1
|
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.
Collapse
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
| |
Collapse
|
2
|
Shen Z, Tang CM, Liu GY. Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids? Mil Med Res 2022; 9:3. [PMID: 35012680 PMCID: PMC8744291 DOI: 10.1186/s40779-021-00362-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.
Collapse
Affiliation(s)
- Zhen Shen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.,Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Guang-Yu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| |
Collapse
|
3
|
Sheppard RJ, Barraclough TG, Jansen VAA. The Evolution of Plasmid Transfer Rate in Bacteria and Its Effect on Plasmid Persistence. Am Nat 2021; 198:473-488. [PMID: 34559608 DOI: 10.1086/716063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractPlasmids are extrachromosomal segments of DNA that can transfer genes between bacterial cells. Many plasmid genes benefit bacteria but cause harm to human health by granting antibiotic resistance to pathogens. Transfer rate is a key parameter for predicting plasmid dynamics, but observed rates are highly variable, and the effects of selective forces on their evolution are unclear. We apply evolutionary analysis to plasmid conjugation models to investigate selective pressures affecting plasmid transfer rate, emphasizing host versus plasmid control, the costs of plasmid transfer, and the role of recipient cells. Our analyses show that plasmid-determined transfer rates can be predicted with three parameters (host growth rate, plasmid loss rate, and the cost of plasmid transfer on growth) under some conditions. We also show that low-frequency genetic variation in transfer rate can accumulate, facilitating rapid adaptation to changing conditions. Furthermore, reduced transfer rates due to host control have limited effects on plasmid prevalence until low enough to prevent plasmid persistence. These results provide a framework to predict plasmid transfer rate evolution in different environments and demonstrate the limited impact of host mechanisms to control the costs incurred when plasmids are present.
Collapse
|
4
|
Dimitriu T, Matthews AC, Buckling A. Increased copy number couples the evolution of plasmid horizontal transmission and plasmid-encoded antibiotic resistance. Proc Natl Acad Sci U S A 2021; 118:e2107818118. [PMID: 34326267 PMCID: PMC8346908 DOI: 10.1073/pnas.2107818118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Conjugative plasmids are mobile elements that spread horizontally between bacterial hosts and often confer adaptive phenotypes, including antimicrobial resistance (AMR). Theory suggests that opportunities for horizontal transmission favor plasmids with higher transfer rates, whereas selection for plasmid carriage favors less-mobile plasmids. However, little is known about the mechanisms leading to variation in transmission rates in natural plasmids or the resultant effects on their bacterial host. We investigated the evolution of AMR plasmids confronted with different immigration rates of susceptible hosts. Plasmid RP4 did not evolve in response to the manipulations, but plasmid R1 rapidly evolved up to 1,000-fold increased transfer rates in the presence of susceptible hosts. Most evolved plasmids also conferred on their hosts the ability to grow at high concentrations of antibiotics. This was because plasmids evolved greater copy numbers as a function of mutations in the copA gene controlling plasmid replication, causing both higher transfer rates and AMR. Reciprocally, plasmids with increased conjugation rates also evolved when selecting for high levels of AMR, despite the absence of susceptible hosts. Such correlated selection between plasmid transfer and AMR could increase the spread of AMR within populations and communities.
Collapse
Affiliation(s)
- Tatiana Dimitriu
- Department of Biosciences, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Andrew C Matthews
- Department of Biosciences, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Angus Buckling
- Department of Biosciences, University of Exeter, Cornwall TR10 9FE, United Kingdom
| |
Collapse
|
5
|
Teles PFS, Boiago MM, Frigo A, Rampazzo L, Araújo DN, Kich JD, Rebelatto R, Furian TQ, Stefani LM. Genetic Similarities of Escherichia Coli Isolated from Different Substrates of the Broiler Production Chain. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2021. [DOI: 10.1590/1806-9061-2020-1361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- PFS Teles
- Universidade do Estado de Santa Catarina, Brazil
| | - MM Boiago
- Universidade do Estado de Santa Catarina, Brazil
| | - A Frigo
- Universidade do Estado de Santa Catarina, Brazil
| | - L Rampazzo
- Universidade do Estado de Santa Catarina, Brazil
| | - DN Araújo
- Universidade do Estado de Santa Catarina, Brazil
| | - JD Kich
- Empresa Brasileira de Pesquisa Agropecuária, Brazil
| | - R Rebelatto
- Empresa Brasileira de Pesquisa Agropecuária, Brazil
| | - TQ Furian
- Universidade Federal do Rio Grande do Sul, Brazil
| | - LM Stefani
- Universidade do Estado de Santa Catarina, Brazil
| |
Collapse
|
6
|
Safari F, Sharifi M, Farajnia S, Akbari B, Karimi Baba Ahmadi M, Negahdaripour M, Ghasemi Y. The interaction of phages and bacteria: the co-evolutionary arms race. Crit Rev Biotechnol 2019; 40:119-137. [PMID: 31793351 DOI: 10.1080/07388551.2019.1674774] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the dawn of life, bacteria and phages are locked in a constant battle and both are perpetually changing their tactics to overcome each other. Bacteria use various strategies to overcome the invading phages, including adsorption inhibition, restriction-modification (R/E) systems, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, abortive infection (Abi), etc. To counteract, phages employ intelligent tactics for the nullification of bacterial defense systems, such as accessing host receptors, evading R/E systems, and anti-CRISPR proteins. Intense knowledge about the details of these defense pathways is the basis for their broad utilities in various fields of research from microbiology to biotechnology. Hence, in this review, we discuss some strategies used by bacteria to inhibit phage infections as well as phage tactics to circumvent bacterial defense systems. In addition, the application of these strategies will be described as a lesson learned from bacteria and phage combats. The ecological factors that affect the evolution of bacterial immune systems is the other issue represented in this review.
Collapse
Affiliation(s)
- Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Sharifi
- Department of Emergency Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
7
|
Torres ACD, Marin SY, Costa CS, Martins NRS. An Overview on Marek’s Disease Virus Evolution and Evidence for Increased Virulence in Brazil. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2019. [DOI: 10.1590/1806-9061-2018-0870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- ACD Torres
- Universidade Federal de Minas Gerais, Brazil
| | - SY Marin
- Universidade Federal de Minas Gerais, Brazil
| | - CS Costa
- Universidade Federal de Minas Gerais, Brazil
| | - NRS Martins
- Universidade Federal de Minas Gerais, Brazil
| |
Collapse
|
8
|
Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance. Plasmid 2018; 99:82-88. [PMID: 30240700 DOI: 10.1016/j.plasmid.2018.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 01/03/2023]
Abstract
Naturally occurring plasmids have medical importance given that they frequently code for virulence or antibiotic resistance. In many cases, plasmids impose a fitness cost to their hosts, meaning that the growth rate of plasmid-bearing cells is lower than that of plasmid-free cells. However, this does not fit with the fact that plasmids are ubiquitous in nature nor that plasmids and their hosts adapt to each other very fast - as has been shown in laboratory evolutionary assays. Even when plasmids are costly, they seem to largely interact in such a way that the cost of two plasmids is lower than the cost of one of them alone. Moreover, it has been argued that transfer rates are too low to compensate for plasmid costs and segregation. Several mechanisms involving interactions between plasmids and other replicons could overcome this limitation, hence contributing to the maintenance of plasmids in bacterial populations. We examine the importance of these mechanisms from a clinical point of view, particularly the spread of antibiotic resistance genes.
Collapse
|
9
|
Medaney F, Ellis RJ, Raymond B. Ecological and genetic determinants of plasmid distribution inEscherichia coli. Environ Microbiol 2016; 18:4230-4239. [DOI: 10.1111/1462-2920.13552] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/19/2016] [Accepted: 09/26/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Frances Medaney
- School of Biological Science; Royal Holloway University of London; Egham Surrey TW20 0EX UK
| | - Richard J. Ellis
- Specialist Scientific Support Department; Animal and Plant Health Agency, APHA Weybridge, Addlestone; Surrey KT15 3NB UK
| | - Ben Raymond
- School of Biological Science; Royal Holloway University of London; Egham Surrey TW20 0EX UK
- University of Exeter, Penryn Campus; Penryn Cornwall TR10 9FE UK
| |
Collapse
|
10
|
van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
Collapse
Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
11
|
Bose J, Kloesener MH, Schulte RD. Multiple-genotype infections and their complex effect on virulence. ZOOLOGY 2016; 119:339-49. [PMID: 27389395 DOI: 10.1016/j.zool.2016.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 11/17/2022]
Abstract
Multiple infections are common. Although in recent years our understanding of multiple infections has increased significantly, it has also become clear that a diversity of aspects has to be considered to understand the interplay between co-infecting parasite genotypes of the same species and its implications for virulence and epidemiology, resulting in high complexity. Here, we review different interaction mechanisms described for multiple infections ranging from competition to cooperation. We also list factors influencing the interaction between co-infecting parasite genotypes and their influence on virulence. Finally, we emphasise the importance of between-host effects and their evolution for understanding multiple infections and their implications.
Collapse
Affiliation(s)
- Joy Bose
- Department of Behavioral Biology, University of Osnabrueck, Barbarastr. 11, D-49076 Osnabrueck, Germany
| | - Michaela H Kloesener
- Department of Behavioral Biology, University of Osnabrueck, Barbarastr. 11, D-49076 Osnabrueck, Germany
| | - Rebecca D Schulte
- Department of Behavioral Biology, University of Osnabrueck, Barbarastr. 11, D-49076 Osnabrueck, Germany.
| |
Collapse
|
12
|
Size Does Matter: Staging of Silene latifolia Floral Buds for Transcriptome Studies. Int J Mol Sci 2015; 16:22027-45. [PMID: 26378529 PMCID: PMC4613295 DOI: 10.3390/ijms160922027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/30/2015] [Accepted: 09/06/2015] [Indexed: 01/07/2023] Open
Abstract
Dioecious plants in the Caryophyllaceae family are susceptible to infection by members of the anthericolous smut fungi. In our studies of the Silene latifolia/Microbotryum lychnidis-dioicae pathosystem, we were interested in characterizing the plant-pathogen interaction at the molecular level before and during teliosporogenesis. This takes place during floral bud development, and we hoped to capture the interaction by Illumina Next-Gen RNA-Sequencing. Using previous literature that documented the stages of the floral buds for S. latifolia, we examined the floral buds from plants grown and infected under growth chamber conditions, using the disserting microscope to determine the stage of floral buds based on the morphology. We compiled the information and determined the size of floral buds that correspond to the desired stages of development for tissue collection, for the purpose of RNA-sequencing. This offers a practical approach for researchers who require a large number of floral buds/tissue categorized by stages of development, ascertaining whether infected/uninfected buds are at comparable stages of development and whether this also holds true for male vs. female buds. We also document our experience in infecting the plants and some of the unusual morphologies we observed after infection.
Collapse
|
13
|
Dimitriu T, Misevic D, Lindner AB, Taddei F. Mobile genetic elements are involved in bacterial sociality. Mob Genet Elements 2015; 5:7-11. [PMID: 26435881 PMCID: PMC4588217 DOI: 10.1080/2159256x.2015.1006110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/19/2014] [Accepted: 01/07/2015] [Indexed: 12/02/2022] Open
Abstract
Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requires mechanisms ensuring that benefits are directed preferentially to cooperators. In order to investigate the reasons for the mobility of public good genes, we designed a synthetic bacterial system where we control and quantify the transfer of public good production genes. In our recent study, we have experimentally shown that horizontal transfer helps maintain public good production in the face of both non-producer organisms and non-producer plasmids. Transfer spreads genes to neighboring cells, thus increasing relatedness and directing a higher proportion of public good benefits to producers. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods. The promotion of cooperation may be a general consequence of horizontal gene transfer in prokaryotes. Our work has an intriguing parallel, cultural transmission, where horizontal transfer, such as teaching, may preferentially promote cooperative behaviors.
Collapse
Affiliation(s)
- Tatiana Dimitriu
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| | - Dusan Misevic
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| | - Ariel B Lindner
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| | - François Taddei
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| |
Collapse
|
14
|
Molina CA, Vilchez S. Cooperation and bacterial pathogenicity: an approach to social evolution. REVISTA CHILENA DE HISTORIA NATURAL 2014. [DOI: 10.1186/s40693-014-0014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
15
|
Abstract
Many bacterial species are social, producing costly secreted "public good" molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria.
Collapse
|
16
|
Morton ER, Platt TG, Fuqua C, Bever JD. Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids. Proc Biol Sci 2014; 281:20132173. [PMID: 24500159 PMCID: PMC3924060 DOI: 10.1098/rspb.2013.2173] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/07/2014] [Indexed: 11/12/2022] Open
Abstract
Plasmids play an important role in shaping bacterial evolution and adaptation to heterogeneous environments. As modular genetic elements that are often conjugative, the selective pressures that act on plasmid-borne genes are distinct from those that act on the chromosome. Many bacteria are co-infected by multiple plasmids that impart niche-specific phenotypes. Thus, in addition to host-plasmid dynamics, interactions between co-infecting plasmids are likely to be important drivers of plasmid population dynamics, evolution and ecology. Agrobacterium tumefaciens is a facultative plant pathogen that commonly harbours two distinct megaplasmids. Virulence depends on the presence of the tumour-inducing (Ti) plasmid, with benefits that are primarily restricted to the disease environment. Here, we demonstrate that a second megaplasmid, the At plasmid, confers a competitive advantage in the rhizosphere. To assess the individual and interactive costs of these plasmids, we generated four isogenic derivatives: plasmidless, pAt only, pTi only and pAtpTi, and performed pairwise competitions under carbon-limiting conditions. These studies reveal a low cost to the virulence plasmid when outside of the disease environment, and a strikingly high cost to the At plasmid. In addition, the costs of pAt and pTi in the same host were significantly lower than predicted based on single plasmid costs, signifying the first demonstration of non-additivity between naturally occurring co-resident plasmids. Based on these empirically demonstrated costs and benefits, we developed a resource-consumer model to generate predictions about the frequencies of these genotypes in relevant environments, showing that non-additivity between co-residing plasmids allows for their stable coexistence across environments.
Collapse
Affiliation(s)
- Elise R. Morton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | | | | |
Collapse
|
17
|
Boldin B, Diekmann O. An extension of the classification of evolutionarily singular strategies in Adaptive Dynamics. J Math Biol 2013; 69:905-40. [DOI: 10.1007/s00285-013-0725-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 06/05/2013] [Indexed: 12/01/2022]
|
18
|
Mc Ginty SÉ, Lehmann L, Brown SP, Rankin DJ. The interplay between relatedness and horizontal gene transfer drives the evolution of plasmid-carried public goods. Proc Biol Sci 2013; 280:20130400. [PMID: 23760639 PMCID: PMC3652439 DOI: 10.1098/rspb.2013.0400] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/09/2013] [Indexed: 12/22/2022] Open
Abstract
Plasmids carry a wide range of genes that are often involved in bacterial social behaviour. The question of why such genes are frequently mobile has received increasing attention. Here, we use an explicit population genetic approach to model the evolution of plasmid-borne bacterial public goods production. Our findings highlight the importance of both transmission and relatedness as factors driving the evolution of plasmid-borne public goods production. We partition the effects of plasmid transfer of social traits into those of infectivity and the effect of increased relatedness. Our results demonstrate that, owing to its effect on relatedness, plasmid mobility increases the invasion and stability of public goods, in a way not seen in individually beneficial traits. In addition, we show that plasmid transfer increases relatedness when public goods production is rare but this effect declines when production is common, with both scenarios leading to an increase in the frequency of plasmid-borne public goods. Plasmids remain important vectors for the spread of social genes involved in bacterial virulence thus an understanding of their dynamics is highly relevant from a public health perspective.
Collapse
Affiliation(s)
- Sorcha É Mc Ginty
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Building Y27, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | | | | | | |
Collapse
|
19
|
Bever JD, Platt TG, Morton ER. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu Rev Microbiol 2013. [PMID: 22726216 DOI: 10.1146/annurev-micro-092611-150107.microbial] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology.
Collapse
Affiliation(s)
- James D Bever
- Department of Biology, Indiana University, Bloomington, 47405, USA.
| | | | | |
Collapse
|
20
|
Alizon S, de Roode JC, Michalakis Y. Multiple infections and the evolution of virulence. Ecol Lett 2013; 16:556-67. [PMID: 23347009 DOI: 10.1111/ele.12076] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 10/30/2012] [Accepted: 12/17/2012] [Indexed: 12/13/2022]
Abstract
Infections that consist of multiple parasite strains or species are common in the wild and are a major public health concern. Theory suggests that these infections have a key influence on the evolution of infectious diseases and, more specifically, on virulence evolution. However, we still lack an overall vision of the empirical support for these predictions. We argue that within-host interactions between parasites largely determine how virulence evolves and that experimental data support model predictions. Then, we explore the main limitation of the experimental study of such 'mixed infections', which is that it draws conclusions on evolutionary outcomes from studies conducted at the individual level. We also discuss differences between coinfections caused by different strains of the same species or by different species. Overall, we argue that it is possible to make sense out of the complexity inherent to multiple infections and that experimental evolution settings may provide the best opportunity to further our understanding of virulence evolution.
Collapse
Affiliation(s)
- Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM1, UM2), Montpellier, France.
| | | | | |
Collapse
|
21
|
Bever JD, Platt TG, Morton ER. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu Rev Microbiol 2012; 66:265-83. [PMID: 22726216 PMCID: PMC3525954 DOI: 10.1146/annurev-micro-092611-150107] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology.
Collapse
Affiliation(s)
- James D. Bever
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Thomas G. Platt
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Elise R. Morton
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| |
Collapse
|
22
|
Harrison E, Brockhurst MA. Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol 2012; 20:262-7. [PMID: 22564249 DOI: 10.1016/j.tim.2012.04.003] [Citation(s) in RCA: 203] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 11/30/2022]
Abstract
Conjugative plasmids are key agents of horizontal gene transfer (HGT) that accelerate bacterial adaptation by vectoring ecologically important traits between strains and species. However, although many conjugative plasmids carry beneficial traits, all plasmids exert physiological costs-of-carriage on bacteria. The existence of conjugative plasmids, therefore, presents a paradox because non-beneficial plasmids should be lost to purifying selection, whereas beneficial genes carried on plasmids should be integrated into the bacterial chromosome. Several ecological solutions to the paradox have been proposed, but none account for co-adaptation of bacteria and conjugative plasmids. Drawing upon evidence from experimental evolution, we argue that HGT via conjugation can only be fully understood in a coevolutionary framework.
Collapse
Affiliation(s)
- Ellie Harrison
- Institute of Integrative Biology, University of Liverpool, Bioscience Building, Liverpool, UK
| | | |
Collapse
|
23
|
Vehicles, replicators, and intercellular movement of genetic information: evolutionary dissection of a bacterial cell. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:874153. [PMID: 22567533 PMCID: PMC3332184 DOI: 10.1155/2012/874153] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/06/2012] [Accepted: 02/08/2012] [Indexed: 11/18/2022]
Abstract
Prokaryotic biosphere is vastly diverse in many respects. Any given bacterial cell may harbor in different combinations viruses, plasmids, transposons, and other genetic elements along with their chromosome(s). These agents interact in complex environments in various ways causing multitude of phenotypic effects on their hosting cells. In this discussion I perform a dissection for a bacterial cell in order to simplify the diversity into components that may help approach the ocean of details in evolving microbial worlds. The cell itself is separated from all the genetic replicators that use the cell vehicle for preservation and propagation. I introduce a classification that groups different replicators according to their horizontal movement potential between cells and according to their effects on the fitness of their present host cells. The classification is used to discuss and improve the means by which we approach general evolutionary tendencies in microbial communities. Moreover, the classification is utilized as a tool to help formulating evolutionary hypotheses and to discuss emerging bacterial pathogens as well as to promote understanding on the average phenotypes of different replicators in general. It is also discussed that any given biosphere comprising prokaryotic cell vehicles and genetic replicators may naturally evolve to have horizontally moving replicators of various types.
Collapse
|
24
|
Abstract
As social interactions are increasingly recognized as important determinants of microbial fitness, sociobiology is being enlisted to better understand the evolution of clinically relevant microbes and, potentially, to influence their evolution to aid human health. Of special interest are situations in which there exists a "tragedy of the commons," where natural selection leads to a net reduction in fitness for all members of a population. Here, I demonstrate the existence of a tragedy of the commons among antibiotic resistance plasmids of bacteria. In serial transfer culture, plasmids evolved a greater ability to superinfect already-infected bacteria, increasing plasmid fitness when evolved genotypes were rare. Evolved plasmids, however, fell victim to their own success, reducing the density of their bacterial hosts when they became common and suffering reduced fitness through vertical transmission. Social interactions can thus be an important determinant of evolution for the molecular endosymbionts of bacteria. These results also identify an avenue of evolution that reduces proliferation of both antibiotic resistance genes and their bacterial hosts.
Collapse
Affiliation(s)
- Jeff Smith
- Department of Biology, Emory University, Atlanta, GA, USA.
| |
Collapse
|
25
|
Hall AR, Scanlan PD, Leggett HC, Buckling A. Multiplicity of infection does not accelerate infectivity evolution of viral parasites in laboratory microcosms. J Evol Biol 2011; 25:409-15. [PMID: 22168551 DOI: 10.1111/j.1420-9101.2011.02434.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coinfection with multiple parasite genotypes [multiplicity of infection (MOI)] creates within-host competition and opportunities for parasite recombination and is therefore predicted to be important for both parasite and host evolution. We tested for a difference in the infectivity of viral parasites (lytic phage Φ2) and resistance of their bacterial hosts (Pseudomonas fluorescens SBW25) under both high and low MOI during coevolution in laboratory microcosms. Results show that MOI has no effect on infectivity and resistance evolution during coevolution over ∼80 generations of host growth, and this is true when the experiment is initiated with wild-type viruses and hosts, or with viruses and hosts that have already been coevolving for ∼330 generations. This suggests that MOI does not have a net effect of accelerating parasite adaptation to hosts through recombination, or slowing adaptation to hosts through between-parasite conflict in this system.
Collapse
Affiliation(s)
- A R Hall
- Department of Zoology, University of Oxford, Oxford, UK College of Life & Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, UK
| | | | | | | |
Collapse
|
26
|
|
27
|
Alizon S, Michalakis Y. THE TRANSMISSION-VIRULENCE TRADE-OFF AND SUPERINFECTION: COMMENTS TO SMITH. Evolution 2011; 65:3633-8; discussion 3639-41. [DOI: 10.1111/j.1558-5646.2011.01432.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|