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Sikora M, Wąsik S, Semaniak J, Drulis-Kawa Z, Wiśniewska-Wrona M, Arabski M. Chitosan-based matrix as a carrier for bacteriophages. Appl Microbiol Biotechnol 2024; 108:6. [PMID: 38165478 PMCID: PMC10761466 DOI: 10.1007/s00253-023-12838-0] [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: 04/13/2023] [Revised: 09/21/2023] [Accepted: 10/03/2023] [Indexed: 01/03/2024]
Abstract
Wound healing is a dynamic and complex process where infection prevention is essential. Chitosan, thanks to its bactericidal activity against gram-positive and gram-negative bacteria, as well as anti-inflammatory and hemostatic properties, is an excellent candidate to design dressings for difficult-to-heal wound treatment. The great advantage of this biopolymer is its capacity to be chemically modified, which allows for the production of various functional forms, depending on the needs and subsequent use. Moreover, chitosan can be an excellent polymer matrix for bacteriophage (phage) packing as a novel alternative/supportive antibacterial therapy approach. This study is focused on the preparation and characteristics of chitosan-based material in the form of a film with the addition of Pseudomonas lytic phages (KTN4, KT28, and LUZ19), which would exhibit antibacterial activity as a potential dressing that accelerates the wound healing. We investigated the method of producing a polymer based on microcrystalline chitosan (MKCh) to serve as the matrix for phage deposition. We described some important parameters such as average molar mass, swelling capacity, surface morphology, phage release profile, and antibacterial activity tested in the Pseudomonas aeruginosa bacterial model. The chitosan polysaccharide turned out to interact with phage particles immobilizing them within a material matrix. Nevertheless, with the high hydrophilicity and swelling features of the prepared material, the external solution of bacterial culture was absorbed and phages went in direct contact with bacteria causing their lysis in the polymer matrix. KEY POINTS: • A novel chitosan-based matrix with the addition of active phages was prepared • Phage interactions with the chitosan matrix were determined as electrostatic • Phages in the matrix work through direct contact with the bacterial cells.
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Affiliation(s)
- Monika Sikora
- Department of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
- Lukasiewicz Research Network-Lodz Institute of Technology, Lodz, Poland
| | - Sławomir Wąsik
- Institute of Physics, Jan Kochanowski University in Kielce, Kielce, Poland
- Central Office of Measures, Warsaw, Poland
| | - Jacek Semaniak
- Institute of Physics, Jan Kochanowski University in Kielce, Kielce, Poland
- Central Office of Measures, Warsaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | | | - Michał Arabski
- Department of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland.
- Central Office of Measures, Warsaw, Poland.
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Wang X, Wang S, Huang M, He Y, Guo S, Yang K, Wang N, Sun T, Yang H, Yang T, Xu Y, Shen Q, Friman VP, Wei Z. Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness. mBio 2024; 15:e0301623. [PMID: 38780276 PMCID: PMC11237578 DOI: 10.1128/mbio.03016-23] [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: 11/06/2023] [Accepted: 03/21/2024] [Indexed: 05/25/2024] Open
Abstract
Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities. IMPORTANCE Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Mingcong Huang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yilin He
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Saisai Guo
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ningqi Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Tianyu Sun
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Hongwu Yang
- China National Tobacco Corporation Hunan Company, Changsha, Hunan, China
| | - Tianjie Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
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3
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Shaw CL, Bilich R, Duffy MA. A common multi-host parasite shows genetic structuring at the host species and population levels. Parasitology 2024:1-10. [PMID: 38616414 DOI: 10.1017/s0031182024000428] [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] [Indexed: 04/16/2024]
Abstract
Although individual parasite species commonly infect many populations across physical space as well as multiple host species, the extent to which parasites traverse physical and phylogenetic distances is unclear. Population genetic analyses of parasite populations can reveal how parasites move across space or between host species, including helping assess whether a parasite is more likely to infect a different host species in the same location or the same host species in a different location. Identifying these transmission barriers could be exploited for effective disease control. Here, we analysed population genetic structuring of the parasite Pasteuria ramosa in daphniid host species from different lakes. Outbreaks occurred most often in the common host species Daphnia dentifera and Daphnia retrocurva. The genetic distance between parasite samples tended to be smaller when samples were collected from the same lake, the same host species and closer in time. Within lakes, the parasite showed structure by host species and sampling date; within a host species, the parasite showed structure by lake and sampling date. However, despite this structuring, we found the same parasite genotype infecting closely related host species, and we sometimes found the same genotype in nearby lakes. Thus, P. ramosa experiences challenges infecting different host species and moving between populations, but doing so is possible. In addition, the structuring by sampling date indicates potential adaptation to or coevolution with host populations and supports prior findings that parasite population structure is dynamic during outbreaks.
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Affiliation(s)
- Clara L Shaw
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Rebecca Bilich
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Meghan A Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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Gibson AK, Mundim FM, Ramirez AL, Timper P. Do biological control agents adapt to local pest genotypes? A multiyear test across geographic scales. Evol Appl 2024; 17:e13682. [PMID: 38617827 PMCID: PMC11009426 DOI: 10.1111/eva.13682] [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: 12/08/2023] [Revised: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 04/16/2024] Open
Abstract
Parasite local adaptation has been a major focus of (co)evolutionary research on host-parasite interactions. Studies of wild host-parasite systems frequently find that parasites paired with local, sympatric host genotypes perform better than parasites paired with allopatric host genotypes. In contrast, there are few such tests in biological control systems to establish whether biological control parasites commonly perform better on sympatric pest genotypes. This knowledge gap prevents the optimal design of biological control programs: strong local adaptation could argue for the use of sympatric parasites to achieve consistent pest control. To address this gap, we tested for local adaptation of the biological control bacterium Pasteuria penetrans to the root-knot nematode Meloidogyne arenaria, a global threat to a wide range of crops. We measured the probability and intensity of P. penetrans infection on sympatric and allopatric M. arenaria over the course of 4 years. Our design accounted for variation in adaptation across scales by conducting tests within and across fields, and we isolated the signature of parasite adaptation by comparing parasites collected over the course of the growing season. Our results are largely inconsistent with local adaptation of P. penetrans to M. arenaria: in 3 of 4 years, parasites performed similarly well in sympatric and allopatric combinations. In 1 year, however, infection probability was 28% higher for parasites paired with hosts from their sympatric plot, relative to parasites paired with hosts from other plots within the same field. These mixed results argue for population genetic data to characterize the scale of gene flow and genetic divergence in this system. Overall, our findings do not provide strong support for using P. penetrans from local fields to enhance biological control of Meloidogyne.
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Affiliation(s)
| | - Fabiane M. Mundim
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of BiologyUtah State UniversityLoganUtahUSA
| | - Abbey L. Ramirez
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Patricia Timper
- United States Department of Agriculture Agricultural Research ServiceTiftonGeorgiaUSA
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Yang K, Wang X, Hou R, Lu C, Fan Z, Li J, Wang S, Xu Y, Shen Q, Friman VP, Wei Z. Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease. MICROBIOME 2023; 11:16. [PMID: 36721270 PMCID: PMC9890766 DOI: 10.1186/s40168-023-01463-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/09/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. 'primary phages') and (2) that 'secondary phages' that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly 'helping' the pathogen. RESULTS Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, 'secondary phages' that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and 'secondary phages' were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen. CONCLUSIONS Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Video Abstract.
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Affiliation(s)
- Keming Yang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiaofang Wang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Rujiao Hou
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chunxia Lu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhe Fan
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jingxuan Li
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shuo Wang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yangchun Xu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qirong Shen
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ville-Petri Friman
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland.
| | - Zhong Wei
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Shaw CL, Duffy MA. Rapid evolution of a bacterial parasite during outbreaks in two Daphnia populations. Ecol Evol 2023; 13:e9676. [PMID: 36694542 PMCID: PMC9843074 DOI: 10.1002/ece3.9676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 01/18/2023] Open
Abstract
Myriad ecological and evolutionary factors can influence whether a particular parasite successfully transmits to a new host during a disease outbreak, with consequences for the structure and diversity of parasite populations. However, even though the diversity and evolution of parasite populations are of clear fundamental and applied importance, we have surprisingly few studies that track how genetic structure of parasites changes during naturally occurring outbreaks in non-human populations. Here, we used population genetic approaches to reveal how genotypes of a bacterial parasite, Pasteuria ramosa, change over time, focusing on how infecting P. ramosa genotypes change during the course of epidemics in Daphnia populations in two lakes. We found evidence for genetic change - and, therefore, evolution - of the parasite during outbreaks. In one lake, P. ramosa genotypes were structured by sampling date; in both lakes, genetic distance between groups of P. ramosa isolates increased with time between sampling. Diversity in parasite populations remained constant over epidemics, although one epidemic (which was large) had low genetic diversity while the other epidemic (which was small) had high genetic diversity. Our findings demonstrate that patterns of parasite evolution differ between outbreaks; future studies exploring the feedbacks among epidemic size, host diversity, and parasite genetic diversity would improve our understanding of parasite dynamics and evolution.
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Affiliation(s)
- Clara L. Shaw
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA,Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Meghan A. Duffy
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
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Liu ZH, Chiang MT, Lin HY. Lytic Bacteriophage as a Biomaterial to Prevent Biofilm Formation and Promote Neural Growth. Tissue Eng Regen Med 2022; 19:987-1000. [PMID: 35648339 DOI: 10.1007/s13770-022-00462-4] [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: 01/12/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Although non-lytic filamentous bacteriophages have been made into biomaterial to guide tissue growth, they had limited ability to prevent bacterial infection. In this work a lytic bacteriophage was used to make an antibacterial biomaterial for neural tissue repair. METHODS Lytic phages were chemically bound to the surface of a chitosan film through glutaraldehyde crosslinking. After the chemical reaction, the contact angle of the sample surface and the remaining lytic potential of the phages were measured. The numbers of bacteria on the samples were measured and examined under scanning electron microscopy. Transmission electron microscopy (TEM) was used to observe the phages and phage-infected bacteria. A neuroblast cell line was cultured on the samples to evaluate the sample's biocompatibility. RESULTS The phages conjugated to the chitosan film preserved their lytic potential and reduced 68% of bacterial growth on the sample surface at 120 min (p < 0.001). The phage-linked surface had a significantly higher contact angle than that of the control chitosan (p < 0.05). After 120 min a bacterial biofilm appeared on the control chitosan, while the phage-linked sample effectively prevented biofilm formation. The TEM images demonstrated that the phage attached and lysed the bacteria on the phage-linked sample at 120 min. The phage-linked sample significantly promoted the neuroblast cell attachment (p < 0.05) and proliferation (p < 0.01). The neuroblast on the phage-linked sample demonstrated more cell extensions after day 1. CONCLUSION The purified lytic phages were proven to be a highly bioactive nanomaterial. The phage-chitosan composite material not only promoted neural cell proliferation but also effectively prevent bacterial growth, a major cause of implant failure and removal.
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Affiliation(s)
- Zi-Hao Liu
- Graduate Institute of Chemical Engineering, National Taipei University of Technology, 3, Zhongxiao E Rd, Taipei, 106, Taiwan
| | - Ming-Tse Chiang
- Graduate Institute of Chemical Engineering, National Taipei University of Technology, 3, Zhongxiao E Rd, Taipei, 106, Taiwan
| | - Hsin-Yi Lin
- Graduate Institute of Chemical Engineering, National Taipei University of Technology, 3, Zhongxiao E Rd, Taipei, 106, Taiwan.
- Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, 3, Zhongxiao E Rd, Taipei, 106, Taiwan.
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Shaw CL, Bilich R, O'Brien B, Cáceres CE, Hall SR, James TY, Duffy MA. Genotypic variation in an ecologically important parasite is associated with host species, lake and spore size. Parasitology 2021; 148:1303-1312. [PMID: 34103104 PMCID: PMC8383271 DOI: 10.1017/s0031182021000949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/11/2021] [Accepted: 05/31/2021] [Indexed: 11/10/2022]
Abstract
Genetic variation in parasites has important consequences for host–parasite interactions. Prior studies of the ecologically important parasite Metschnikowia bicuspidata have suggested low genetic variation in the species. Here, we collected M. bicuspidata from two host species (Daphnia dentifera and Ceriodaphnia dubia) and two regions (Michigan and Indiana, USA). Within a lake, outbreaks tended to occur in one host species but not the other. Using microsatellite markers, we identified six parasite genotypes grouped within three distinct clades, one of which was rare. Of the two main clades, one was generally associated with D. dentifera, with lakes in both regions containing a single genotype. The other M. bicuspidata clade was mainly associated with C. dubia, with a different genotype dominating in each region. Despite these associations, both D. dentifera- and C. dubia-associated genotypes were found infecting both hosts in lakes. However, in lab experiments, the D. dentifera-associated genotype infected both D. dentifera and C. dubia, but the C. dubia-associated genotype, which had spores that were approximately 30% smaller, did not infect D. dentifera. We hypothesize that variation in spore size might help explain patterns of cross-species transmission. Future studies exploring the causes and consequences of variation in spore size may help explain patterns of infection and the maintenance of genotypic diversity in this ecologically important system.
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Affiliation(s)
- Clara L. Shaw
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI48109, USA
| | - Rebecca Bilich
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI48109, USA
| | - Bruce O'Brien
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI48109, USA
| | - Carla E. Cáceres
- Department of Evolution, Ecology, & Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801, USA
| | - Spencer R. Hall
- Department of Biology, Indiana University, Bloomington, IN47405, USA
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI48109, USA
| | - Meghan A. Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI48109, USA
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Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales. mSystems 2021; 6:e0083221. [PMID: 34427532 PMCID: PMC8407120 DOI: 10.1128/msystems.00832-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.
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Wale N, Duffy MA. The Use and Underuse of Model Systems in Infectious Disease Ecology and Evolutionary Biology. Am Nat 2021; 198:69-92. [PMID: 34143716 DOI: 10.1086/714595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractEver since biologists began studying the ecology and evolution of infectious diseases (EEID), laboratory-based model systems have been important for developing and testing theory. Yet what EEID researchers mean by the term "model systems" and what they want from them is unclear. This uncertainty hinders our ability to maximally exploit these systems, identify knowledge gaps, and establish effective new model systems. Here, we borrow a definition of model systems from the biomolecular sciences to assess how EEID researchers are (and are not) using 10 key model systems. According to this definition, model systems in EEID are not being used to their fullest and, in fact, cannot even be considered model systems. Research using these systems consistently addresses only two of the three fundamental processes that underlie disease dynamics-transmission and disease, but not recovery. Furthermore, studies tend to focus on only a few scales of biological organization that matter for disease ecology and evolution. Moreover, the field lacks an infrastructure to perform comparative analyses. We aim to begin a discussion of what we want from model systems, which would further progress toward a thorough, holistic understanding of EEID.
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Controlled-release of free bacteriophage nanoparticles from 3D-plotted hydrogel fibrous structure as potential antibacterial wound dressing. J Control Release 2021; 331:154-163. [DOI: 10.1016/j.jconrel.2021.01.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/03/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022]
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12
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Essarioui A, LeBlanc N, Otto-Hanson L, Schlatter DC, Kistler HC, Kinkel LL. Inhibitory and nutrient use phenotypes among coexisting Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil. Environ Microbiol 2019; 22:976-985. [PMID: 31424591 DOI: 10.1111/1462-2920.14782] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 06/22/2019] [Accepted: 08/14/2019] [Indexed: 11/29/2022]
Abstract
Bacteria and fungi are key components of virtually all natural habitats, yet the significance of fungal-bacterial inhibitory interactions for the ecological and evolutionary dynamics of specific bacterial and fungal populations in natural habitats have been overlooked. More specifically, despite the broad consensus that antibiotics play a key role in providing a fitness advantage to competing microbes, the significance of antibiotic production in mediating cross-kingdom coevolutionary interactions has received relatively little attention. Here, we characterize reciprocal inhibition among Streptomyces and Fusarium populations from prairie soil, and explore antibiotic inhibition in relation to niche overlap among sympatric and allopatric populations. We found evidence for local adaptation between Fusarium and Streptomyces populations as indicated by significantly greater inhibition among sympatric than allopatric populations. Additionally, for both taxa, there was a significant positive correlation between the strength of inhibition against the other taxon and the intensity of resource competition from that taxon among sympatric but not allopatric populations. These data suggest that coevolutionary antagonistic interactions between Fusarium and Streptomyces are driven by resource competition, and support the hypothesis that antibiotics act as weapons in mediating bacterial-fungal interactions in soil.
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Affiliation(s)
- Adil Essarioui
- National Institute of Agronomic Research, Regional Center of Errachidia, Errachidia, Morocco.,Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas LeBlanc
- Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
| | - Lindsey Otto-Hanson
- Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
| | | | - Harold Corby Kistler
- USDA-ARS Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Linda L Kinkel
- Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
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13
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Common J, Morley D, Westra ER, van Houte S. CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180098. [PMID: 30905285 PMCID: PMC6452269 DOI: 10.1098/rstb.2018.0098] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2018] [Indexed: 01/22/2023] Open
Abstract
CRISPR-Cas is an adaptive prokaryotic immune system that prevents phage infection. By incorporating phage-derived 'spacer' sequences into CRISPR loci on the host genome, future infections from the same phage genotype can be recognized and the phage genome cleaved. However, the phage can escape CRISPR degradation by mutating the sequence targeted by the spacer, allowing them to re-infect previously CRISPR-immune hosts, and theoretically leading to coevolution. Previous studies have shown that phage can persist over long periods in populations of Streptococcus thermophilus that can acquire CRISPR-Cas immunity, but it has remained less clear whether this coexistence was owing to coevolution, and if so, what type of coevolutionary dynamics were involved. In this study, we performed highly replicated serial transfer experiments over 30 days with S. thermophilus and a lytic phage. Using a combination of phenotypic and genotypic data, we show that CRISPR-mediated resistance and phage infectivity coevolved over time following an arms race dynamic, and that asymmetry between phage infectivity and host resistance within this system eventually causes phage extinction. This work provides further insight into the way CRISPR-Cas systems shape the population and coevolutionary dynamics of bacteria-phage interactions. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | | | | | - Stineke van Houte
- ESI and CEC, Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
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14
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Larsen ML, Wilhelm SW, Lennon JT. Nutrient stoichiometry shapes microbial coevolution. Ecol Lett 2019; 22:1009-1018. [DOI: 10.1111/ele.13252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/10/2018] [Accepted: 02/18/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Megan L. Larsen
- Department of Biology Indiana University Bloomington IN47405USA
| | - Steven W. Wilhelm
- Department of Microbiology University of Tennessee Knoxville TN37996 USA
| | - Jay T. Lennon
- Department of Biology Indiana University Bloomington IN47405USA
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15
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Week B, Nuismer SL. The measurement of coevolution in the wild. Ecol Lett 2019; 22:717-725. [PMID: 30775838 DOI: 10.1111/ele.13231] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/14/2018] [Accepted: 01/11/2019] [Indexed: 11/27/2022]
Abstract
Coevolution has long been thought to drive the exaggeration of traits, promote major evolutionary transitions such as the evolution of sexual reproduction and influence epidemiological dynamics. Despite coevolution's long suspected importance, we have yet to develop a quantitative understanding of its strength and prevalence because we lack generally applicable statistical methods that yield numerical estimates for coevolution's strength and significance in the wild. Here, we develop a novel method that derives maximum likelihood estimates for the strength of direct pairwise coevolution by coupling a well-established coevolutionary model to spatially structured phenotypic data. Applying our method to two well-studied interactions reveals evidence for coevolution in both systems. Broad application of this approach has the potential to further resolve long-standing evolutionary debates such as the role species interactions play in the evolution of sexual reproduction and the organisation of ecological communities.
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Affiliation(s)
- Bob Week
- Department of Biological Sciences, University of Idaho, Idaho, NW, USA
| | - Scott L Nuismer
- Department of Biological Sciences, University of Idaho, Idaho, NW, USA
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16
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Sun B, Ma L, Li S, Williams CM, Wang Y, Hao X, Du W. Phenology and the physiological niche are co‐adapted in a desert‐dwelling lizard. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bao‐Jun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- Department of Integrative Biology University of California Berkeley California
| | - Liang Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shu‐Ran Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | | | - Yang Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Xin Hao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Wei‐Guo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming China
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17
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Best A, Ashby B, White A, Bowers R, Buckling A, Koskella B, Boots M. Host-parasite fluctuating selection in the absence of specificity. Proc Biol Sci 2018; 284:rspb.2017.1615. [PMID: 29093222 PMCID: PMC5698645 DOI: 10.1098/rspb.2017.1615] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time, to our knowledge, that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection.
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Affiliation(s)
- Alex Best
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.,Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Andy White
- Department of Mathematics and the Maxwell Institute for Mathematical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Roger Bowers
- Department of Mathematical Sciences, Division of Applied Mathematics, The University of Liverpool, Mathematical Sciences Building, Liverpool L69 7ZL, UK
| | - Angus Buckling
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Treliever Road, Penryn, Cornwall TR10 9EZ, UK
| | - Britt Koskella
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Mike Boots
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.,Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Treliever Road, Penryn, Cornwall TR10 9EZ, UK
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18
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Höckerstedt LM, Siren JP, Laine AL. Effect of spatial connectivity on host resistance in a highly fragmented natural pathosystem. J Evol Biol 2018; 31:844-852. [PMID: 29569292 PMCID: PMC6032904 DOI: 10.1111/jeb.13268] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 02/06/2023]
Abstract
Both theory and experimental evolution studies predict migration to influence the outcome of antagonistic coevolution between hosts and their parasites, with higher migration rates leading to increased diversity and evolutionary potential. Migration rates are expected to vary in spatially structured natural pathosystems, yet how spatial structure generates variation in coevolutionary trajectories across populations occupying the same landscape has not been tested. Here, we studied the effect of spatial connectivity on host evolutionary potential in a natural pathosystem characterized by a stable Plantago lanceolata host network and a highly dynamic Podosphaera plantaginis parasite metapopulation. We designed a large inoculation experiment to test resistance of five isolated and five well‐connected host populations against sympatric and allopatric pathogen strains, over 4 years. Contrary to our expectations, we did not find consistently higher resistance against sympatric pathogen strains in the well‐connected populations. Instead, host local adaptation varied considerably among populations and through time with greater fluctuations observed in the well‐connected populations. Jointly, our results suggest that in populations where pathogens have successfully established, they have the upper hand in the coevolutionary arms race, but hosts may be better able to respond to pathogen‐imposed selection in the well‐connected than in the isolated populations. Hence, the ongoing and extensive fragmentation of natural habitats may increase vulnerability to diseases.
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Affiliation(s)
| | - Jukka Pekka Siren
- Department of Computer Science, School of Sciences, Aalto University, Espoo, Finland
| | - Anna-Liisa Laine
- Faculty of Environmental and Biological Sciences, University of Helsinki, Helsinki, Finland
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19
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Blanquart F, Valero M, Alves-de-Souza C, Dia A, Lepelletier F, Bigeard E, Jeanthon C, Destombe C, Guillou L. Evidence for parasite-mediated selection during short-lasting toxic algal blooms. Proc Biol Sci 2017; 283:rspb.2016.1870. [PMID: 27798309 PMCID: PMC5095388 DOI: 10.1098/rspb.2016.1870] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022] Open
Abstract
Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in ‘Red Queen’ dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics.
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Affiliation(s)
- François Blanquart
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Myriam Valero
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,CNRS, UMI 3614, Pontifica Universidad Catolica de Chile, Universidad Austral de Chile, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Catharina Alves-de-Souza
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristovão, Rio de Janeiro, RJ, Brazil
| | - Aliou Dia
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Frédéric Lepelletier
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Estelle Bigeard
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Christian Jeanthon
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Christophe Destombe
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,CNRS, UMI 3614, Pontifica Universidad Catolica de Chile, Universidad Austral de Chile, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Laure Guillou
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France .,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
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20
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Hillesland KL. Evolution on the bright side of life: microorganisms and the evolution of mutualism. Ann N Y Acad Sci 2017; 1422:88-103. [PMID: 29194650 DOI: 10.1111/nyas.13515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 01/15/2023]
Abstract
Mutualistic interactions, where two interacting species have a net beneficial effect on each other's fitness, play a crucial role in the survival and evolution of many species. Despite substantial empirical and theoretical work in past decades, the impact of these interactions on natural selection is not fully understood. In addition, mutualisms between microorganisms have been largely ignored, even though they are ecologically important and can be used as tools to bridge the gap between theory and empirical work. Here, I describe two problems with our current understanding of natural selection in mutualism and highlight the properties of microbial mutualisms that could help solve them. One problem is that bias and methodological problems have limited our understanding of the variety of mechanisms by which species may adapt to mutualism. Another problem is that it is rare for experiments testing coevolution in mutualism to address whether each species has adapted to evolutionary changes in its partner. These problems can be addressed with genome resequencing and time-shift experiments, techniques that are easier to perform in microorganisms. In addition, microbial mutualisms may inspire novel insights and hypotheses about natural selection in mutualism.
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21
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Auld SKJR, Brand J. Environmental variation causes different (co) evolutionary routes to the same adaptive destination across parasite populations. Evol Lett 2017; 1:245-254. [PMID: 30283653 PMCID: PMC6121849 DOI: 10.1002/evl3.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
Epidemics are engines for host-parasite coevolution, where parasite adaptation to hosts drives reciprocal adaptation in host populations. A key challenge is to understand whether parasite adaptation and any underlying evolution and coevolution is repeatable across ecologically realistic populations that experience different environmental conditions, or if each population follows a completely unique evolutionary path. We established twenty replicate pond populations comprising an identical suite of genotypes of crustacean host, Daphnia magna, and inoculum of their parasite, Pasteuria ramosa. Using a time-shift experiment, we compared parasite infection traits before and after epidemics and linked patterns of parasite evolution with shifts in host genotype frequencies. Parasite adaptation to the sympatric suite of host genotypes came at a cost of poorer performance on foreign genotypes across populations and environments. However, this consistent pattern of parasite adaptation was driven by different types of frequency-dependent selection that was contingent on an ecologically relevant environmental treatment (whether or not there was physical mixing of water within ponds). In unmixed ponds, large epidemics drove rapid and strong host-parasite coevolution. In mixed ponds, epidemics were smaller and host evolution was driven mainly by the mixing treatment itself; here, host evolution and parasite evolution were clear, but coevolution was absent. Population mixing breaks an otherwise robust coevolutionary cycle. These findings advance our understanding of the repeatability of (co)evolution across noisy, ecologically realistic populations.
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Affiliation(s)
- Stuart K. J. R. Auld
- Biological and Environmental SciencesUniversity of StirlingStirlingUnited Kingdom
| | - June Brand
- Biological and Environmental SciencesUniversity of StirlingStirlingUnited Kingdom
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22
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Lin DM, Koskella B, Lin HC. Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World J Gastrointest Pharmacol Ther 2017; 8:162-173. [PMID: 28828194 PMCID: PMC5547374 DOI: 10.4292/wjgpt.v8.i3.162] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/12/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
The practice of phage therapy, which uses bacterial viruses (phages) to treat bacterial infections, has been around for almost a century. The universal decline in the effectiveness of antibiotics has generated renewed interest in revisiting this practice. Conventionally, phage therapy relies on the use of naturally-occurring phages to infect and lyse bacteria at the site of infection. Biotechnological advances have further expanded the repertoire of potential phage therapeutics to include novel strategies using bioengineered phages and purified phage lytic proteins. Current research on the use of phages and their lytic proteins against multidrug-resistant bacterial infections, suggests phage therapy has the potential to be used as either an alternative or a supplement to antibiotic treatments. Antibacterial therapies, whether phage- or antibiotic-based, each have relative advantages and disadvantages; accordingly, many considerations must be taken into account when designing novel therapeutic approaches for preventing and treating bacterial infection. Although much about phages and human health is still being discovered, the time to take phage therapy serious again seems to be rapidly approaching.
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23
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Baltrus DA. Adaptation, specialization, and coevolution within phytobiomes. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:109-116. [PMID: 28545003 DOI: 10.1016/j.pbi.2017.04.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 04/26/2017] [Indexed: 05/03/2023]
Abstract
Growth patterns of individual plants and evolutionary trajectories of plant communities are intimately linked with and are critically affected by host-associated microbiomes. Research across systems has begun to shed light on how these phytobiomes are established under laboratory and natural conditions, and have cultivated hope that a better understanding of the governing principles for host-microbe interactions can guide attempts to engineer microbiomes to boost agricultural yields. One important, yet relatively understudied, parameter in regards to phytobiome membership is the degree to which specialization and coevolution between plant species and microbes provides structure to these communities. In this article, I provide an overview of mechanisms enabling adaptation and specialization of phytobiome communities to host plants as well as the potential for plants themselves to recruit and cultivate beneficial interactions. I further explore the possibility of host-beneficial microbe coevolution and suggest particular situations that could promote the evolution of such close-knit partnerships. It is my hope that this overview will encourage future experiments that can begin to fill in this black box of ecological and evolutionary interactions across phytobiomes.
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Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, United States; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, United States.
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24
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Parratt SR, Barrès B, Penczykowski RM, Laine AL. Local adaptation at higher trophic levels: contrasting hyperparasite-pathogen infection dynamics in the field and laboratory. Mol Ecol 2017; 26:1964-1979. [PMID: 27859910 PMCID: PMC5412677 DOI: 10.1111/mec.13928] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/25/2016] [Accepted: 11/01/2016] [Indexed: 12/23/2022]
Abstract
Predicting and controlling infectious disease epidemics is a major challenge facing the management of agriculture, human and wildlife health. Co-evolutionarily derived patterns of local adaptation among pathogen populations have the potential to generate variation in disease epidemiology; however, studies of local adaptation in disease systems have mostly focused on interactions between competing pathogens or pathogens and their hosts. In nature, parasites and pathogens are also subject to attack by hyperparasitic natural enemies that can severely impact upon their infection dynamics. However, few studies have investigated whether this interaction varies across combinations of pathogen-hyperparasite strains, and whether this influences hyperparasite incidence in natural pathogen populations. Here, we test whether the association between a hyperparasitic fungus, Ampelomyces, and a single powdery mildew host, Podosphaera plantaginis, varies among genotype combinations, and whether this drives hyperparasite incidence in nature. Laboratory inoculation studies reveal that genotype, genotype × genotype interactions and local adaptation affect hyperparasite infection. However, observations of a natural pathogen metapopulation reveal that spatial rather than genetic factors predict the risk of hyperparasite presence. Our results highlight how sensitive the outcome of biocontrol using hyperparasites is to selection of hyperparasite strains.
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Affiliation(s)
- Steven R Parratt
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Benoit Barrès
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Rachel M Penczykowski
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
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25
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Wang X, Wei Z, Li M, Wang X, Shan A, Mei X, Jousset A, Shen Q, Xu Y, Friman V. Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs. Evolution 2017; 71:733-746. [PMID: 27925169 PMCID: PMC5347860 DOI: 10.1111/evo.13143] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
Parasites and competitors are important for regulating pathogen densities and subsequent disease dynamics. It is, however, unclear to what extent this is driven by ecological and evolutionary processes. Here, we used experimental evolution to study the eco-evolutionary feedbacks among Ralstonia solanacearum bacterial pathogen, Ralstonia-specific phage parasite, and Bacillus amyloliquefaciens competitor bacterium in the laboratory and plant rhizosphere. We found that while the phage had a small effect on pathogen densities on its own, it considerably increased the R. solanacearum sensitivity to antibiotics produced by B. amyloliquefaciens. Instead of density effects, this synergy was due to phage-driven increase in phage resistance that led to trade-off with the resistance to B. amyloliquefaciens antibiotics. While no evidence was found for pathogen resistance evolution to B. amyloliquefaciens antibiotics, the fitness cost of adaptation (reduced growth) was highest when the pathogen had evolved in the presence of both parasite and competitor. Qualitatively similar patterns were found between laboratory and greenhouse experiments even though the evolution of phage resistance was considerably attenuated in the tomato rhizosphere. These results suggest that evolutionary trade-offs can impose strong constraints on disease dynamics and that combining phages and antibiotic-producing bacteria could be an efficient way to control agricultural pathogens.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Xueqi Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Anqi Shan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Xinlan Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
- Institute for Environmental Biology, Ecology & BiodiversityUtrecht UniversityPadualaan 83584CHUtrechtthe Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic‐based FertilizersNanjing Agricultural UniversityWeigang 1Nanjing210095China
| | - Ville‐Petri Friman
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUnited Kingdom
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26
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Macke E, Tasiemski A, Massol F, Callens M, Decaestecker E. Life history and eco-evolutionary dynamics in light of the gut microbiota. OIKOS 2017. [DOI: 10.1111/oik.03900] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emilie Macke
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | | | - François Massol
- Univ. Lille; CNRS UMR 8198 Evo-Eco-Paleo SPICI group Lille France
| | - Martijn Callens
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | - Ellen Decaestecker
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
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27
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Greenspoon PB, Mideo N. Parasite transmission among relatives halts Red Queen dynamics. Evolution 2017; 71:747-755. [PMID: 27996079 DOI: 10.1111/evo.13157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/25/2016] [Indexed: 11/26/2022]
Abstract
The theory that coevolving hosts and parasites create a fluctuating selective environment for one another (i.e., produce Red Queen dynamics) has deep roots in evolutionary biology; yet empirical evidence for Red Queen dynamics remains scarce. Fluctuating coevolutionary dynamics underpin the Red Queen hypothesis for the evolution of sex, as well as hypotheses explaining the persistence of genetic variation under sexual selection, local parasite adaptation, the evolution of mutation rate, and the evolution of nonrandom mating. Coevolutionary models that exhibit Red Queen dynamics typically assume that hosts and parasites encounter one another randomly. However, if related individuals aggregate into family groups or are clustered spatially, related hosts will be more likely to encounter parasites transmitted by genetically similar individuals. Using a model that incorporates familial parasite transmission, we show that a slight degree of familial parasite transmission is sufficient to halt coevolutionary fluctuations. Our results predict that evidence for Red Queen dynamics, and its evolutionary consequences, are most likely to be found in biological systems in which hosts and parasites mix mainly at random, and are less likely to be found in systems with familial aggregation. This presents a challenge to the Red Queen hypothesis and other hypotheses that depend on coevolutionary cycling.
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Affiliation(s)
- Philip B Greenspoon
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
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28
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Baltrus DA, McCann HC, Guttman DS. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:152-168. [PMID: 27798954 PMCID: PMC6638251 DOI: 10.1111/mpp.12506] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
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Affiliation(s)
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey UniversityAuckland 0632New Zealand
| | - David S. Guttman
- Department of Cell and Systems BiologyUniversity of TorontoTorontoON M5S 3B2Canada
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoON M5S 3B2Canada
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29
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Ford SA, Williams D, Paterson S, King KC. Co-evolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection. Mol Ecol 2016; 26:1778-1789. [PMID: 27862515 PMCID: PMC6849518 DOI: 10.1111/mec.13906] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/15/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022]
Abstract
Microbes that protect their hosts from pathogenic infection are widespread components of the microbiota of both plants and animals. It has been found that interactions between 'defensive' microbes and pathogens can be genotype-specific and even underlie the variation in host resistance to pathogenic infection. These observations suggest a dynamic co-evolutionary association between pathogens and defensive microbes, but direct evidence of co-evolution is lacking. We tested the hypothesis that defensive microbes and pathogens could co-evolve within host populations by co-passaging a microbe with host-defensive properties (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within Caenorhabditis elegans nematodes. Using both phenotypic and genomic analyses across evolutionary time, we found patterns of pathogen local adaptation and defensive microbe-pathogen co-evolution via fluctuating selection dynamics. Moreover, co-evolution with defensive microbes resulted in more rapid and divergent pathogen evolution compared to pathogens evolved independently in host populations. Taken together, our results indicate the potential for defensive microbes and pathogens to co-evolve, driving interaction specificity and pathogen evolutionary divergence in the absence of host evolution.
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Affiliation(s)
- Suzanne A Ford
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - David Williams
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB, UK
| | - Steve Paterson
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB, UK
| | - Kayla C King
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
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30
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Kraemer SA, Kassen R. Temporal patterns of local adaptation in soil pseudomonads. Proc Biol Sci 2016; 283:20161652. [PMID: 27708150 PMCID: PMC5069515 DOI: 10.1098/rspb.2016.1652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/13/2016] [Indexed: 12/25/2022] Open
Abstract
Strong divergent selection leading to local adaptation is often invoked to explain the staggering diversity of bacteria in microbial ecosystems. However, examples of specialization by bacterial clones to alternative niches in nature are rare. Here, we investigate the extent of local adaptation in natural isolates of pseudomonads and their relatives to their soil environments across both space and time. Though most isolates grew well in most environments, patchily distributed low-quality environments were found to drive specialization. In contrast to experimental evolution work on microbial adaptation, temporal adaptation was stronger than spatial adaptation among the isolates and environments we sampled. Time-shift analysis of fitness across two seasons of growth revealed an unexpectedly strong effect of preadaptation. This pattern of apparent future adaptation may be caused by unknown abiotic properties of these environments, phages, bacterial competitors or general mechanisms of ecological niche release, and warrants future study.
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Affiliation(s)
- Susanne A Kraemer
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Rees Kassen
- University of Ottawa, Ottawa, Ontario, Canada
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31
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Host and Parasite Evolution in a Tangled Bank. Trends Parasitol 2016; 32:863-873. [PMID: 27599631 DOI: 10.1016/j.pt.2016.08.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 01/29/2023]
Abstract
Most hosts and parasites exist in diverse communities wherein they interact with other species, spanning the parasite-mutualist continuum. These additional interactions have the potential to impose selection on hosts and parasites and influence the patterns and processes of their evolution. Yet, host-parasite interactions are almost exclusively studied in species pairs. A wave of new research has incorporated a multispecies community context, showing that additional ecological interactions can alter components of host and parasite fitness, as well as interaction specificity and virulence. Here, we synthesize these findings to assess the effects of increased species diversity on the patterns and processes of host and parasite evolution. We argue that our understanding of host-parasite interactions would benefit from a richer biotic perspective.
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32
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Kalske A, Leimu R, Scheepens JF, Mutikainen P. Spatiotemporal variation in local adaptation of a specialist insect herbivore to its long-lived host plant. Evolution 2016; 70:2110-22. [PMID: 27436540 DOI: 10.1111/evo.13013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 07/06/2016] [Accepted: 07/12/2016] [Indexed: 02/04/2023]
Abstract
Local adaptation of interacting species to one another indicates geographically variable reciprocal selection. This process of adaptation is central in the organization and maintenance of genetic variation across populations. Given that the strength of selection and responses to it often vary in time and space, the strength of local adaptation should in theory vary between generations and among populations. However, such spatiotemporal variation has rarely been explicitly demonstrated in nature and local adaptation is commonly considered to be relatively static. We report persistent local adaptation of the short-lived herbivore Abrostola asclepiadis to its long-lived host plant Vincetoxicum hirundinaria over three successive generations in two studied populations and considerable temporal variation in local adaptation in six populations supporting the geographic mosaic theory. The observed variation in local adaptation among populations was best explained by geographic distance and population isolation, suggesting that gene flow reduces local adaptation. Changes in herbivore population size did not conclusively explain temporal variation in local adaptation. Our results also imply that short-term studies are likely to capture only a part of the existing variation in local adaptation.
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Affiliation(s)
- Aino Kalske
- Section of Ecology, Department of Biology, University of Turku, FI-20014, Turku, Finland. .,Current Address: Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York, 14853.
| | - Roosa Leimu
- Seed International, Oxford, United Kingdom.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom
| | - J F Scheepens
- Section of Ecology, Department of Biology, University of Turku, FI-20014, Turku, Finland.,Current Address: Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Pia Mutikainen
- Institute of Integrative Biology, ETH-Zürich, ETH-Zentrum, CH-8092, Zürich, Switzerland
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33
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Koskella B, Parr N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0297. [PMID: 26150663 PMCID: PMC4528495 DOI: 10.1098/rstb.2014.0297] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.
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Affiliation(s)
- Britt Koskella
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall, UK
| | - Nicole Parr
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall, UK
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34
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Krysiak-Baltyn K, Martin GJO, Stickland AD, Scales PJ, Gras SL. Computational models of populations of bacteria and lytic phage. Crit Rev Microbiol 2016; 42:942-68. [PMID: 26828960 DOI: 10.3109/1040841x.2015.1114466] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The use of phages to control and reduce numbers of unwanted bacteria can be traced back to the early 1900s, when phages were explored as a tool to treat infections before the wide scale use of antibiotics. Recently, phage therapy has received renewed interest as a method to treat multiresistant bacteria. Phages are also widely used in the food industry to prevent the growth of certain bacteria in foods, and are currently being explored as a tool for use in bioremediation and wastewater treatment. Despite the large body of biological research on phages, relatively little attention has been given to computational modeling of the population dynamics of phage and bacterial interactions. The earliest model was described by Campbell in the 1960s. Subsequent modifications to this model include partial or complete resistance, multiple phage binding sites, and spatial heterogeneity. This review provides a general introduction to modeling of the population dynamics of bacteria and phage. The review introduces the basic model and relevant concepts and evaluates more complex variations of the basic model published to date, including a model of disease epidemics caused by infectious bacteria. Finally, the shortcomings and potential ways to improve the models are discussed.
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Affiliation(s)
- Konrad Krysiak-Baltyn
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Gregory J O Martin
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Anthony D Stickland
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Peter J Scales
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Sally L Gras
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
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35
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Penczykowski RM, Laine A, Koskella B. Understanding the ecology and evolution of host-parasite interactions across scales. Evol Appl 2016; 9:37-52. [PMID: 27087838 PMCID: PMC4780374 DOI: 10.1111/eva.12294] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/18/2015] [Indexed: 12/19/2022] Open
Abstract
Predicting the emergence, spread and evolution of parasites within and among host populations requires insight to both the spatial and temporal scales of adaptation, including an understanding of within-host up through community-level dynamics. Although there are very few pathosystems for which such extensive data exist, there has been a recent push to integrate studies performed over multiple scales or to simultaneously test for dynamics occurring across scales. Drawing on examples from the literature, with primary emphasis on three diverse host-parasite case studies, we first examine current understanding of the spatial structure of host and parasite populations, including patterns of local adaptation and spatial variation in host resistance and parasite infectivity. We then explore the ways to measure temporal variation and dynamics in host-parasite interactions and discuss the need to examine change over both ecological and evolutionary timescales. Finally, we highlight new approaches and syntheses that allow for simultaneous analysis of dynamics across scales. We argue that there is great value in examining interplay among scales in studies of host-parasite interactions.
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Affiliation(s)
- Rachel M. Penczykowski
- Department of BiosciencesMetapopulation Research CentreUniversity of HelsinkiHelsinkiFinland
| | - Anna‐Liisa Laine
- Department of BiosciencesMetapopulation Research CentreUniversity of HelsinkiHelsinkiFinland
| | - Britt Koskella
- BiosciencesUniversity of ExeterTremoughUK
- Integrative BiologyUniversity of CaliforniaBerkeleyUSA
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36
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Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev 2015; 40:258-72. [PMID: 26657537 PMCID: PMC5831537 DOI: 10.1093/femsre/fuv048] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 01/21/2023] Open
Abstract
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. New viruses infecting bacteria are increasingly being discovered in many environments through sequence-based explorations. To understand their role in microbial ecosystems, computational tools are indispensable to prioritize and guide experimental efforts. This review assesses and discusses a range of bioinformatic approaches to predict bacteriophage–host relationships when all that is known is their genome sequence.
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Affiliation(s)
- Robert A Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Bas E Dutilh
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
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37
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Koskella B, Vos M. Adaptation in Natural Microbial Populations. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054458] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California 94720;
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Penryn Campus, Cornwall TR10 9FE, United Kingdom;
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38
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Lion S, Gandon S. Evolution of spatially structured host-parasite interactions. J Evol Biol 2015; 28:10-28. [DOI: 10.1111/jeb.12551] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 01/19/2023]
Affiliation(s)
- S. Lion
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE; Montpellier Cedex 5 France
| | - S. Gandon
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE; Montpellier Cedex 5 France
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