship between iron bioavailability and Salmonella Typhimurium fitness in raw and pasteurized liquid whole egg. Food Microbiol 2022; 104:104008. [DOI: 10.1016/j.fm.2022.104008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
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17
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Li Q, Liu L, Guo A, Zhang X, Liu W, Ruan Y. Formation of Multispecies Biofilms and Their Resistance to Disinfectants in Food Processing Environments: A Review. J Food Prot 2021; 84:2071-2083. [PMID: 34324690 DOI: 10.4315/jfp-21-071] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT In food processing environments, various microorganisms can adhere and aggregate on the surface of equipment, resulting in the formation of multispecies biofilms. Complex interactions among microorganisms may affect the formation of multispecies biofilms and resistance to disinfectants, which are food safety and quality concerns. This article reviews the various interactions among microorganisms in multispecies biofilms, including competitive, cooperative, and neutral interactions. Then, the preliminary mechanisms underlying the formation of multispecies biofilms are discussed in relation to factors, such as quorum-sensing signal molecules, extracellular polymeric substances, and biofilm-regulated genes. Finally, the resistance mechanisms of common contaminating microorganisms to disinfectants in food processing environments are also summarized. This review is expected to facilitate a better understanding of interspecies interactions and provide some implications for the control of multispecies biofilms in food processing. HIGHLIGHTS
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Affiliation(s)
- Qun Li
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Ling Liu
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Ailing Guo
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China.,National Research and Development Center for Egg Processing, Wuhan, Hubei 430070, People's Republic of China
| | - Xinshuai Zhang
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Wukang Liu
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Yao Ruan
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
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18
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Escherichia coli small molecule metabolism at the host-microorganism interface. Nat Chem Biol 2021; 17:1016-1026. [PMID: 34552219 DOI: 10.1038/s41589-021-00807-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Escherichia coli are a common component of the human microbiota, and isolates exhibit probiotic, commensal and pathogenic roles in the host. E. coli members often use diverse small molecule chemistry to regulate intrabacterial, intermicrobial and host-bacterial interactions. While E. coli are considered to be a well-studied model organism in biology, much of their chemical arsenal has only more recently been defined, and much remains to be explored. Here we describe chemical signaling systems in E. coli in the context of the broader field of metabolism at the host-bacteria interface and the role of this signaling in disease modulation.
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19
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Maes S, De Reu K, Van Weyenberg S, Lories B, Heyndrickx M, Steenackers H. Pseudomonas putida as a potential biocontrol agent against Salmonella Java biofilm formation in the drinking water system of broiler houses. BMC Microbiol 2020; 20:373. [PMID: 33308162 PMCID: PMC7731557 DOI: 10.1186/s12866-020-02046-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/19/2020] [Indexed: 11/18/2022] Open
Abstract
Background Environmental biofilms can induce attachment and protection of other microorganisms including pathogens, but can also prevent them from invasion and colonization. This opens the possibility for so-called biocontrol strategies, wherein microorganisms are applied to control the presence of other microbes. The potential for both positive and negative interactions between microbes, however, raises the need for in depth characterization of the sociobiology of candidate biocontrol agents (BCAs). The inside of the drinking water system (DWS) of broiler houses is an interesting niche to apply BCAs, because contamination of these systems with pathogens plays an important role in the infection of broiler chickens and consequently humans. In this study, Pseudomonas putida, which is part of the natural microbiota in the DWS of broiler houses, was evaluated as BCA against the broiler pathogen Salmonella Java. Results To study the interaction between these species, an in vitro model was developed simulating biofilm formation in the drinking water system of broilers. Dual-species biofilms of P. putida strains P1, P2, and P3 with S. Java were characterized by competitive interactions, independent of P. putida strain, S. Java inoculum density and application order. When equal inocula of S. Java and P. putida strains P1 or P3 were simultaneously applied, the interaction was characterized by mutual inhibition, whereas P. putida strain P2 showed an exploitation of S. Java. Lowering the inoculum density of S. Java changed the interaction with P. putida strain P3 also into an exploitation of S. Java. A further increase in S. Java inhibition was established by P. putida strain P3 forming a mature biofilm before applying S. Java. Conclusions This study provides the first results showing the potential of P. putida as BCA against S. Java in the broiler environment. Future work should include more complex microbial communities residing in the DWS, additional Salmonella strains as well as chemicals typically used to clean and disinfect the system. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02046-5.
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Affiliation(s)
- Sharon Maes
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Koen De Reu
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Stephanie Van Weyenberg
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Bram Lories
- Faculty of Bioscience Engineering, Department of Microbial and Molecular Systems (M2S), Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Leuven, Belgium
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium.,Faculty of Veterinary Medicine, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Hans Steenackers
- Faculty of Bioscience Engineering, Department of Microbial and Molecular Systems (M2S), Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Leuven, Belgium.
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20
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Kügler S, Cooper RE, Boessneck J, Küsel K, Wichard T. Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands. Biometals 2020; 33:415-433. [PMID: 33026607 PMCID: PMC7676072 DOI: 10.1007/s10534-020-00258-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023]
Abstract
Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Rebecca E Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Johanna Boessneck
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- The German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany.
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21
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Himoto T, Masaki T. Current Trends of Essential Trace Elements in Patients with Chronic Liver Diseases. Nutrients 2020; 12:nu12072084. [PMID: 32674425 PMCID: PMC7400835 DOI: 10.3390/nu12072084] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Essential trace elements play crucial roles in the maintenance of health, since they are involved in many metabolic pathways. A deficiency or an excess of some trace elements, including zinc, selenium, iron, and copper, frequently causes these metabolic disorders such as impaired glucose tolerance and dyslipidemia. The liver largely regulates most of the metabolism of trace elements, and accordingly, an impairment of liver functions can result in numerous metabolic disorders. The administration or depletion of these trace elements can improve such metabolic disorders and liver dysfunction. Recent advances in molecular biological techniques have helped to elucidate the putative mechanisms by which liver disorders evoke metabolic abnormalities that are due to deficiencies or excesses of these trace elements. A genome-wide association study revealed that a genetic polymorphism affected the metabolism of a specific trace element. Gut dysbiosis was also responsible for impairment of the metabolism of a trace element. This review focuses on the current trends of four trace elements in chronic liver diseases, including chronic hepatitis, liver cirrhosis, nonalcoholic fatty liver disease, and autoimmune liver diseases. The novel mechanisms by which the trace elements participated in the pathogenesis of the chronic liver diseases are also mentioned.
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Affiliation(s)
- Takashi Himoto
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, 281-1, Hara, Mure-Cho, Takamatsu, Kagawa 761-0123, Japan
- Correspondence: ; Tel.: +81-87-870-1240; Fax: +81-87-870-1202
| | - Tsutomu Masaki
- Department of Gastroenterology and Neurology, Kagawa University School of Medicine, Kagawa 761-0123, Japan;
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22
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Perraud Q, Cantero P, Roche B, Gasser V, Normant VP, Kuhn L, Hammann P, Mislin GLA, Ehret-Sabatier L, Schalk IJ. Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms. Mol Cell Proteomics 2020; 19:589-607. [PMID: 32024770 PMCID: PMC7124469 DOI: 10.1074/mcp.ra119.001829] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/23/2019] [Indexed: 12/31/2022] Open
Abstract
Bacteria secrete siderophores to access iron, a key nutrient poorly bioavailable and the source of strong competition between microorganisms in most biotopes. Many bacteria also use siderophores produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa, an opportunistic pathogen, produces two siderophores, pyoverdine and pyochelin, and is also able to use a panel of exosiderophores. We first investigated expression of the various iron-uptake pathways of P. aeruginosa in three different growth media using proteomic and RT-qPCR approaches and observed three different phenotypic patterns, indicating complex phenotypic plasticity in the expression of the various iron-uptake pathways. We then investigated the phenotypic plasticity of iron-uptake pathway expression in the presence of various exosiderophores (present individually or as a mixture) under planktonic growth conditions, as well as in an epithelial cell infection assay. In all growth conditions tested, catechol-type exosiderophores were clearly more efficient in inducing the expression of their corresponding transporters than the others, showing that bacteria opt for the use of catechol siderophores to access iron when they are present in the environment. In parallel, expression of the proteins of the pyochelin pathway was significantly repressed under most conditions tested, as well as that of proteins of the pyoverdine pathway, but to a lesser extent. There was no effect on the expression of the heme and ferrous uptake pathways. Overall, these data provide precise insights on how P. aeruginosa adjusts the expression of its various iron-uptake pathways (phenotypic plasticity and switching) to match varying levels of iron and competition.
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Affiliation(s)
- Quentin Perraud
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Paola Cantero
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Béatrice Roche
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Véronique Gasser
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Vincent P Normant
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, F-67084 Strasbourg Cedex, France
| | - Philippe Hammann
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, F-67084 Strasbourg Cedex, France
| | - Gaëtan L A Mislin
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Laurence Ehret-Sabatier
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Isabelle J Schalk
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.
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23
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Cooperation and Cheating through a Secreted Aminopeptidase in the Pseudomonas aeruginosa RpoS Response. mBio 2020; 11:mBio.03090-19. [PMID: 32184248 PMCID: PMC7078477 DOI: 10.1128/mbio.03090-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bacterial stress responses are generally considered protective measures taken by individual cells. Enabled by an experimental evolution approach, we describe a contrasting property, collective nutrient acquisition, in the RpoS-dependent stress response of the opportunistic human pathogen P. aeruginosa. Specifically, we identify the secreted P. aeruginosa aminopeptidase (PaAP) as an essential RpoS-controlled function in extracellular proteolysis. As a secreted “public good,” PaAP permits cheating by rpoS mutants that save the metabolic costs of expressing RpoS-controlled genes dispensable under the given growth conditions. Proteolytic enzymes are important virulence factors in P. aeruginosa pathogenesis and constitute a potential target for antimicrobial therapy. More broadly, our work contributes to recent findings in higher organisms that stress affects not only individual fitness and competitiveness but also cooperative behavior. The global stress response controlled by the alternative sigma factor RpoS protects enteric bacteria from a variety of environmental stressors. The role of RpoS in other, nonenteric bacteria, such as the opportunistic pathogen Pseudomonas aeruginosa, is less well understood. Here, we employed experimental social evolution to reveal that cooperative behavior via secreted public goods is an important function in the RpoS response of P. aeruginosa. Using whole-genome sequencing, we identified rpoS loss-of-function mutants among isolates evolved in a protein growth medium that requires extracellular proteolysis. We found that rpoS mutants comprise up to 25% of the evolved population and that they behave as social cheaters, with low fitness in isolation but high fitness in mixed culture with the cooperating wild type. We conclude that rpoS mutants cheat because they exploit an RpoS-controlled public good produced by the wild type, the secreted aminopeptidase PaAP, and because they do not carry the metabolic costs of expressing PaAP and many other gene products in the large RpoS regulon. Our results suggest that PaAP is an integral part of a proteolytic sequence in P. aeruginosa that permits the utilization of protein as a nutrient source. Our work broadens the scope of stress response functions in bacteria.
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24
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Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol 2020; 18:152-163. [PMID: 31748738 PMCID: PMC7116523 DOI: 10.1038/s41579-019-0284-4] [Citation(s) in RCA: 409] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 01/06/2023]
Abstract
Iron is an essential trace element for most organisms. A common way for bacteria to acquire this nutrient is through the secretion of siderophores, which are secondary metabolites that scavenge iron from environmental stocks and deliver it to cells via specific receptors. While there has been tremendous interest in understanding the molecular basis of siderophore synthesis, uptake and regulation, questions about the ecological and evolutionary consequences of siderophore secretion have only recently received increasing attention. In this Review, we outline how eco-evolutionary questions can complement the mechanistic perspective and help to obtain a more integrated view of siderophores. In particular, we explain how secreted diffusible siderophores can affect other community members, leading to cooperative, exploitative and competitive interactions between individuals. These social interactions in turn can spur co-evolutionary arms races between strains and species, lead to ecological dependencies between them and potentially contribute to the formation of stable communities. In brief, this Review shows that siderophores are much more than just iron carriers: they are important mediators of interactions between members of microbial assemblies and the eukaryotic hosts they inhabit.
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Affiliation(s)
- Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Özhan Özkaya
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
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25
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Sathe S, Mathew A, Agnoli K, Eberl L, Kümmerli R. Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia. Evol Lett 2019; 3:610-622. [PMID: 31844554 PMCID: PMC6906993 DOI: 10.1002/evl3.144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Explaining how cooperation can persist in the presence of cheaters, exploiting the cooperative acts, is a challenge for evolutionary biology. Microbial systems have proved extremely useful to test evolutionary theory and identify mechanisms maintaining cooperation. One of the most widely studied system is the secretion and sharing of iron‐scavenging siderophores by Pseudomonas bacteria, with many insights gained from this system now being considered as hallmarks of bacterial cooperation. Here, we introduce siderophore secretion by the bacterium Burkholderia cenocepacia H111 as a novel parallel study system, and show that this system behaves differently. For ornibactin, the main siderophore of this species, we discovered a novel mechanism of how cheating can be prevented. Particularly, we found that secreted ornibactin cannot be exploited by ornibactin‐defective mutants because ornibactin receptor and synthesis genes are co‐expressed from the same operon, such that disruptive mutations in synthesis genes compromise receptor availability required for siderophore uptake and cheating. For pyochelin, the secondary siderophore of this species, we found that cheating was possible, but the relative success of cheaters was positive frequency dependent, thus diametrically opposite to the Pseudomonas and other microbial systems. Altogether, our results highlight that expanding our repertoire of microbial study systems leads to new discoveries and suggest that there is an enormous diversity of social interactions out there in nature, and we might have only looked at the tip of the iceberg so far.
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Affiliation(s)
- Santosh Sathe
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Kirsty Agnoli
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland
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26
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Smith RP, Doiron A, Muzquiz R, Fortoul MC, Haas M, Abraham T, Quinn RJ, Barraza I, Chowdhury K, Nemzer LR. The public and private benefit of an impure public good determines the sensitivity of bacteria to population collapse in a snowdrift game. Environ Microbiol 2019; 21:4330-4342. [DOI: 10.1111/1462-2920.14796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Robert P. Smith
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Aimee Doiron
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Rodrigo Muzquiz
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Marla C. Fortoul
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Meghan Haas
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Tom Abraham
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Rebecca J. Quinn
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Ivana Barraza
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Khadija Chowdhury
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Louis R. Nemzer
- Department of Chemistry and Physics Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
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27
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Bruce JB, West SA, Griffin AS. Functional amyloids promote retention of public goods in bacteria. Proc Biol Sci 2019; 286:20190709. [PMID: 31138071 DOI: 10.1098/rspb.2019.0709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The growth and virulence of bacteria depends upon a number of factors that are secreted into the environment. These factors can diffuse away from the producing cells, to be either lost or used by cells that do not produce them (cheats). Mechanisms that act to reduce the loss of secreted factors through diffusion are expected to be favoured. One such mechanism may be the production of Fap fibrils, needle-like fibres on the cell surface observed in P. aeruginosa, which can transiently bind several secreted metabolites produced by cells. We test whether Fap fibrils help retain a secreted factor, the iron-scavenging molecule pyoverdine, and hence reduce the potential for exploitation by non-producing, cheating cells. We found that: (i) wild-type cells retain more iron-chelating metabolites than fibril non-producers; (ii) purified Fap fibrils can prevent the loss of the iron-chelators PQS ( Pseudomonas quinolone signal) and pyoverdine; and (iii) pyoverdine non-producers have higher fitness in competition with fibril non-producers than with wild-type cells. Our results suggest that by limiting the loss of a costly public good, Fap fibrils may play an important role in stabilizing cooperative production of secreted factors.
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Affiliation(s)
- John B Bruce
- Department of Zoology, University of Oxford , Oxford , UK
| | - Stuart A West
- Department of Zoology, University of Oxford , Oxford , UK
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28
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Rezzoagli C, Granato ET, Kümmerli R. In-vivo microscopy reveals the impact of Pseudomonas aeruginosa social interactions on host colonization. ISME JOURNAL 2019; 13:2403-2414. [PMID: 31123320 DOI: 10.1038/s41396-019-0442-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/20/2019] [Accepted: 04/24/2019] [Indexed: 12/21/2022]
Abstract
Pathogenic bacteria engage in social interactions to colonize hosts, which include quorum-sensing-mediated communication and the secretion of virulence factors that can be shared as "public goods" between individuals. While in-vitro studies demonstrated that cooperative individuals can be displaced by "cheating" mutants freeriding on social acts, we know less about social interactions in infections. Here, we developed a live imaging system to track virulence factor expression and social strain interactions in the human pathogen Pseudomonas aeruginosa colonizing the gut of Caenorhabditis elegans. We found that shareable siderophores and quorum-sensing systems are expressed during infections, affect host gut colonization, and benefit non-producers. However, non-producers were unable to successfully cheat and outcompete producers. Our results indicate that the limited success of cheats is due to a combination of the down-regulation of virulence factors over the course of the infection, the fact that each virulence factor examined contributed to but was not essential for host colonization, and the potential for negative frequency-dependent selection. Our findings shed new light on bacterial social interactions in infections and reveal potential limits of therapeutic approaches that aim to capitalize on social dynamics between strains for infection control.
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Affiliation(s)
- Chiara Rezzoagli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland. .,Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
| | | | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland. .,Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
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29
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Schiessl KT, Ross-Gillespie A, Cornforth DM, Weigert M, Bigosch C, Brown SP, Ackermann M, Kümmerli R. Individual- versus group-optimality in the production of secreted bacterial compounds. Evolution 2019; 73:675-688. [PMID: 30793292 DOI: 10.1111/evo.13701] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/01/2019] [Indexed: 01/10/2023]
Abstract
How unicellular organisms optimize the production of compounds is a fundamental biological question. While it is typically thought that production is optimized at the individual-cell level, secreted compounds could also allow for optimization at the group level, leading to a division of labor where a subset of cells produces and shares the compound with everyone. Using mathematical modeling, we show that the evolution of such division of labor depends on the cost function of compound production. Specifically, for any trait with saturating benefits, linear costs promote the evolution of uniform production levels across cells. Conversely, production costs that diminish with higher output levels favor the evolution of specialization-especially when compound shareability is high. When experimentally testing these predictions with pyoverdine, a secreted iron-scavenging compound produced by Pseudomonas aeruginosa, we found linear costs and, consistent with our model, detected uniform pyoverdine production levels across cells. We conclude that for shared compounds with saturating benefits, the evolution of division of labor is facilitated by a diminishing cost function. More generally, we note that shifts in the level of selection from individuals to groups do not solely require cooperation, but critically depend on mechanistic factors, including the distribution of compound synthesis costs.
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Affiliation(s)
- Konstanze T Schiessl
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, 8600, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH Zurich), Zürich, 8092, Switzerland.,Current Address: Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, 10027, New York
| | - Adin Ross-Gillespie
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
| | - Daniel M Cornforth
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - Michael Weigert
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
| | - Colette Bigosch
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH Zurich), Zürich, 8092, Switzerland
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - Martin Ackermann
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, 8600, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH Zurich), Zürich, 8092, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, Zürich, 8057, Switzerland
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30
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A single mutation in rapP induces cheating to prevent cheating in Bacillus subtilis by minimizing public good production. Commun Biol 2018; 1:133. [PMID: 30272012 PMCID: PMC6123732 DOI: 10.1038/s42003-018-0136-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
Cooperation is beneficial to group behaviors like multicellularity, but is vulnerable to exploitation by cheaters. Here we analyze mechanisms that protect against exploitation of extracellular surfactin in swarms of Bacillus subtilis. Unexpectedly, the reference strain NCIB 3610 displays inherent resistance to surfactin-non-producing cheaters, while a different wild isolate is susceptible. We trace this interstrain difference down to a single amino acid change in the plasmid-borne regulator RapP, which is necessary and sufficient for cheater mitigation. This allele, prevalent in many Bacillus species, optimizes transcription of the surfactin operon to the minimum needed for full cooperation. When combined with a strain lacking rapP, NCIB 3610 acts as a cheater itself—except it does not harm the population at high proportions since it still produces enough surfactin. This strategy of minimal production is thus a doubly advantageous mechanism to limit exploitation of public goods, and is readily evolved from existing regulatory networks. Lyons and Kolter describe a single-point mutation in the plasmid-borne gene rapP of Bacillus subtilis that optimizes surfactin transcription to express the minimum required for cooperation. The decrease in the production of this public good significantly prevented the exploitation of cooperative traits by cheaters.
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31
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Butaitė E, Kramer J, Wyder S, Kümmerli R. Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities. Environ Microbiol 2018; 20:3629-3642. [PMID: 30003663 DOI: 10.1111/1462-2920.14355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/20/2018] [Accepted: 06/25/2018] [Indexed: 11/28/2022]
Abstract
Many bacteria rely on the secretion of siderophores to scavenge iron from the environment. Laboratory studies revealed that abiotic and biotic factors together determine how much siderophores bacteria make, and whether siderophores can be exploited by non-producing cheaters or be deployed by producers to inhibit competitors. Here, we explore whether these insights apply to natural communities, by comparing the production of the siderophore pyoverdine among 930 Pseudomonas strains from 48 soil and pond communities. We found that pH, iron content, carbon concentration and community diversity determine pyoverdine production levels, and the extent to which strains are either stimulated or inhibited by heterologous (non-self) pyoverdines. While pyoverdine non-producers occurred in both habitats, their prevalence was higher in soils. Environmental and genetic analyses suggest that non-producers can evolve as cheaters, exploiting heterologous pyoverdine, but also due to pyoverdine disuse in environments with increased iron availability. Overall, we found that environmental factors explained between-strain variation in pyoverdine production much better in soils than in ponds, presumably because high strain mixing in ponds impedes local adaption. Our study sheds light on the complexity of natural bacterial communities, and provides first insights into the multivariate nature of siderophore-based iron acquisition and competition among environmental pseudomonads.
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Affiliation(s)
- Elena Butaitė
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jos Kramer
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Stefan Wyder
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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32
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Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi. Proc Natl Acad Sci U S A 2018; 115:7581-7586. [PMID: 29954861 DOI: 10.1073/pnas.1805791115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The secretion of small Fe-binding molecules called siderophores is an important microbial strategy for survival in Fe-limited environments. Siderophore production is often regulated by quorum sensing (QS), a microbial counting technique that allows organisms to alter gene expression based on cell density. However, the identity and quantities of siderophores produced under QS regulation are rarely studied in the context of their roles in Fe uptake. We investigated the link between QS, siderophores, and Fe uptake in the model marine organism Vibrio harveyi where QS is thought to repress siderophore production. We find that V. harveyi uses a single QS- and Fe-repressed gene cluster to produce both cell-associated siderophores (amphiphilic enterobactins) as well as several related soluble siderophores, which we identify and quantify using liquid chromatography-coupled (LC)-MS as well as tandem high-resolution MS (LC-HR-MS/MS). Measurements of siderophore production show that soluble siderophores are present at ∼100× higher concentrations than amphi-enterobactin and that over the course of growth V. harveyi decreases amphi-enterobactin concentrations but accumulates soluble siderophores. 55Fe radio-tracer uptake experiments demonstrate that these soluble siderophores play a significant role in Fe uptake and that the QS-dictated concentrations of soluble siderophores in stationary phase are near the limit of cellular uptake capacities. We propose that cell-associated and soluble siderophores are beneficial to V. harveyi in different environmental and growth contexts and that QS allows V. harveyi to exploit "knowledge" of its population size to avoid unnecessary siderophore production.
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33
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Parijs I, Steenackers HP. Competitive inter-species interactions underlie the increased antimicrobial tolerance in multispecies brewery biofilms. ISME JOURNAL 2018; 12:2061-2075. [PMID: 29858577 DOI: 10.1038/s41396-018-0146-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 11/09/2022]
Abstract
Genetic diversity often enhances the tolerance of microbial communities against antimicrobial treatment. However the sociobiology underlying this antimicrobial tolerance remains largely unexplored. Here we analyze how inter-species interactions can increase antimicrobial tolerance. We apply our approach to 17 industrially relevant multispecies biofilm models, based on species isolated from 58 contaminating biofilms in three breweries. Sulfathiazole was used as antimicrobial agent because it showed the highest activity out of 22 biofilm inhibitors tested. Our analysis reveals that competitive interactions dominate among species within brewery biofilms. We show that antimicrobial treatment can reduce the level of competition and therefore cause a subset of species to bloom. The result is a 1.2-42.7-fold lower percentage inhibition of these species and increased overall tolerance. In addition, we show that the presence of Raoultella can also directly enhance the inherent tolerance of Pseudomonas to antimicrobial treatment, either because the species protect each other or because they induce specific tolerance phenotypes as a response to competitors. Overall, our study emphasizes that the dominance of competitive interactions is central to the enhanced antimicrobial tolerance of the multispecies biofilms, and that the activity of antimicrobials against multispecies biofilms cannot be predicted based on their effect against monocultures.
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Affiliation(s)
- Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20 - box 2460, B-3001, Leuven, Belgium
| | - Hans P Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20 - box 2460, B-3001, Leuven, Belgium.
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34
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Iebba V, Guerrieri F, Di Gregorio V, Levrero M, Gagliardi A, Santangelo F, Sobolev AP, Circi S, Giannelli V, Mannina L, Schippa S, Merli M. Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy. Sci Rep 2018; 8:8210. [PMID: 29844325 PMCID: PMC5974022 DOI: 10.1038/s41598-018-26509-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
In liver cirrhosis (LC), impaired intestinal functions lead to dysbiosis and possible bacterial translocation (BT). Bacteria or their byproducts within the bloodstream can thus play a role in systemic inflammation and hepatic encephalopathy (HE). We combined 16S sequencing, NMR metabolomics and network analysis to describe the interrelationships of members of the microbiota in LC biopsies, faeces, peripheral/portal blood and faecal metabolites with clinical parameters. LC faeces and biopsies showed marked dysbiosis with a heightened proportion of Enterobacteriaceae. Our approach showed impaired faecal bacterial metabolism of short-chain fatty acids (SCFAs) and carbon/methane sources in LC, along with an enhanced stress-related response. Sixteen species, mainly belonging to the Proteobacteria phylum, were shared between LC peripheral and portal blood and were functionally linked to iron metabolism. Faecal Enterobacteriaceae and trimethylamine were positively correlated with blood proinflammatory cytokines, while Ruminococcaceae and SCFAs played a protective role. Within the peripheral blood and faeces, certain species (Stenotrophomonas pavanii, Methylobacterium extorquens) and metabolites (methanol, threonine) were positively related to HE. Cirrhotic patients thus harbour a 'functional dysbiosis' in the faeces and peripheral/portal blood, with specific keystone species and metabolites related to clinical markers of systemic inflammation and HE.
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Affiliation(s)
- Valerio Iebba
- Istituto Pasteur Cenci Bolognetti Foundation, Public Health and Infectious Diseases Department, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Guerrieri
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Vincenza Di Gregorio
- Gastroenterology, Department of Clinical Medicine, Sapienza University of Rome, Viale dell'Università 37, 00185, Rome, Italy
| | - Massimo Levrero
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), Centre Léon Bérard, Lyon, France
| | - Antonella Gagliardi
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Floriana Santangelo
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anatoly P Sobolev
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185, Rome, Italy
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, CNR, via Salaria km 29.300, 00015, Monterotondo, (RM), Italy
| | - Simone Circi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185, Rome, Italy
| | - Valerio Giannelli
- Gastroenterology, Department of Clinical Medicine, Sapienza University of Rome, Viale dell'Università 37, 00185, Rome, Italy
| | - Luisa Mannina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185, Rome, Italy
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, CNR, via Salaria km 29.300, 00015, Monterotondo, (RM), Italy
| | - Serena Schippa
- Public Health and Infectious Diseases Department, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Manuela Merli
- Gastroenterology, Department of Clinical Medicine, Sapienza University of Rome, Viale dell'Università 37, 00185, Rome, Italy.
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35
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Bauer MA, Kainz K, Carmona-Gutierrez D, Madeo F. Microbial wars: Competition in ecological niches and within the microbiome. MICROBIAL CELL (GRAZ, AUSTRIA) 2018; 5:215-219. [PMID: 29796386 PMCID: PMC5961915 DOI: 10.15698/mic2018.05.628] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/03/2018] [Indexed: 12/22/2022]
Abstract
Many microbial communities live in highly competitive surroundings, in which the fight for resources determines their survival and genetic persistence. Humans live in a close relationship with microbial communities, which includes the health- and disease-determining interactions with our microbiome. Accordingly, the understanding of microbial competitive activities are essential at physiological and pathophysiological levels. Here we provide a brief overview on microbial competition and discuss some of its roles and consequences that directly affect humans.
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Affiliation(s)
- Maria A. Bauer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Frank Madeo
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
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36
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Leinweber A, Weigert M, Kümmerli R. The bacterium Pseudomonas aeruginosa senses and gradually responds to interspecific competition for iron. Evolution 2018; 72:1515-1528. [PMID: 29665015 PMCID: PMC6314444 DOI: 10.1111/evo.13491] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/07/2018] [Indexed: 12/20/2022]
Abstract
Phenotypic plasticity in response to competition is a well-described phenomenon in higher organisms. Here, we show that also bacteria have the ability to sense the presence of competitors and mount fine-tuned responses to match prevailing levels of competition. In our experiments, we studied interspecific competition for iron between the bacterium Pseudomonas aeruginosa (PA) and its competitor Burkholderia cenocepacia (BC). We focused on the ability of PA to phenotypically adjust the production of pyoverdine, an iron-scavenging siderophore. We found that PA upregulates pyoverdine production early on during competition under condition of low iron availability. This plastic upregulation was fine-tuned in response to the level of competition imposed by BC, and seems to confer a relative fitness benefit to PA in the form of an earlier initiation of growth. At later time points, however, PA showed reduced growth in mixed compared to monoculture, suggesting that competitive responses are costly. Altogether, our results demonstrate that phenotypic plasticity in siderophore production plays an important role in interspecific competition for iron. Upregulating siderophore production may be a powerful strategy to lock iron away from competing species, and to reserve this nutrient for strain members possessing the compatible receptor for uptake.
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Affiliation(s)
- Anne Leinweber
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Weigert
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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37
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Weigert M, Kümmerli R. The physical boundaries of public goods cooperation between surface-attached bacterial cells. Proc Biol Sci 2018; 284:rspb.2017.0631. [PMID: 28701557 DOI: 10.1098/rspb.2017.0631] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/02/2017] [Indexed: 01/17/2023] Open
Abstract
Bacteria secrete a variety of compounds important for nutrient scavenging, competition mediation and infection establishment. While there is a general consensus that secreted compounds can be shared and therefore have social consequences for the bacterial collective, we know little about the physical limits of such bacterial social interactions. Here, we address this issue by studying the sharing of iron-scavenging siderophores between surface-attached microcolonies of the bacterium Pseudomonas aeruginosa Using single-cell fluorescence microscopy, we show that siderophores, secreted by producers, quickly reach non-producers within a range of 100 µm, and significantly boost their fitness. Producers in turn respond to variation in sharing efficiency by adjusting their pyoverdine investment levels. These social effects wane with larger cell-to-cell distances and on hard surfaces. Thus, our findings reveal the boundaries of compound sharing, and show that sharing is particularly relevant between nearby yet physically separated bacteria on soft surfaces, matching realistic natural conditions such as those encountered in soft tissue infections.
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Affiliation(s)
- Michael Weigert
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland .,Department of Biology I, Division of Microbiology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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38
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Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities. Nat Commun 2017; 8:414. [PMID: 28871205 PMCID: PMC5583256 DOI: 10.1038/s41467-017-00509-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 06/29/2017] [Indexed: 11/17/2022] Open
Abstract
All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have become model organisms to study social dilemmas in laboratory systems, we know little about their relevance in natural communities. Here, we show that social interactions mediated by a single shareable compound necessary for growth (the iron-scavenging pyoverdine) have important consequences for competitive dynamics in soil and pond communities of Pseudomonas bacteria. We find that pyoverdine non- and low-producers co-occur in many natural communities. While non-producers have genes coding for multiple pyoverdine receptors and are able to exploit compatible heterologous pyoverdines from other community members, producers differ in the pyoverdine types they secrete, offering protection against exploitation from non-producers with incompatible receptors. Our findings indicate that there is both selection for cheating and cheating resistance, which could drive antagonistic co-evolution and diversification in natural bacterial communities. Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.
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39
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Maintenance of Microbial Cooperation Mediated by Public Goods in Single- and Multiple-Trait Scenarios. J Bacteriol 2017; 199:JB.00297-17. [PMID: 28847922 DOI: 10.1128/jb.00297-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microbes often form densely populated communities, which favor competitive and cooperative interactions. Cooperation among bacteria often occurs through the production of metabolically costly molecules produced by certain individuals that become available to other neighboring individuals; such molecules are called public goods. This type of cooperation is susceptible to exploitation, since nonproducers of a public good can benefit from it while saving the cost of its production (cheating), gaining a fitness advantage over producers (cooperators). Thus, in mixed cultures, cheaters can increase in frequency in the population, relative to cooperators. Sometimes, and as predicted by simple game-theoretic arguments, such increases in the frequency of cheaters cause loss of the cooperative traits by exhaustion of the public goods, eventually leading to a collapse of the entire population. In other cases, however, both cooperators and cheaters remain in coexistence. This raises the question of how cooperation is maintained in microbial populations. Several strategies to prevent cheating have been studied in the context of a single trait and a unique environmental constraint. In this review, we describe current knowledge on the evolutionary stability of microbial cooperation and discuss recent discoveries describing the mechanisms operating in multiple-trait and multiple-constraint settings. We conclude with a consideration of the consequences of these complex interactions, and we briefly discuss the potential role of social interactions involving multiple traits and multiple environmental constraints in the evolution of specialization and division of labor in microbes.
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40
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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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41
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Synergistic cooperation promotes multicellular performance and unicellular free-rider persistence. Nat Commun 2017; 8:15707. [PMID: 28580966 PMCID: PMC5465372 DOI: 10.1038/ncomms15707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/20/2017] [Indexed: 12/17/2022] Open
Abstract
The evolution of multicellular life requires cooperation among cells, which can be undermined by intra-group selection for selfishness. Theory predicts that selection to avoid non-cooperators limits social interactions among non-relatives, yet previous evolution experiments suggest that intra-group conflict is an outcome, rather than a driver, of incipient multicellular life cycles. Here we report the evolution of multicellularity via two distinct mechanisms of group formation in the unicellular budding yeast Kluyveromyces lactis. Cells remain permanently attached following mitosis, giving rise to clonal clusters (staying together); clusters then reversibly assemble into social groups (coming together). Coming together amplifies the benefits of multicellularity and allows social clusters to collectively outperform solitary clusters. However, cooperation among non-relatives also permits fast-growing unicellular lineages to 'free-ride' during selection for increased size. Cooperation and competition for the benefits of multicellularity promote the stable coexistence of unicellular and multicellular genotypes, underscoring the importance of social and ecological context during the transition to multicellularity.
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42
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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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43
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Xie Y, Qiu N, Wang G. Toward a better guard of coastal water safety-Microbial distribution in coastal water and their facile detection. MARINE POLLUTION BULLETIN 2017; 118:5-16. [PMID: 28215556 DOI: 10.1016/j.marpolbul.2017.02.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/19/2017] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
Prosperous development in marine-based tourism has raised increasing concerns over the sanitary quality of coastal waters with potential microbial contamination. The World Health Organization has set stringent standards over a list of pathogenic microorganisms posing potential threats to people with frequent coastal water exposure and has asked for efficient detection procedures for pathogen facile identification. Inspection of survey events regarding the occurrence of marine pathogens in recreational beaches in recent years has reinforced the need for the development of a rapid identification procedure. In this review, we examine the possibility of recruiting uniform molecular assays to identify different marine pathogens and the feasibility of appropriate biomarkers, including enterochelin biosynthetic genes, for general toxicity assays. The focus is not only on bacterial pathogens but also on other groups of infectious pathogens. The ultimate goal is the development of a handy method to more efficiently and rapidly detect marine pathogens.
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Affiliation(s)
- Yunxuan Xie
- Tianjin University Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Ning Qiu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Guangyi Wang
- Tianjin University Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China.
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44
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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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45
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Asfahl KL, Schuster M. Social interactions in bacterial cell-cell signaling. FEMS Microbiol Rev 2016; 41:92-107. [PMID: 27677972 DOI: 10.1093/femsre/fuw038] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/19/2016] [Accepted: 08/14/2016] [Indexed: 01/16/2023] Open
Abstract
Cooperation and conflict in microorganisms is being recognized as an important factor in the organization and function of microbial communities. Many of the cooperative behaviors described in bacteria are governed through a cell-cell signaling process generally termed quorum sensing. Communication and cooperation in diverse microorganisms exhibit predictable trends that behave according to social evolutionary theory, notably that public goods dilemmas produce selective pressures for divergence in social phenotypes including cheating. In this review, we relate the general features of quorum sensing and social adaptation in microorganisms to established evolutionary theory. We then describe physiological and molecular mechanisms that have been shown to stabilize cooperation in microbes, thereby preventing a tragedy of the commons. Continued study of the role of communication and cooperation in microbial ecology and evolution is important to clinical treatment of pathogens, as well as to our fundamental understanding of cooperative selection at all levels of life.
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Affiliation(s)
- Kyle L Asfahl
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331-3804, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331-3804, USA
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46
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Driscoll WW, Hackett JD, Ferrière R. Eco-evolutionary feedbacks between private and public goods: evidence from toxic algal blooms. Ecol Lett 2015; 19:81-97. [PMID: 26612461 DOI: 10.1111/ele.12533] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Accepted: 09/07/2015] [Indexed: 01/18/2023]
Abstract
The importance of 'eco-evolutionary feedbacks' in natural systems is currently unclear. Here, we advance a general hypothesis for a particular class of eco-evolutionary feedbacks with potentially large, long-lasting impacts in complex ecosystems. These eco-evolutionary feedbacks involve traits that mediate important interactions with abiotic and biotic features of the environment and a self-driven reversal of selection as the ecological impact of the trait varies between private (small scale) and public (large scale). Toxic algal blooms may involve such eco-evolutionary feedbacks due to the emergence of public goods. We review evidence that toxin production by microalgae may yield 'privatised' benefits for individual cells or colonies under pre- and early-bloom conditions; however, the large-scale, ecosystem-level effects of toxicity associated with bloom states yield benefits that are necessarily 'public'. Theory predicts that the replacement of private with public goods may reverse selection for toxicity in the absence of higher level selection. Indeed, blooms often harbor significant genetic and functional diversity: bloom populations may undergo genetic differentiation over a scale of days, and even genetically similar lineages may vary widely in toxic potential. Intriguingly, these observations find parallels in terrestrial communities, suggesting that toxic blooms may serve as useful models for eco-evolutionary dynamics in nature. Eco-evolutionary feedbacks involving the emergence of a public good may shed new light on the potential for interactions between ecology and evolution to influence the structure and function of entire ecosystems.
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Affiliation(s)
- William W Driscoll
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, 5106, MN, USA.,Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), CNRS UMR 8197, 46 rue d'Ulm, Paris, F-75005, USA.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85716, AZ, USA
| | - Jeremiah D Hackett
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85716, AZ, USA
| | - Régis Ferrière
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), CNRS UMR 8197, 46 rue d'Ulm, Paris, F-75005, USA.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85716, AZ, USA
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47
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Estrela S, Morris JJ, Kerr B. Private benefits and metabolic conflicts shape the emergence of microbial interdependencies. Environ Microbiol 2015; 18:1415-27. [DOI: 10.1111/1462-2920.13028] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/12/2015] [Accepted: 08/15/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Sylvie Estrela
- Department of Biology and BEACON Center for the Study of Evolution in Action; University of Washington; Seattle WA 98195 USA
| | - J. Jeffrey Morris
- Department of Biology; University of Alabama at Birmingham; Birmingham AL 35294 USA
- BEACON Center for the Study of Evolution in Action; Michigan State University; East Lansing MI 48824 USA
| | - Benjamin Kerr
- Department of Biology and BEACON Center for the Study of Evolution in Action; University of Washington; Seattle WA 98195 USA
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