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De Gasperin O, Blacher P, Sarton-Lohéac S, Grasso G, Corliss MK, Nicole S, Chérasse S, Aron S, Chapuisat M. A supergene-controlling social structure in Alpine ants also affects the dispersal ability and fecundity of each sex. Proc Biol Sci 2024; 291:20240494. [PMID: 38864332 DOI: 10.1098/rspb.2024.0494] [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: 11/15/2023] [Accepted: 04/18/2024] [Indexed: 06/13/2024] Open
Abstract
Social organization, dispersal and fecundity coevolve, but whether they are genetically linked remains little known. Supergenes are prime candidates for coupling adaptive traits and mediating sex-specific trade-offs. Here, we test whether a supergene that controls social structure in Formica selysi also influences dispersal-related traits and fecundity within each sex. In this ant species, single-queen colonies contain only the ancestral supergene haplotype M and produce MM queens and M males, while multi-queen colonies contain the derived haplotype P and produce MP queens, PP queens and P males. By combining multiple experiments, we show that the M haplotype induces phenotypes with higher dispersal potential and higher fecundity in both sexes. Specifically, MM queens, MP queens and M males are more aerodynamic and more fecund than PP queens and P males, respectively. Differences between MP and PP queens from the same colonies reveal a direct genetic effect of the supergene on dispersal-related traits and fecundity. The derived haplotype P, associated with multi-queen colonies, produces queens and males with reduced dispersal abilities and lower fecundity. More broadly, similarities between the Formica and Solenopsis systems reveal that supergenes play a major role in linking behavioural, morphological and physiological traits associated with intraspecific social polymorphisms.
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Affiliation(s)
- Ornela De Gasperin
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
- Red de Ecoetología, Instituto de Ecología, A. C. , Xalapa, Veracruz 91073, Mexico
| | - Pierre Blacher
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Solenn Sarton-Lohéac
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Guglielmo Grasso
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
- University of Manchester , Manchester M13 9PL, UK
| | - Mia Kotur Corliss
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Sidonie Nicole
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | | | - Serge Aron
- Universite libre de Bruxelles , Brussels 1050, Belgium
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
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2
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Shi M, Wang X. Event-triggered predictive control for cooperation-competition multi-agent systems under DoS attacks. ISA TRANSACTIONS 2024; 149:16-25. [PMID: 38664115 DOI: 10.1016/j.isatra.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
This paper concerns the bipartite consensus problem of multi-agent systems(MASs) with competitive- cooperative network topology under denial-of-service (DoS) attacks. Firstly, this work extensively analyzes the competitive phenomena that may exist in the information interchange of agents in contrast to the single cooperative behavior between agents. Based on this, some necessary conditions are provided for the system to attain the bipartite consensus. In addition, the event-triggered mechanism (ETM) effectively lowers unnecessary information sharing between agents and eliminates Zeno behavior. Furthermore, the predictive method provides the system with exceptional resistance against common energy-limited DoS attacks and the ability to compensate for information loss caused by DoS attacks. Finally, a numerical simulation proves that the proposed approach is feasible.
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Affiliation(s)
- Ming Shi
- College of Electronic and Information Engineering, Southwest University, Chongqing 400715, China.
| | - Xin Wang
- College of Electronic and Information Engineering, Southwest University, Chongqing 400715, China.
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3
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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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4
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Cheng H, Sysoeva L, Wang H, Yuan H, Zhang T, Meng X. Evolution of Cooperation in Spatio-Temporal Evolutionary Games with Public Goods Feedback. Bull Math Biol 2024; 86:67. [PMID: 38700758 DOI: 10.1007/s11538-024-01296-y] [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: 01/24/2024] [Accepted: 04/08/2024] [Indexed: 05/23/2024]
Abstract
In biology, evolutionary game-theoretical models often arise in which players' strategies impact the state of the environment, driving feedback between strategy and the surroundings. In this case, cooperative interactions can be applied to studying ecological systems, animal or microorganism populations, and cells producing or actively extracting a growth resource from their environment. We consider the framework of eco-evolutionary game theory with replicator dynamics and growth-limiting public goods extracted by population members from some external source. It is known that the two sub-populations of cooperators and defectors can develop spatio-temporal patterns that enable long-term coexistence in the shared environment. To investigate this phenomenon and unveil the mechanisms that sustain cooperation, we analyze two eco-evolutionary models: a well-mixed environment and a heterogeneous model with spatial diffusion. In the latter, we integrate spatial diffusion into replicator dynamics. Our findings reveal rich strategy dynamics, including bistability and bifurcations, in the temporal system and spatial stability, as well as Turing instability, Turing-Hopf bifurcations, and chaos in the diffusion system. The results indicate that effective mechanisms to promote cooperation include increasing the player density, decreasing the relative timescale, controlling the density of initial cooperators, improving the diffusion rate of the public goods, lowering the diffusion rate of the cooperators, and enhancing the payoffs to the cooperators. We provide the conditions for the existence, stability, and occurrence of bifurcations in both systems. Our analysis can be applied to dynamic phenomena in fields as diverse as human decision-making, microorganism growth factors secretion, and group hunting.
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Affiliation(s)
- Haihui Cheng
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, People's Republic of China
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, T6G 2G1, Canada
| | - Liubov Sysoeva
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, T6G 2G1, Canada
| | - Hao Wang
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, T6G 2G1, Canada
| | - Hairui Yuan
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, People's Republic of China
| | - Tonghua Zhang
- Department of Mathematics, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Xinzhu Meng
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, People's Republic of China.
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Luo N, Lu J, Şimşek E, Silver A, Yao Y, Ouyang X, West SA, You L. The collapse of cooperation during range expansion of Pseudomonas aeruginosa. Nat Microbiol 2024; 9:1220-1230. [PMID: 38443483 PMCID: PMC7615952 DOI: 10.1038/s41564-024-01627-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
Cooperation is commonly believed to be favourable in spatially structured environments, as these systems promote genetic relatedness that reduces the likelihood of exploitation by cheaters. Here we show that a Pseudomonas aeruginosa population that exhibited cooperative swarming was invaded by cheaters when subjected to experimental evolution through cycles of range expansion on solid media, but not in well-mixed liquid cultures. Our results suggest that cooperation is disfavoured in a more structured environment, which is the opposite of the prevailing view. We show that spatial expansion of the population prolongs cooperative swarming, which was vulnerable to cheating. Our findings reveal a mechanism by which spatial structures can suppress cooperation through modulation of the quantitative traits of cooperation, a process that leads to population divergence towards distinct colonization strategies.
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Affiliation(s)
- Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emrah Şimşek
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Anita Silver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yi Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Xiaoyi Ouyang
- School of Physics, Peking University, Beijing, China
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, UK
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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6
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Vega-Heredia S, Giffard-Mena I, Reverter M. Bacterial and viral co-infections in aquaculture under climate warming: co-evolutionary implications, diagnosis, and treatment. DISEASES OF AQUATIC ORGANISMS 2024; 158:1-20. [PMID: 38602294 DOI: 10.3354/dao03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Climate change and the associated environmental temperature fluctuations are contributing to increases in the frequency and severity of disease outbreaks in both wild and farmed aquatic species. This has a significant impact on biodiversity and also puts global food production systems, such as aquaculture, at risk. Most infections are the result of complex interactions between multiple pathogens, and understanding these interactions and their co-evolutionary mechanisms is crucial for developing effective diagnosis and control strategies. In this review, we discuss current knowledge on bacteria-bacteria, virus-virus, and bacterial and viral co-infections in aquaculture as well as their co-evolution in the context of global warming. We also propose a framework and different novel methods (e.g. advanced molecular tools such as digital PCR and next-generation sequencing) to (1) precisely identify overlooked co-infections, (2) gain an understanding of the co-infection dynamics and mechanisms by knowing species interactions, and (3) facilitate the development multi-pathogen preventive measures such as polyvalent vaccines. As aquaculture disease outbreaks are forecasted to increase both due to the intensification of practices to meet the protein demand of the increasing global population and as a result of global warming, understanding and treating co-infections in aquatic species has important implications for global food security and the economy.
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Affiliation(s)
- Sarahí Vega-Heredia
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México, Egresada del Programa de Ecología Molecular y Biotecnología, carretera transpeninsular Ensenada-Tijuana No. 3917, C.P. 22860, México
| | - Ivone Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México
| | - Miriam Reverter
- School of Biological and Marine Sciences, Plymouth University, Drake Circus, Devon PL4 8AA, UK
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7
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Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT. Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon. Mol Biol Evol 2024; 41:msae045. [PMID: 38415839 PMCID: PMC11043216 DOI: 10.1093/molbev/msae045] [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: 11/21/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/29/2024] Open
Abstract
Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.
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Affiliation(s)
- Liang Sun
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Kyle T David
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - John F Wolters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Steven D Karlen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Carla Gonçalves
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Dana A Opulente
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Xiaofan Zhou
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Antonis Rokas
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
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8
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Mutlu A, Vanderpool EJ, Rumbaugh KP, Diggle SP, Griffin AS. Exploiting cooperative pathogen behaviour for enhanced antibiotic potency: A Trojan horse approach. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001454. [PMID: 38687006 PMCID: PMC11084615 DOI: 10.1099/mic.0.001454] [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: 12/01/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Antimicrobial resistance poses an escalating global threat, rendering traditional drug development approaches increasingly ineffective. Thus, novel alternatives to antibiotic-based therapies are needed. Exploiting pathogen cooperation as a strategy for combating resistant infections has been proposed but lacks experimental validation. Empirical findings demonstrate the successful invasion of cooperating populations by non-cooperating cheats, effectively reducing virulence in vitro and in vivo. The idea of harnessing cooperative behaviours for therapeutic benefit involves exploitation of the invasive capabilities of cheats to drive medically beneficial traits into infecting populations of cells. In this study, we employed Pseudomonas aeruginosa quorum sensing cheats to drive antibiotic sensitivity into both in vitro and in vivo resistant populations. We demonstrated the successful invasion of cheats, followed by increased antibiotic effectiveness against cheat-invaded populations, thereby establishing an experimental proof of principle for the potential application of the Trojan strategy in fighting resistant infections.
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Affiliation(s)
- Alper Mutlu
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Stephen P. Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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9
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Bingham A, Sur A, Shaw LB, Murphy HA. The effect of cooperator recognition on competition among clones in spatially structured microbial communities. PLoS One 2024; 19:e0299546. [PMID: 38547104 PMCID: PMC10977701 DOI: 10.1371/journal.pone.0299546] [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: 07/31/2023] [Accepted: 02/12/2024] [Indexed: 04/02/2024] Open
Abstract
In spatially structured microbial communities, clonal growth of stationary cells passively generates clusters of related individuals. This can lead to stable cooperation without the need for recognition mechanisms. However, recent research suggests that some biofilm-forming microbes may have mechanisms of kin recognition. To explore this unexpected observation, we studied the effects of different types of cooperation in a microbial colony using spatially explicit, agent-based simulations of two interacting strains. We found scenarios that favor a form of kin recognition in spatially structured microbial communities. In the presence of a "cheater" strain, a strain with greenbeard cooperation was able to increase in frequency more than a strain with obligate cooperation. This effect was most noticeable in high density colonies and when the cooperators were not as abundant as the cheaters. We also studied whether a polychromatic greenbeard, in which cells only cooperate with their own type, could provide a numerical benefit beyond a simple, binary greenbeard. We found the greatest benefit to a polychromatic greenbeard when cooperation is highly effective. These results suggest that in some ecological scenarios, recognition mechanisms may be beneficial even in spatially structured communities.
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Affiliation(s)
- Adrienna Bingham
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
| | - Aparajita Sur
- Department of Mathematics, William & Mary, Williamsburg, VA, United States of America
| | - Leah B. Shaw
- Department of Mathematics, William & Mary, Williamsburg, VA, United States of America
| | - Helen A. Murphy
- Department of Biology, William & Mary, Williamsburg, VA, United States of America
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10
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Romdhane S, Huet S, Spor A, Bru D, Breuil MC, Philippot L. Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly. ENVIRONMENTAL MICROBIOME 2024; 19:18. [PMID: 38504378 PMCID: PMC10953230 DOI: 10.1186/s40793-024-00559-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors. RESULTS We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any "home field advantage" during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering. CONCLUSIONS Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.
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Affiliation(s)
- Sana Romdhane
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France.
| | - Sarah Huet
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Aymé Spor
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - David Bru
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Marie-Christine Breuil
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Laurent Philippot
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
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11
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Erdos Z, Studholme DJ, Sharma MD, Chandler D, Bass C, Raymond B. Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits. PLoS Pathog 2024; 20:e1011775. [PMID: 38527086 PMCID: PMC10994555 DOI: 10.1371/journal.ppat.1011775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/04/2024] [Accepted: 03/09/2024] [Indexed: 03/27/2024] Open
Abstract
Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, Akanthomyces muscarius. Starting with a genetically diverse stock we selected for speed of kill, parasite yield or infectivity by manipulating competition within and between hosts and between-populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in timing of sporulation and spore production in vitro. We found that early sporulation led to reduced competitive fitness but could increase yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits-virulence and spore production-that are often in conflict in other parasites.
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Affiliation(s)
- Zoltan Erdos
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | | | - Manmohan D. Sharma
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - David Chandler
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
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12
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Hesse E, O’Brien S. Ecological dependencies and the illusion of cooperation in microbial communities. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001442. [PMID: 38385784 PMCID: PMC10924460 DOI: 10.1099/mic.0.001442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Ecological dependencies - where organisms rely on other organisms for survival - are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amino acids. Legume plants similarly rely on nitrogen-fixing rhizobia to convert atmospheric nitrogen to ammonia. In some cases, dependencies can arise via loss-of-function mutations that allow one partner to benefit from the actions of another. It is common in microbiology to label ecological dependencies between species as cooperation - making it necessary to invoke cooperation-specific frameworks to explain the phenomenon. However, in many cases, such traits are not (at least initially) cooperative, because they are not selected for because of the benefits they confer on a partner species. In contrast, dependencies in microbial communities may originate from fitness benefits gained from genomic-streamlining (i.e. Black Queen Dynamics). Here, we outline how the Black Queen Hypothesis predicts the formation of metabolic dependencies via loss-of-function mutations in microbial communities, without needing to invoke any cooperation-specific explanations. Furthermore we outline how the Black Queen Hypothesis can act as a blueprint for true cooperation as well as discuss key outstanding questions in the field. The nature of interactions in microbial communities can predict the ability of natural communities to withstand and recover from disturbances. Hence, it is vital to gain a deeper understanding of the factors driving these dynamic interactions over evolutionary time.
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Affiliation(s)
- Elze Hesse
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Siobhán O’Brien
- Moyne Institute of Preventive Medicine, Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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13
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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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14
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Song L, Xu L, Wu T, Shi Z, Kareem HA, Wang Z, Dai Q, Guo C, Pan J, Yang M, Wei X, Wang Y, Wei G, Shen X. Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition. THE ISME JOURNAL 2024; 18:wrad028. [PMID: 38365238 PMCID: PMC10833071 DOI: 10.1093/ismejo/wrad028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 02/18/2024]
Abstract
The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.
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Affiliation(s)
- Li Song
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Xu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tong Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenkun Shi
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hafiz Abdul Kareem
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuo Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingyun Dai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenghao Guo
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junfeng Pan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomeng Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihui Shen
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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15
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Smith P, Schuster M. The fitness benefit of pyoverdine cross-feeding by Pseudomonas protegens Pf-5. Environ Microbiol 2024; 26:e16554. [PMID: 38097191 DOI: 10.1111/1462-2920.16554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Under iron-limiting conditions, fluorescent pseudomonads acquire iron from the environment by secreting strain-specific, iron-chelating siderophores termed pyoverdines (PVD). The rhizosphere bacterium Pseudomonas protegens Pf-5 produces its own PVD but also can cross-feed on PVDs produced by other species. Previous work has found that Pf-5 continues to produce its own PVD when allowed to cross-feed, raising questions about the benefit of heterologous PVD utilisation. Here, we investigate this question using a defined, unidirectional P. protegens Pf-5/Pseudomonas aeruginosa PAO1 cross-feeding model. Quantifying the production of PVD in the presence of heterologous PVD produced by PAO1, we show that cross-feeding Pf-5 strains reduce the production of their own PVD, while non-cross-feeding Pf-5 strains increase the production of PVD. Measuring the fitness of cross-feeding and non-cross-feeding Pf-5 strains in triple coculture with PAO1, we find that cross-feeding provides a fitness benefit to Pf-5 when the availability of heterologous PVD is high. We conclude that cross-feeding can reduce the costs of self-PVD production and may thus aid in the colonisation of iron-limited environments that contain compatible siderophores produced by other resident microbes. Taken together, these results expand our understanding of the mechanisms of interspecific competition for iron in microbial communities.
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Affiliation(s)
- Parker Smith
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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16
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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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17
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Schaal KA, Manhes P, Velicer GJ. Ecological histories determine the success of social exploitation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571652. [PMID: 38168390 PMCID: PMC10760085 DOI: 10.1101/2023.12.14.571652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Ecological context often modifies biotic interactions, yet effects of ecological history are poorly understood. In experiments with the bacterium Myxococcus xanthus , resource-level histories of genotypes interacting during cooperative multicellular development were found to strongly regulate social fitness. Yet how developmental spore production responded to variation in resource-level histories between interactants differed greatly between cooperators and cheaters; relative-fitness advantages gained by cheating after high-resource growth were generally reduced or absent if one or both parties experienced low-resource growth. Low-resource growth also eliminated facultative exploitation in some pairwise mixes of cooperation-proficient natural isolates that occurs when both strains have grown under resource abundance. Our results contrast with previous studies in which cooperator fitness correlated positively with resource level and suggest that resource-level variation may be important in regulating whether exploitation of cooperators occurs in a natural context.
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18
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Masroni MSB, Lee KW, Lee VKM, Ng SB, Law CT, Poon KS, Lee BTK, Liu Z, Tan YP, Chng WL, Tucker S, Ngo LSM, Yip GWC, Nga ME, Hue SSS, Putti TC, Bay BH, Lin Q, Zhou L, Hartman M, Loh TP, Lakshmanan M, Lee SY, Tergaonkar V, Chua H, Lee AVH, Yeo EYM, Li MH, Chang CF, Kee Z, Tan KML, Tan SY, Koay ESC, Archetti M, Leong SM. Dynamic altruistic cooperation within breast tumors. Mol Cancer 2023; 22:206. [PMID: 38093346 PMCID: PMC10720132 DOI: 10.1186/s12943-023-01896-7] [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: 06/05/2023] [Accepted: 11/05/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Social behaviors such as altruism, where one self-sacrifices for collective benefits, critically influence an organism's survival and responses to the environment. Such behaviors are widely exemplified in nature but have been underexplored in cancer cells which are conventionally seen as selfish competitive players. This multidisciplinary study explores altruism and its mechanism in breast cancer cells and its contribution to chemoresistance. METHODS MicroRNA profiling was performed on circulating tumor cells collected from the blood of treated breast cancer patients. Cancer cell lines ectopically expressing candidate miRNA were used in co-culture experiments and treated with docetaxel. Ecological parameters like relative survival and relative fitness were assessed using flow cytometry. Functional studies and characterization performed in vitro and in vivo include proliferation, iTRAQ-mass spectrometry, RNA sequencing, inhibition by small molecules and antibodies, siRNA knockdown, CRISPR/dCas9 inhibition and fluorescence imaging of promoter reporter-expressing cells. Mathematical modeling based on evolutionary game theory was performed to simulate spatial organization of cancer cells. RESULTS Opposing cancer processes underlie altruism: an oncogenic process involving secretion of IGFBP2 and CCL28 by the altruists to induce survival benefits in neighboring cells under taxane exposure, and a self-sacrificial tumor suppressive process impeding proliferation of altruists via cell cycle arrest. Both processes are regulated concurrently in the altruists by miR-125b, via differential NF-κB signaling specifically through IKKβ. Altruistic cells persist in the tumor despite their self-sacrifice, as they can regenerate epigenetically from non-altruists via a KLF2/PCAF-mediated mechanism. The altruists maintain a sparse spatial organization by inhibiting surrounding cells from adopting the altruistic fate via a lateral inhibition mechanism involving a GAB1-PI3K-AKT-miR-125b signaling circuit. CONCLUSIONS Our data reveal molecular mechanisms underlying manifestation, persistence and spatial spread of cancer cell altruism. A minor population behave altruistically at a cost to itself producing a collective benefit for the tumor, suggesting tumors to be dynamic social systems governed by the same rules of cooperation in social organisms. Understanding cancer cell altruism may lead to more holistic models of tumor evolution and drug response, as well as therapeutic paradigms that account for social interactions. Cancer cells constitute tractable experimental models for fields beyond oncology, like evolutionary ecology and game theory.
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Affiliation(s)
- Muhammad Sufyan Bin Masroni
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Kee Wah Lee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, MD10, 4 Medical Drive, Singapore, 117594, Singapore
| | - Victor Kwan Min Lee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
- NUS Centre for Cancer Research (N2CR), MD6, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Siok Bian Ng
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
- NUS Centre for Cancer Research (N2CR), MD6, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Chao Teng Law
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Kok Siong Poon
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Bernett Teck-Kwong Lee
- Centre for Biomedical Informatics, Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, NTU Main Campus, 59 Nanyang Drive, Level 4, Singapore, 636921, Singapore
| | - Zhehao Liu
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, MD10, 4 Medical Drive, Singapore, 117594, Singapore
| | - Yuen Peng Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Wee Ling Chng
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Steven Tucker
- Tucker Medical Pte Ltd, Novena Specialist Centre, 8 Sinaran Drive #04-03, Singapore, 307470, Singapore
| | - Lynette Su-Mien Ngo
- Raffles Cancer Centre, Raffles Hospital, 585 North Bridge Road, Singapore, 188770, Singapore
- Current address: Curie Oncology Pte Ltd, Mount Elizabeth Novena Specialist Centre, 38 Irrawaddy Road, Level 8, #08-29/30, Singapore, 329563, Singapore
| | - George Wai Cheong Yip
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, MD10, 4 Medical Drive, Singapore, 117594, Singapore
- NUS Centre for Cancer Research (N2CR), MD6, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Min En Nga
- Department of Pathology, National University Hospital, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Susan Swee Shan Hue
- Department of Pathology, National University Hospital, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Thomas Choudary Putti
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Boon Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, MD10, 4 Medical Drive, Singapore, 117594, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Lihan Zhou
- MiRXES Pte Ltd, JTC MedTech Hub, 2 Tukang Innovation Grove #08-01, Singapore, 618305, Singapore
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 8, Singapore, 119228, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Level 3 NUH Main Building, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Sook Yee Lee
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Vinay Tergaonkar
- NUS Centre for Cancer Research (N2CR), MD6, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Huiwen Chua
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Adeline Voon Hui Lee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Eric Yew Meng Yeo
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Mo-Huang Li
- CellSievo Pte Ltd, Block 289A, Bukit Batok Street 25, #15-218, Singapore, 650289, Singapore
| | - Chan Fong Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117594, Singapore
| | - Zizheng Kee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Karen Mei-Ling Tan
- Department of Laboratory Medicine, National University Hospital, Level 3 NUH Main Building, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
- Singapore Institute For Clinical Sciences, Brenner Centre for Molecular Medicine, 30 Medical Drive, Singapore, 117609, Singapore.
| | - Soo Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
- NUS Centre for Cancer Research (N2CR), MD6, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore.
- Department of Pathology, National University Hospital, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore.
| | - Evelyn Siew-Chuan Koay
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
- Department of Laboratory Medicine, National University Hospital, Level 3 NUH Main Building, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
| | - Marco Archetti
- Department of Biology, Pennsylvania State University, W210 Millennium Science Complex, University Park, PA, 16802, USA.
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Level 3 NUH Main Building, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
- NUS Centre for Cancer Research (N2CR), MD6, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore.
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19
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Belcher LJ, Dewar AE, Hao C, Katz Z, Ghoul M, West SA. SOCfinder: a genomic tool for identifying social genes in bacteria. Microb Genom 2023; 9:001171. [PMID: 38117204 PMCID: PMC10763506 DOI: 10.1099/mgen.0.001171] [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: 07/12/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023] Open
Abstract
Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify genes that control cooperative or otherwise social traits. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. We introduce SOCfinder as a new tool to find bacterial genes that control cooperative or otherwise social traits. SOCfinder combines information from several methods, considering if a gene is likely to [1] code for an extracellular protein [2], have a cooperative functional annotation, or [3] be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (P. aeruginosa and B. subtilis) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder.
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Affiliation(s)
| | - Anna E. Dewar
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Zohar Katz
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Stuart A. West
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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20
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Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, Leavitt LaBella A, Groenewald M, Zhou X, Shen XX, Rokas A, Todd Hittinger C. Functional and evolutionary integration of a fungal gene with a bacterial operon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568075. [PMID: 38045280 PMCID: PMC10690196 DOI: 10.1101/2023.11.21.568075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.
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Affiliation(s)
- Liang Sun
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Kyle T. David
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Steven D. Karlen
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Carla Gonçalves
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Dana A. Opulente
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223
| | | | - Xiaofan Zhou
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Xing-Xing Shen
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Antonis Rokas
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
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21
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Leeks A, Bono LM, Ampolini EA, Souza LS, Höfler T, Mattson CL, Dye AE, Díaz-Muñoz SL. Open questions in the social lives of viruses. J Evol Biol 2023; 36:1551-1567. [PMID: 37975507 PMCID: PMC11281779 DOI: 10.1111/jeb.14203] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 11/19/2023]
Abstract
Social interactions among viruses occur whenever multiple viral genomes infect the same cells, hosts, or populations of hosts. Viral social interactions range from cooperation to conflict, occur throughout the viral world, and affect every stage of the viral lifecycle. The ubiquity of these social interactions means that they can determine the population dynamics, evolutionary trajectory, and clinical progression of viral infections. At the same time, social interactions in viruses raise new questions for evolutionary theory, providing opportunities to test and extend existing frameworks within social evolution. Many opportunities exist at this interface: Insights into the evolution of viral social interactions have immediate implications for our understanding of the fundamental biology and clinical manifestation of viral diseases. However, these opportunities are currently limited because evolutionary biologists only rarely study social evolution in viruses. Here, we bridge this gap by (1) summarizing the ways in which viruses can interact socially, including consequences for social evolution and evolvability; (2) outlining some open questions raised by viruses that could challenge concepts within social evolution theory; and (3) providing some illustrative examples, data sources, and conceptual questions, for studying the natural history of social viruses.
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Affiliation(s)
- Asher Leeks
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA
| | - Lisa M. Bono
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Elizabeth A. Ampolini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lucas S. Souza
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Thomas Höfler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Courtney L. Mattson
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA
| | - Anna E. Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Samuel L. Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA
- Genome Center, University of California Davis, Davis, California, USA
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22
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Guadarrama-Orozco KD, Perez-Gonzalez C, Kota K, Cocotl-Yañez M, Jiménez-Cortés JG, Díaz-Guerrero M, Hernández-Garnica M, Munson J, Cadet F, López-Jácome LE, Estrada-Velasco ÁY, Fernández-Presas AM, García-Contreras R. To cheat or not to cheat: cheatable and non-cheatable virulence factors in Pseudomonas aeruginosa. FEMS Microbiol Ecol 2023; 99:fiad128. [PMID: 37827541 DOI: 10.1093/femsec/fiad128] [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: 07/23/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023] Open
Abstract
Important bacterial pathogens such as Pseudomonas aeruginosa produce several exoproducts such as siderophores, degradative enzymes, biosurfactants, and exopolysaccharides that are used extracellularly, benefiting all members of the population, hence being public goods. Since the production of public goods is a cooperative trait, it is in principle susceptible to cheating by individuals in the population who do not invest in their production, but use their benefits, hence increasing their fitness at the expense of the cooperators' fitness. Among the most studied virulence factors susceptible to cheating are siderophores and exoproteases, with several studies in vitro and some in animal infection models. In addition to these two well-known examples, cheating with other virulence factors such as exopolysaccharides, biosurfactants, eDNA production, secretion systems, and biofilm formation has also been studied. In this review, we discuss the evidence of the susceptibility of each of those virulence factors to cheating, as well as the mechanisms that counteract this behavior and the possible consequences for bacterial virulence.
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Affiliation(s)
- Katya Dafne Guadarrama-Orozco
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Caleb Perez-Gonzalez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Kokila Kota
- Ramapo College of New Jersey, Biology Department, Mahwah, NJ 07430, USA
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Jesús Guillermo Jiménez-Cortés
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Mariel Hernández-Garnica
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Julia Munson
- Ramapo College of New Jersey, Biology Department, Mahwah, NJ 07430, USA
| | - Frederic Cadet
- PEACCEL, Artificial Intelligence Department, AI for Biologics, Paris, 75013, France
| | - Luis Esaú López-Jácome
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389 Mexico City, Mexico
| | - Ángel Yahir Estrada-Velasco
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Ana María Fernández-Presas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
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23
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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24
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Kalambokidis M, Travisano M. Multispecies interactions shape the transition to multicellularity. Proc Biol Sci 2023; 290:20231055. [PMID: 37727086 PMCID: PMC10509594 DOI: 10.1098/rspb.2023.1055] [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: 05/12/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
The origin of multicellularity transformed the adaptive landscape on Earth, opening diverse avenues for further innovation. The transition to multicellular life is understood as the evolution of cooperative groups which form a new level of individuality. Despite the potential for community-level interactions, most studies have not addressed the competitive context of this transition, such as competition between species. Here, we explore how interspecific competition shapes the emergence of multicellularity in an experimental system with two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis, where multicellularity evolves in response to selection for faster settling ability. We find that the multispecies context slows the rate of the transition to multicellularity, and the transition to multicellularity significantly impacts community composition. Multicellular K. lactis emerges first and sweeps through populations in monocultures faster than in cocultures with S. cerevisiae. Following the transition, the between-species competitive dynamics shift, likely in part to intraspecific cooperation in K. lactis. Hence, we document an eco-evolutionary feedback across the transition to multicellularity, underscoring how ecological context is critical for understanding the causes and consequences of innovation. By including two species, we demonstrate that cooperation and competition across several biological scales shapes the origin and persistence of multicellularity.
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Affiliation(s)
- Maria Kalambokidis
- Department of Ecology, Evolution, University of Minnesota, St. Paul, MN 55108, USA
- Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Travisano
- Department of Ecology, Evolution, University of Minnesota, St. Paul, MN 55108, USA
- The BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
- Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
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25
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Zhao K, Yang X, Zeng Q, Zhang Y, Li H, Yan C, Li JS, Liu H, Du L, Wu Y, Huang G, Huang T, Zhang Y, Zhou H, Wang X, Chu Y, Zhou X. Evolution of lasR mutants in polymorphic Pseudomonas aeruginosa populations facilitates chronic infection of the lung. Nat Commun 2023; 14:5976. [PMID: 37749088 PMCID: PMC10519970 DOI: 10.1038/s41467-023-41704-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
Chronic infection with the bacterial pathogen Pseudomonas aeruginosa often leads to coexistence of heterogeneous populations carrying diverse mutations. In particular, loss-of-function mutations affecting the quorum-sensing regulator LasR are often found in bacteria isolated from patients with lung chronic infection and cystic fibrosis. Here, we study the evolutionary dynamics of polymorphic P. aeruginosa populations using isolates longitudinally collected from patients with chronic obstructive pulmonary disease (COPD). We find that isolates deficient in production of different sharable extracellular products are sequentially selected in COPD airways, and lasR mutants appear to be selected first due to their quorum-sensing defects. Polymorphic populations including lasR mutants display survival advantages in animal models of infection and modulate immune responses. Our study sheds light on the multistage evolution of P. aeruginosa populations during their adaptation to host lungs.
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Affiliation(s)
- Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China.
| | - Xiting Yang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Qianglin Zeng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yige Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Heyue Li
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Chaochao Yan
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Jing Shirley Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Huan Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Liangming Du
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yi Wu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Gui Huang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Ting Huang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yamei Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Hui Zhou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Xinrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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26
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O'Brien S, Culbert CT, Barraclough TG. Community composition drives siderophore dynamics in multispecies bacterial communities. BMC Ecol Evol 2023; 23:45. [PMID: 37658316 PMCID: PMC10472669 DOI: 10.1186/s12862-023-02152-8] [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: 11/29/2022] [Accepted: 08/17/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e., interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence drive intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2 to 15 species. RESULTS We find, contrary to our prediction, that siderophore production is favoured at higher levels of community species richness, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. CONCLUSIONS Our results suggest that maintaining a diverse soil microbiota could partly contribute to the maintenance of siderophore production in natural communities.
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Affiliation(s)
- Siobhán O'Brien
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Christopher T Culbert
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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27
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Arenzon JJ, Peliti L. Emergent cooperative behavior in transient compartments. Phys Rev E 2023; 108:034409. [PMID: 37849208 DOI: 10.1103/physreve.108.034409] [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: 05/01/2023] [Accepted: 09/07/2023] [Indexed: 10/19/2023]
Abstract
We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors sampled from an infinite pool. After the fragmentation, these transient compartments grow until the maximal number of individuals per compartment is attained. Eventually, all compartments are merged and well mixed, and the whole process is repeated. We show that cooperators, even if interacting only through mean-field intragroup interactions that favor defectors, may perform well because of the intergroup competition and the size diversity among the compartments. These cycles of isolation and coalescence may therefore be important in maintaining diversity among different species or strategies and may help to understand the underlying mechanisms of the scaffolding processes in the transition to multicellularity.
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Affiliation(s)
- Jeferson J Arenzon
- Instituto de Física, Universidade Federal do Rio Grande do Sul, CP 15051, 91501-970 Porto Alegre RS, Brazil
- Instituto Nacional de Ciência e Tecnologia-Sistemas Complexos, 22290-180 Rio de Janeiro RJ, Brazil
| | - Luca Peliti
- Santa Marinella Research Institute, 00058 Santa Marinella (RM), Italy
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28
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Travers-Cook TJ, Jokela J, Buser CC. The evolutionary ecology of fungal killer phenotypes. Proc Biol Sci 2023; 290:20231108. [PMID: 37583325 PMCID: PMC10427833 DOI: 10.1098/rspb.2023.1108] [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: 05/17/2023] [Accepted: 07/20/2023] [Indexed: 08/17/2023] Open
Abstract
Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.
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Affiliation(s)
- Thomas J. Travers-Cook
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Jukka Jokela
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Claudia C. Buser
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
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29
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Debeljak P, Bayer B, Sun Y, Herndl GJ, Obernosterer I. Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. MICROBIOME 2023; 11:187. [PMID: 37596690 PMCID: PMC10439609 DOI: 10.1186/s40168-023-01600-3] [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: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer. RESULTS Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae. CONCLUSION The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.
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Affiliation(s)
- Pavla Debeljak
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France.
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria.
- SupBiotech, Villejuif, France.
| | - Barbara Bayer
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ying Sun
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ (Royal Netherlands Institute for Sea Research), Den Burg, 1790 AB, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
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Ozan M, Helanterä H, d'Ettorre P, Sundström L. Queen fecundity, worker entourage and cuticular chemistry in the ant Formica fusca. Proc Biol Sci 2023; 290:20230861. [PMID: 37554034 PMCID: PMC10410219 DOI: 10.1098/rspb.2023.0861] [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: 04/12/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
Cooperative breeding entails conflicts over reproductive shares that may be settled in different ways. In ants, where several queens simultaneously reproduce in a colony, both queens and workers may influence the reproductive apportionment and offspring quality. Queens may vary in their intrinsic fecundity, which may influence the size of the worker entourage attending individual queens, and this may eventually dictate the reproductive output of a queen. We tested whether the reproductive success of queens is affected by the size of their worker entourage, their fecundity at the onset of the reproductive season, and whether the queen cuticular hydrocarbon profile carries information on fecundity. We show that in the ant Formica fusca both queen fecundity and egg hatching success increase with the size of their entourage, and that newly hatched larvae produced by initially highly fecund queens are smaller. Furthermore, higher relatedness among workers increased queen fecundity. Finally, the queens that received a large worker entourage differed in the cuticular chemistry from those that received a small worker entourage. Our results thus show that workers play a pivotal role in determining queen fitness, that high intracolony relatedness among workers enhances the overall reproductive output in the colony, and that queen fecundity is reflected in their cuticular hydrocarbon profile.
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Affiliation(s)
- Martina Ozan
- Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Finland
- Tvärminne Zoological Station, University of Helsinki, J.A. Palménintie 260, 10900 Hanko, Finland
| | - Heikki Helanterä
- Tvärminne Zoological Station, University of Helsinki, J.A. Palménintie 260, 10900 Hanko, Finland
- Faculty of Science, Ecology and Genetics Research Unit, University of Oulu, 90014, Finland
| | - Patrizia d'Ettorre
- Laboratoire d'Ethologie Expérimentale et Comparée, UR 4443, Université Sorbonne Paris Nord, Villetaneuse, France
- Institut Universitaire de France (IUF), Paris, France
| | - Liselotte Sundström
- Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Finland
- Tvärminne Zoological Station, University of Helsinki, J.A. Palménintie 260, 10900 Hanko, Finland
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Pike VL, Stevens EJ, Griffin AS, King KC. Within- and between-host dynamics of producer and non-producer pathogens. Parasitology 2023; 150:805-812. [PMID: 37394480 PMCID: PMC10478067 DOI: 10.1017/s0031182023000586] [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: 02/13/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 07/04/2023]
Abstract
For infections to be maintained in a population, pathogens must compete to colonize hosts and transmit between them. We use an experimental approach to investigate within-and-between host dynamics using the pathogen Pseudomonas aeruginosa and the animal host Caenorhabditis elegans. Within-host interactions can involve the production of goods that are beneficial to all pathogens in the local environment but susceptible to exploitation by non-producers. We exposed the nematode host to ‘producer’ and two ‘non-producer’ bacterial strains (specifically for siderophore production and quorum sensing), in single infections and coinfections, to investigate within-host colonization. Subsequently, we introduced infected nematodes to pathogen-naive populations to allow natural transmission between hosts. We find that producer pathogens are consistently better at colonizing hosts and transmitting between them than non-producers during coinfection and single infection. Non-producers were poor at colonizing hosts and between-host transmission, even when coinfecting with producers. Understanding pathogen dynamics across these multiple levels will ultimately help us predict and control the spread of infections, as well as contribute to explanations for the persistence of cooperative genotypes in natural populations.
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Affiliation(s)
| | | | | | - Kayla C. King
- Department of Biology, University of Oxford, Oxford, UK
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada
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Morwool P, Dimitriu T, Crickmore N, Raymond B. Group Selection as a Basis for Screening Mutagenized Libraries of Public Goods (Bacillus thuringiensis Cry Toxins). Appl Environ Microbiol 2023; 89:e0051223. [PMID: 37358425 PMCID: PMC10370297 DOI: 10.1128/aem.00512-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/26/2023] [Indexed: 06/27/2023] Open
Abstract
The pesticidal toxins of Bacillus thuringiensis (Bt) supply the active proteins for genetically modified insect-resistant crops. There is therefore keen interest in finding new toxins, or improving known toxins, in order to increase the mortality of various targets. The production and screening of large libraries of mutagenized toxins are among the means of identifying improved toxins. Since Cry toxins are public goods, and do not confer advantages to producers in competition, conventional directed evolution approaches cannot be used here. Instead, thousands of individual mutants have to be sequenced and assayed individually, a costly and time-consuming process. In this study, we tested a group selection-based approach that could be used to screen an uncharacterized pool of Cry toxin mutants. This involved selecting for infectivity between subpopulations of Bt clones within metapopulations of infected insects in three rounds of passage. We also tested whether additional mutagenesis from exposure to ethyl methanesulfonate could increase infectivity or supply additional Cry toxin diversity during passage. Sequencing of pools of mutants at the end of selection showed that we could effectively screen out Cry toxin variants that had reduced toxicity with our group selection approach. The addition of extra mutagenesis during passage decreased the efficiency of selection for infectivity and did not produce any additional novel toxin diversity. Toxins with loss-of-function mutations tend to dominate mutagenized libraries, and so a process for screening out these mutants without time-consuming sequencing and characterization steps could be beneficial when applied to larger libraries. IMPORTANCE Insecticidal toxins from the bacterium Bacillus thuringiensis are widely exploited in genetically modified plants. This application creates a demand for novel insecticidal toxins that can be used to better manage resistant pests or control new or recalcitrant target species. An important means of producing novel toxins is via high-throughput mutagenesis and screening of existing toxins, a lengthy and resource-intensive process. This study describes the development and testing of an efficient means of screening a test library of mutagenized insecticidal toxins. Here, we showed that it is possible to screen out loss-of-function mutations with low infectivity within a pool without the need to characterize and sequence each mutant individually. This has the potential to improve the efficiency of processes used to identify novel proteins.
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Affiliation(s)
| | | | - Neil Crickmore
- Department of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Ben Raymond
- University of Exeter, Penryn, United Kingdom
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Fant L, Mazzarisi O, Panizon E, Grilli J. Stable cooperation emerges in stochastic multiplicative growth. Phys Rev E 2023; 108:L012401. [PMID: 37583239 DOI: 10.1103/physreve.108.l012401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/01/2023] [Indexed: 08/17/2023]
Abstract
Understanding the evolutionary stability of cooperation is a central problem in biology, sociology, and economics. There exist only a few known mechanisms that guarantee the existence of cooperation and its robustness to cheating. Here, we introduce a mechanism for the emergence of cooperation in the presence of fluctuations. We consider agents whose wealth changes stochastically in a multiplicative fashion. Each agent can share part of her wealth as a public good, which is equally distributed among all the agents. We show that, when agents operate with long-time horizons, cooperation produces an advantage at the individual level, as it effectively screens agents from the deleterious effect of environmental fluctuations.
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Affiliation(s)
- Lorenzo Fant
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Onofrio Mazzarisi
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany
| | - Emanuele Panizon
- Quantitative Life Sciences section, The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34014 Trieste, Italy
| | - Jacopo Grilli
- Quantitative Life Sciences section, The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34014 Trieste, Italy
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Bose APH, Dabernig-Heinz J, Oberkofler J, Koch L, Grimm J, Sefc KM, Jordan A. Aggression and spatial positioning of kin and non-kin fish in social groups. Behav Ecol 2023; 34:673-681. [PMID: 37434638 PMCID: PMC10332448 DOI: 10.1093/beheco/arad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/01/2023] [Accepted: 04/19/2023] [Indexed: 07/13/2023] Open
Abstract
Group-living animals are faced with the challenge of sharing space and local resources amongst group members who may be either relatives or non-relatives. Individuals may reduce the inclusive fitness costs they incur from competing with relatives by either reducing their levels of aggression toward kin, or by maintaining physical separation between kin. In this field study, we used the group-living cichlid Neolamprologus multifasciatus to examine whether within-group aggression is reduced among group members that are kin, and whether kin occupy different regions of their group's territory to reduce kin competition over space and local resources. We determined the kinship relationships among cohabiting adults via microsatellite genotyping and then combined these with spatial and behavioral analyses of groups in the wild. We found that aggressive contests between group members declined in frequency with spatial separation between their shelters. Female kin did not engage in aggressive contests with one another, whereas non-kin females did, despite the fact these females lived at similar distances from one another on their groups' territories. Contests within male-male and male-female dyads did not clearly correlate with kinship. Non-kin male-male and male-female dyads lived at more variable distances from one another on their territories than their corresponding kin dyads. Together, our study indicates that contests among group members can be mediated by relatedness in a sex-dependent manner. We also suggest that spatial relationships can play an important role in determining the extent to which group members compete with one another.
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Affiliation(s)
- Aneesh P H Bose
- Department of Wildlife, Fish & Environmental Studies, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183, Umeå, Sweden
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Universitätsstraße 10, 78464, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | | | - Jan Oberkofler
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Universitätsstraße 10, 78464, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Lukas Koch
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Universitätsstraße 10, 78464, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Jacqueline Grimm
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Alex Jordan
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Universitätsstraße 10, 78464, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
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35
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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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36
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McLean EM, Moorad JA, Tung J, Archie EA, Alberts SC. Genetic variance and indirect genetic effects for affiliative social behavior in a wild primate. Evolution 2023; 77:1607-1621. [PMID: 37094802 PMCID: PMC10309972 DOI: 10.1093/evolut/qpad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
Affiliative social behaviors are linked to fitness components in multiple species. However, the role of genetic variance in shaping such behaviors remains largely unknown, limiting our understanding of how affiliative behaviors can respond to natural selection. Here, we employed the "animal model" to estimate environmental and genetic sources of variance and covariance in grooming behavior in the well-studied Amboseli wild baboon population. We found that the tendency for a female baboon to groom others ("grooming given") is heritable (h2 = 0.22 ± 0.048), and that several environmental variables-including dominance rank and the availability of kin as grooming partners-contribute to variance in this grooming behavior. We also detected small but measurable variance due to the indirect genetic effect of partner identity on the amount of grooming given within dyadic grooming partnerships. The indirect and direct genetic effects for grooming given were positively correlated (r = 0.74 ± 0.09). Our results provide insight into the evolvability of affiliative behavior in wild animals, including the possibility for correlations between direct and indirect genetic effects to accelerate the response to selection. As such they provide novel information about the genetic architecture of social behavior in nature, with important implications for the evolution of cooperation and reciprocity.
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Affiliation(s)
- Emily M McLean
- University Program in Genetics and Genomics, Duke University, Durham, NC, United States
- Division of Natural Sciences and Mathematics, Oxford College, Emory University, Oxford, GA, United States
| | - Jacob A Moorad
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, Scotland
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, United States
- Department of Evolutionary Anthropology, Duke University, Durham, NC, United States
- Population Research Institute, Duke University, Durham, NC, United States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, United States
- Department of Evolutionary Anthropology, Duke University, Durham, NC, United States
- Population Research Institute, Duke University, Durham, NC, United States
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Jiang L, Zhao Y, Yao Y, Lou J, Zhao Y, Hu B. Adding siderophores: A new strategy to reduce greenhouse gas emissions in composting. BIORESOURCE TECHNOLOGY 2023:129319. [PMID: 37315620 DOI: 10.1016/j.biortech.2023.129319] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/10/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Microbial community is the primary driver causing the greenhouse gas emissions in composting. Thus, regulating the microbial communities is a strategy to reduce them. Here, two different siderophores (enterobactin and putrebactin) were added, which could bind and translocate iron by specific microbes, to regulate the composting communities. The results showed that adding enterobactin enriched Acinetobacter and Bacillus with specific receptors by 6.84-fold and 6.78-fold. It promoted carbohydrate degradation and amino acid metabolism. This resulted in a 1.28-fold increase in humic acid content, as well as a 14.02% and 18.27% decrease in CO2 and CH4 emissions, respectively. Meanwhile, adding putrebactin boosted the microbial diversity by 1.21-fold and enhanced potential microbial interactions by 1.76-fold. The attenuated denitrification process led to a 1.51-fold increase in the total nitrogen content and a 27.47% reduction in N2O emissions. Overall, adding siderophores is an efficient strategy to reduce greenhouse gas emissions and promote the compost quality.
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Affiliation(s)
- Liyan Jiang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuqing Yao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingxuan Lou
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou310058, China.
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38
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Teodoro-Paulo J, Alba JM, Charlesworth S, Kant MR, Magalhães S, Duncan AB. Intraspecific variation for host immune activation by the spider mite Tetranychus evansi. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230525. [PMID: 37325599 PMCID: PMC10265008 DOI: 10.1098/rsos.230525] [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: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Many parasites can interfere with their host's defences to maximize their fitness. Here, we investigated if there is heritable variation in the spider mite Tetranychus evansi for traits associated with how they interact with their host plant. We also determined if this variation correlates with mite fecundity. Tetranychus evansi can interfere with jasmonate (JA) defences which are the main determinant of anti-herbivore immunity in plants. We investigated (i) variation in fecundity in the presence and absence of JA defences, making use of a wild-type tomato cultivar and a JA-deficient mutant (defenseless-1), and (ii) variation in the induction of JA defences, in four T. evansi field populations and 59 inbred lines created from an outbred population originating from controlled crosses of the four field populations. We observed a strong positive genetic correlation between fecundity in the presence (on wild-type) and the absence of JA defences (on defenseless-1). However, fecundity did not correlate with the magnitude of induced JA defences in wild-type plants. Our results suggest that the performance of the specialist T. evansi is not related to their ability to manipulate plant defences, either because all lines can adequately reduce levels of defences, or because they are resistant to them.
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Affiliation(s)
- Jéssica Teodoro-Paulo
- cE3c—Centre for Ecology, Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Institut des Sciences de l’Évolution, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Juan M. Alba
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Steven Charlesworth
- cE3c—Centre for Ecology, Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Merijn R. Kant
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Sara Magalhães
- cE3c—Centre for Ecology, Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Alison B. Duncan
- Institut des Sciences de l’Évolution, University of Montpellier, CNRS, IRD, Montpellier, France
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Wang Q, Wei S, Silva AF, Madsen JS. Cooperative antibiotic resistance facilitates horizontal gene transfer. THE ISME JOURNAL 2023; 17:846-854. [PMID: 36949153 PMCID: PMC10203111 DOI: 10.1038/s41396-023-01393-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/24/2023]
Abstract
The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.
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Affiliation(s)
- Qinqin Wang
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Shaodong Wei
- National Food Institute, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ana Filipa Silva
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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Jones CT, Meynell L, Neto C, Susko E, Bielawski JP. The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations. BMC Ecol Evol 2023; 23:11. [PMID: 37046187 PMCID: PMC10100367 DOI: 10.1186/s12862-023-02112-2] [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: 11/10/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Kin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists. Here we take a different explanatory approach based on the recently proposed concept of an "ecological scaffold". We demonstrate that ecological conditions consisting of a patchy nutrient supply that generates a metapopulation structure, episodic mixing of groups, and severe nutrient limitation, can support or "scaffold" the evolution of altruism in a population of microbes by amplifying drift. This contrasts with recent papers in which the ecological scaffold was shown to support selective processes and demonstrates the power of scaffolding even in the absence of selection. RESULTS Using computer simulations motivated by a simple theoretical model, we show that, although an altruistic mutant can be fixed within a single population of non-altruists by drift when nutrients are severely limited, the resulting altruistic population remains vulnerable to non-altruistic mutants. We then show how the imposition of the "ecological scaffold" onto a population of non-altruists alters the balance between selection and drift in a way that supports the fixation and subsequent persistence of altruism despite the possibility of invasion by non-altruists. CONCLUSIONS The fixation of an altruistic mutant by drift is possible when supported by ecological conditions that impose a metapopulation structure, episodic mixing of groups, and severe nutrient limitation. This is significant because it offers an alternative explanation for the evolution of altruism based on drift rather than selection. Given the ubiquity of low-nutrient "oligotrophic" environments in which microbes exist (e.g., the open ocean, deep subsurface soils, or under the polar ice caps) our results suggest that altruistic and cooperative behaviors may be highly prevalent among microbial populations.
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Affiliation(s)
- C T Jones
- Department of Biochemistry and Molecular Biology, Dalhousie University, NS, Halifax, Canada.
| | - L Meynell
- Department of Philosophy, Dalhousie University, Halifax, Canada
| | - C Neto
- Department of Social and Political Sciences, Philosophy, and Anthropology, University of Exeter, Exeter, UK
- Centre for the Study of the Life Sciences, EGENIS, University of Exeter, Exeter, UK
| | - E Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - J P Bielawski
- Department of Biology and Dept. of Mathematics and Statistics, Dalhousie University, Halifax, Canada
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41
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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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42
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Hu K, Wang P, He J, Perc M, Shi L. Complex evolutionary interactions in multiple populations. Phys Rev E 2023; 107:044301. [PMID: 37198848 DOI: 10.1103/physreve.107.044301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 03/22/2023] [Indexed: 05/19/2023]
Abstract
In competitive settings that entail several populations, individuals often engage in intra- and interpopulation interactions that determine their fitness and evolutionary success. With this simple motivation, we here study a multipopulation model where individuals engage in group interactions within their own population and in pairwise interactions with individuals from different populations. We use the evolutionary public goods game and the prisoner's dilemma game to describe these group and pairwise interactions, respectively. We also take into account asymmetry in the extent to which group and pairwise interactions determine the fitness of individuals. We find that interactions across multiple populations reveal new mechanisms through which the evolution of cooperation can be promoted, but this depends on the level of interaction asymmetry. If inter- and intrapopulation interactions are symmetric, the sole presence of multiple populations promotes the evolution of cooperation. Asymmetry in the interactions can further promote cooperation at the expense of the coexistence of the competing strategies. An in-depth analysis of the spatiotemporal dynamics reveals loop-dominated structures and pattern formation that can explain the various evolutionary outcomes. Thus, complex evolutionary interactions in multiple populations reveal an intricate interplay between cooperation and coexistence, and they also open up the path toward further explorations of multipopulation games and biodiversity.
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Affiliation(s)
- Kaipeng Hu
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming 650221, China
| | - Pengyue Wang
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming 650221, China
| | - Junzhou He
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming 650221, China
| | - Matjaž Perc
- Faculty of Natural Sciences and Mathematics, University of Maribor, 2000 Maribor, Slovenia
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404332, Taiwan
- Alma Mater Europaea, 2000 Maribor, Slovenia
- Complexity Science Hub Vienna, 1080 Vienna, Austria
- Department of Physics, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Lei Shi
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming 650221, China
- Interdisciplinary Research Institute of Data Science, Shanghai Lixin University of Accounting and Finance, Shanghai 201209, China
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43
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Garcia-Lopez MT, Serrano MS, Camiletti BX, Gordon A, Estudillo C, Trapero A, Diez CM, Moral J. Study of the competition between Colletotrichum godetiae and C. nymphaeae, two pathogenic species in olive. Sci Rep 2023; 13:5344. [PMID: 37005485 PMCID: PMC10067957 DOI: 10.1038/s41598-023-32585-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Olive anthracnose, a critical olive fruit disease that adversely impacts oil quality, is caused by Colletotrichum species. A dominant Colletotrichum species and several secondary species have been identified in each olive-growing region. This study surveys the interspecific competition between C. godetiae, dominant in Spain, and C. nymphaeae, prevalent in Portugal, to shed light on the cause of this disparity. When Petri-dishes of Potato Dextrose Agar (PDA) and diluted PDA were co-inoculated with spore mixes produced by both species, C. godetiae displaced C. nymphaeae, even if the percentage of spores in the initial spore mix inoculation was just 5 and 95%, respectively. The C. godetiae and C. nymphaeae species showed similar fruit virulence in separate inoculations in both cultivars, the Portuguese cv. Galega Vulgar and the Spanish cv. Hojiblanca, and no cultivar specialization was observed. However, when olive fruits were co-inoculated, the C. godetiae species showed a higher competitive ability and partially displaced the C. nymphaeae species. Furthermore, both Colletotrichum species showed a similar leaf survival rate. Lastly, C. godetiae was more resistant to metallic copper than C. nymphaeae. The work developed here allows a deeper understanding of the competition between C. godetiae and C. nymphaeae, which could lead to developing strategies for more efficient disease risk assessment.
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Affiliation(s)
- M Teresa Garcia-Lopez
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
- Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA
| | - M Socorro Serrano
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Boris X Camiletti
- Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA
| | - Ana Gordon
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Cristina Estudillo
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Antonio Trapero
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Concepcion M Diez
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Juan Moral
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain.
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44
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Daniels M, van Vliet S, Ackermann M. Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community. THE ISME JOURNAL 2023; 17:406-416. [PMID: 36611102 PMCID: PMC9938273 DOI: 10.1038/s41396-022-01312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023]
Abstract
Microbial communities thrive in almost all habitats on earth. Within these communities, cells interact through the release and uptake of metabolites. These interactions can have synergistic or antagonistic effects on individual community members. The collective metabolic activity of microbial communities leads to changes in their local environment. As the environment changes over time, the nature of the interactions between cells can change. We currently lack understanding of how such dynamic feedbacks affect the growth dynamics of individual microbes and of the community as a whole. Here we study how interactions mediated by the exchange of metabolites through the environment change over time within a simple marine microbial community. We used a microfluidic-based approach that allows us to disentangle the effect cells have on their environment from how they respond to their environment. We found that the interactions between two species-a degrader of chitin and a cross-feeder that consumes metabolic by-products-changes dynamically over time as cells modify their environment. Cells initially interact positively and then start to compete at later stages of growth. Our results demonstrate that interactions between microorganisms are not static and depend on the state of the environment, emphasizing the importance of disentangling how modifications of the environment affects species interactions. This experimental approach can shed new light on how interspecies interactions scale up to community level processes in natural environments.
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Affiliation(s)
- Michael Daniels
- Department of Environmental Systems Sciences, Microbial Systems Ecology Group, Institute of Biogeochemistry and Pollutant Dynamics, ETH-Zurich, Zurich, Switzerland. .,Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Duebendorf, Switzerland. .,Interdisciplinary PhD Program Systems Biology, ETH-Zurich and University of Zurich, Zurich, Switzerland.
| | - Simon van Vliet
- grid.6612.30000 0004 1937 0642Biozentrum, University of Basel, Basel, Switzerland
| | - Martin Ackermann
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Sciences, Microbial Systems Ecology Group, Institute of Biogeochemistry and Pollutant Dynamics, ETH-Zurich, Zurich, Switzerland ,Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Duebendorf, Switzerland
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45
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Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics. THE ISME JOURNAL 2023; 17:775-785. [PMID: 36854789 PMCID: PMC10119117 DOI: 10.1038/s41396-023-01381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Predation defense is an important feature of predator-prey interactions adding complexity to ecosystem dynamics. Prey organisms have developed various strategies to escape predation which differ in mode (elude vs. attack), reversibility (inducible vs. permanent), and scope (individual vs. cooperative defenses). While the mechanisms and controls of many singular defenses are well understood, important ecological and evolutionary facets impacting long-term predator-prey dynamics remain underexplored. This pertains especially to trade-offs and interactions between alternative defenses occurring in prey populations evolving under predation pressure. Here, we explored the dynamics of a microbial predator-prey system consisting of bacterivorous flagellates (Poteriospumella lacustris) feeding on Pseudomonas putida. Within five weeks of co-cultivation corresponding to about 35 predator generations, we observed a consistent succession of bacterial defenses in all replicates (n = 16). Initially, bacteria expressed a highly effective cooperative defense based on toxic metabolites, which brought predators close to extinction. This initial strategy, however, was consistently superseded by a second mechanism of predation defense emerging via de novo mutations. Combining experiments with mathematical modeling, we demonstrate how this succession of defenses is driven by the maximization of individual rather than population benefits, highlighting the role of rapid evolution in the breakdown of social cooperation.
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46
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Rattray JB, Brown SP. Beyond Thresholds: Quorum‐Sensing as Quantitatively Varying Reaction Norms to Multiple Environmental Dimensions. Isr J Chem 2023. [DOI: 10.1002/ijch.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
| | - Sam P. Brown
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
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47
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Eco-evolutionary modelling of microbial syntrophy indicates the robustness of cross-feeding over cross-facilitation. Sci Rep 2023; 13:907. [PMID: 36650168 PMCID: PMC9845244 DOI: 10.1038/s41598-023-27421-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
Syntrophic cooperation among prokaryotes is ubiquitous and diverse. It relies on unilateral or mutual aid that may be both catalytic and metabolic in nature. Hypotheses of eukaryotic origins claim that mitochondrial endosymbiosis emerged from mutually beneficial syntrophy of archaeal and bacterial partners. However, there are no other examples of prokaryotic syntrophy leading to endosymbiosis. One potential reason is that when externalized products become public goods, they incite social conflict due to selfish mutants that may undermine any mutualistic interactions. To rigorously evaluate these arguments, here we construct a general mathematical framework of the ecology and evolution of different types of syntrophic partnerships. We do so both in a general microbial and in a eukaryogenetic context. Studying the case where partners cross-feed on each other's self-inhibiting waste, we show that cooperative partnerships will eventually dominate over selfish mutants. By contrast, systems where producers actively secrete enzymes that cross-facilitate their partners' resource consumption are not robust against cheaters over evolutionary time. We conclude that cross-facilitation is unlikely to provide an adequate syntrophic origin for endosymbiosis, but that cross-feeding mutualisms may indeed have played that role.
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48
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Dimitriu T, Souissi W, Morwool P, Darby A, Crickmore N, Raymond B. Selecting for infectivity across metapopulations can increase virulence in the social microbe
Bacillus thuringiensis. Evol Appl 2023; 16:705-720. [PMID: 36969139 PMCID: PMC10033855 DOI: 10.1111/eva.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023] Open
Abstract
Passage experiments that sequentially infect hosts with parasites have long been used to manipulate virulence. However, for many invertebrate pathogens, passage has been applied naively without a full theoretical understanding of how best to select for increased virulence and this has led to very mixed results. Understanding the evolution of virulence is complex because selection on parasites occurs across multiple spatial scales with potentially different conflicts operating on parasites with different life histories. For example, in social microbes, strong selection on replication rate within hosts can lead to cheating and loss of virulence, because investment in public goods virulence reduces replication rate. In this study, we tested how varying mutation supply and selection for infectivity or pathogen yield (population size in hosts) affected the evolution of virulence against resistant hosts in the specialist insect pathogen Bacillus thuringiensis, aiming to optimize methods for strain improvement against a difficult to kill insect target. We show that selection for infectivity using competition between subpopulations in a metapopulation prevents social cheating, acts to retain key virulence plasmids, and facilitates increased virulence. Increased virulence was associated with reduced efficiency of sporulation, and possible loss of function in putative regulatory genes but not with altered expression of the primary virulence factors. Selection in a metapopulation provides a broadly applicable tool for improving the efficacy of biocontrol agents. Moreover, a structured host population can facilitate artificial selection on infectivity, while selection on life-history traits such as faster replication or larger population sizes can reduce virulence in social microbes.
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Affiliation(s)
- Tatiana Dimitriu
- Centre for Ecology and Conservation University of Exeter Penryn UK
| | - Wided Souissi
- School of Life Sciences University of Sussex Brighton UK
| | - Peter Morwool
- Centre for Ecology and Conservation University of Exeter Penryn UK
| | - Alistair Darby
- Centre for Genomic Research, Institute of Integrative Biology University of Liverpool Liverpool UK
| | - Neil Crickmore
- School of Life Sciences University of Sussex Brighton UK
| | - Ben Raymond
- Centre for Ecology and Conservation University of Exeter Penryn UK
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49
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Lear L, Hesse E, Buckling A, Vos M. Copper selects for siderophore-mediated virulence in Pseudomonas aeruginosa. BMC Microbiol 2022; 22:303. [PMID: 36510131 PMCID: PMC9745993 DOI: 10.1186/s12866-022-02720-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/30/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Iron is essential for almost all bacterial pathogens and consequently it is actively withheld by their hosts. However, the production of extracellular siderophores enables iron sequestration by pathogens, increasing their virulence. Another function of siderophores is extracellular detoxification of non-ferrous metals. Here, we experimentally link the detoxification and virulence roles of siderophores by testing whether the opportunistic pathogen Pseudomonas aeruginosa displays greater virulence after exposure to copper. To do this, we incubated P. aeruginosa under different environmentally relevant copper regimes for either two or twelve days. Subsequent growth in a copper-free environment removed phenotypic effects, before we quantified pyoverdine production (the primary siderophore produced by P. aeruginosa), and virulence using the Galleria mellonella infection model. RESULTS Copper selected for increased pyoverdine production, which was positively correlated with virulence. This effect increased with time, such that populations incubated with high copper for twelve days were the most virulent. Replication of the experiment with a non-pyoverdine producing strain of P. aeruginosa demonstrated that pyoverdine production was largely responsible for the change in virulence. CONCLUSIONS We here show a direct link between metal stress and bacterial virulence, highlighting another dimension of the detrimental effects of metal pollution on human health.
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Affiliation(s)
- Luke Lear
- grid.8391.30000 0004 1936 8024European Centre for Environment and Human Health, University of Exeter Medical School, Penryn, Cornwall, TR10 9FE UK
| | - Elze Hesse
- grid.8391.30000 0004 1936 8024College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE UK
| | - Angus Buckling
- grid.8391.30000 0004 1936 8024College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE UK
| | - Michiel Vos
- grid.8391.30000 0004 1936 8024European Centre for Environment and Human Health, University of Exeter Medical School, Penryn, Cornwall, TR10 9FE UK
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50
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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