1
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Litchman E, Villéger S, Zinger L, Auguet JC, Thuiller W, Munoz F, Kraft NJB, Philippot L, Violle C. Refocusing the microbial rare biosphere concept through a functional lens. Trends Ecol Evol 2024:S0169-5347(24)00143-5. [PMID: 38987022 DOI: 10.1016/j.tree.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.
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Affiliation(s)
- Elena Litchman
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA; Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
| | | | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300, CNRS, Institut de Recherche pour le Développement (IRD), Toulouse INP, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | | | - Wilfried Thuiller
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Munoz
- Université Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Agroecology, Dijon, France
| | - Cyrille Violle
- CEFE, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
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2
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Dong J, Qiu L, Zhou X, Liu S. Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana. Mol Ecol 2024; 33:e17414. [PMID: 38801184 DOI: 10.1111/mec.17414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non-genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central-peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation-with-gene-flow models generate the heterogeneous genome landscapes. These elements weight differently between central-island and other central-peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low-recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non-uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana.
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Affiliation(s)
- Jiangxing Dong
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lifei Qiu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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3
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Feltin C, Garneau JR, Morris CE, Bérard A, Torres-Barceló C. Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes. J Gen Virol 2024; 105:001990. [PMID: 38833289 PMCID: PMC11256456 DOI: 10.1099/jgv.0.001990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.
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Affiliation(s)
- Chloé Feltin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Julian R. Garneau
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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4
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Strobel HM, Labador SD, Basu D, Sane M, Corbett KD, Meyer JR. Viral Receptor-Binding Protein Evolves New Function through Mutations That Cause Trimer Instability and Functional Heterogeneity. Mol Biol Evol 2024; 41:msae056. [PMID: 38586942 PMCID: PMC10999833 DOI: 10.1093/molbev/msae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However, recent work has revealed that nonnative, often unstable protein conformations play an important role in mediating evolutionary transitions, raising the question of whether instability can itself potentiate the evolution of new activity. We explored this question in a bacteriophage receptor-binding protein during host-range evolution. We studied the properties of the receptor-binding protein of bacteriophage λ before and after host-range evolution and demonstrated that the evolved protein is relatively unstable and may exist in multiple conformations with unique receptor preferences. Through a combination of structural modeling and in vitro oligomeric state analysis, we found that the instability arises from mutations that interfere with trimer formation. This study raises the intriguing possibility that protein instability might play a previously unrecognized role in mediating host-range expansions in viruses.
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Affiliation(s)
- Hannah M Strobel
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sweetzel D Labador
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Dwaipayan Basu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mrudula Sane
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kevin D Corbett
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Justin R Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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5
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Forni D, Pozzoli U, Cagliani R, Sironi M. Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts. Mol Ecol 2024; 33:e17287. [PMID: 38263702 DOI: 10.1111/mec.17287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod-infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral-encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria-infecting phages resulted to be significantly CpG-depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG-rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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6
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Ascensao JA, Denk J, Lok K, Yu Q, Wetmore KM, Hallatschek O. Rediversification following ecotype isolation reveals hidden adaptive potential. Curr Biol 2024; 34:855-867.e6. [PMID: 38325377 PMCID: PMC10911448 DOI: 10.1016/j.cub.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/09/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about whether communities can regenerate ecological diversity following ecotype removal or extinction and how the rediversified communities would compare to the original ones. Here, we show that simple two-ecotype communities from the E. coli long-term evolution experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different from the original community in ways relevant to the mechanism of ecotype coexistence-for example, in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, although the rediversified community showed unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species where there are even more potential niches, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.
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Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Jonas Denk
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Kristen Lok
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Present affiliation: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - QinQin Yu
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Present affiliation: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Oskar Hallatschek
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
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7
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Doud MB, Gupta A, Li V, Medina SJ, De La Fuente CA, Meyer JR. Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda's fitness landscape and enables speciation. Nat Commun 2024; 15:863. [PMID: 38286804 PMCID: PMC10825149 DOI: 10.1038/s41467-024-45008-5] [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: 08/21/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
A major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, to our knowledge none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage [Formula: see text], a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We use a high-throughput gene editing-phenotyping technology to measure [Formula: see text]'s fitness landscape in the presence of different evolved-[Formula: see text] competitors and find that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulate [Formula: see text]'s evolution on an unchanging landscape and one that recapitulates how the landscape deforms during evolution. [Formula: see text] heterogeneity only evolves in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.
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Affiliation(s)
- Michael B Doud
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Animesh Gupta
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Victor Li
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Sarah J Medina
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Caesar A De La Fuente
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Justin R Meyer
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA.
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8
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Labutin A, Heckel G. Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus Evol 2024; 10:veae002. [PMID: 38361825 PMCID: PMC10868551 DOI: 10.1093/ve/veae002] [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: 03/14/2023] [Revised: 11/08/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
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Affiliation(s)
- Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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9
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Holtzman T, Nechooshtan R, Yosef I, Qimron U. Contracting the Host Range of Bacteriophage T7 Using a Continuous Evolution System. Methods Mol Biol 2024; 2793:85-100. [PMID: 38526725 DOI: 10.1007/978-1-0716-3798-2_6] [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] [Indexed: 03/27/2024]
Abstract
Bacteriophage T7 is an intracellular virus that recognizes its host via tail and tail fiber proteins known as receptor-binding proteins (RBPs). The RBPs attach to a specific lipopolysaccharide (LPS) displayed on the host. While there are various reports of phage host range expansion resulting from mutations in the RBP encoding genes, there is little evidence for contraction of host range. Notably, most experimental systems have not monitored changes in host range in the presence of several hosts simultaneously. Here, we use a continuous evolution system to show that T7 phages grown in the presence of five restrictive strains and one permissive host, each with a different LPS, gradually cease to recognize the restrictive strains. Remarkably, this result was obtained in experiments with six different permissive hosts. The altered specificity is due to mutations in the RBPs as determined by gene sequencing. The results of using this system demonstrate a major role for RBPs in restricting the range of futile infections, and this process can be harnessed to reduce the host range in applications such as recognition and elimination of a specific bacterial serotype by bacteriophages.
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Affiliation(s)
- Tzvi Holtzman
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel.
| | - Ram Nechooshtan
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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10
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Houpt NSB, Kassen R. On the De Novo Emergence of Ecological Interactions during Evolutionary Diversification: A Conceptual Framework and Experimental Test. Am Nat 2023; 202:800-817. [PMID: 38033179 DOI: 10.1086/726895] [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] [Indexed: 12/02/2023]
Abstract
AbstractEcological interactions are crucial to the structure and function of biological communities, but we lack a causal understanding of the forces shaping their emergence during evolutionary diversification. Here we provide a conceptual framework linking different modes of diversification (e.g., ecological diversification), which depend on environmental characteristics, to the evolution of different forms of ecological interactions (e.g., resource partitioning) in asexual lineages. We tested the framework by examining the net interactions in communities of Pseudomonas aeruginosa produced via experimental evolution in nutritionally simple (SIM) or complex (COM) environments by contrasting the productivity and competitive fitness of whole evolved communities relative to their component isolates. As expected, we found that nutritional complexity drove the evolution of communities with net positive interactions whereas SIM communities had similar performance as their component isolates. A follow-up experiment revealed that high fitness in two COM communities was driven by rare variants (frequency <0.1%) that antagonized PA14, the ancestral strain and common competitor used in fitness assays. Our study suggests that the evolution of de novo ecological interactions in asexual lineages is predictable at a broad scale from environmental conditions. Further, our work demonstrates that rare variants can disproportionately impact the function of relatively simple microbial communities.
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11
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Wu R, Davison MR, Nelson WC, Smith ML, Lipton MS, Jansson JK, McClure RS, McDermott JE, Hofmockel KS. Hi-C metagenome sequencing reveals soil phage-host interactions. Nat Commun 2023; 14:7666. [PMID: 37996432 PMCID: PMC10667309 DOI: 10.1038/s41467-023-42967-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.
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Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michelle R Davison
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William C Nelson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Montana L Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan S McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Department of Agronomy, Iowa State University, Ames, IA, USA.
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12
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Borin JM, Lee JJ, Lucia-Sanz A, Gerbino KR, Weitz JS, Meyer JR. Rapid bacteria-phage coevolution drives the emergence of multiscale networks. Science 2023; 382:674-678. [PMID: 37943920 DOI: 10.1126/science.adi5536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023]
Abstract
Interactions between species catalyze the evolution of multiscale ecological networks, including both nested and modular elements that regulate the function of diverse communities. One common assumption is that such complex pattern formation requires spatial isolation or long evolutionary timescales. We show that multiscale network structure can evolve rapidly under simple ecological conditions without spatial structure. In just 21 days of laboratory coevolution, Escherichia coli and bacteriophage Φ21 coevolve and diversify to form elaborate cross-infection networks. By measuring ~10,000 phage-bacteria infections and testing the genetic basis of interactions, we identify the mechanisms that create each component of the multiscale pattern. Our results demonstrate how multiscale networks evolve in parasite-host systems, illustrating Darwin's idea that simple adaptive processes can generate entangled banks of ecological interactions.
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Affiliation(s)
- Joshua M Borin
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin J Lee
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adriana Lucia-Sanz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Krista R Gerbino
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua S Weitz
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institut de Biologie, École Normale Supérieure, 75005 Paris, France
| | - Justin R Meyer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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13
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Doud MB, Gupta A, Li V, Medina SJ, De La Fuente CA, Meyer JR. Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda's fitness landscape and enables speciation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553017. [PMID: 37645887 PMCID: PMC10461988 DOI: 10.1101/2023.08.11.553017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
A major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage λ, a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We used a high-throughput gene editing-phenotyping technology to measure λ's fitness landscape in the presence of different evolved-λ competitors and found that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulated λ's evolution on an unchanging landscape and one that recapitulates how the landscape deforms during evolution. λ heterogeneity only evolved in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.
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Affiliation(s)
- Michael B. Doud
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Animesh Gupta
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Victor Li
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Sarah J. Medina
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Caesar A. De La Fuente
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
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14
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Bumunang EW, Zaheer R, Niu D, Narvaez-Bravo C, Alexander T, McAllister TA, Stanford K. Bacteriophages for the Targeted Control of Foodborne Pathogens. Foods 2023; 12:2734. [PMID: 37509826 PMCID: PMC10379335 DOI: 10.3390/foods12142734] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Foodborne illness is exacerbated by novel and emerging pathotypes, persistent contamination, antimicrobial resistance, an ever-changing environment, and the complexity of food production systems. Sporadic and outbreak events of common foodborne pathogens like Shiga toxigenic E. coli (STEC), Salmonella, Campylobacter, and Listeria monocytogenes are increasingly identified. Methods of controlling human infections linked with food products are essential to improve food safety and public health and to avoid economic losses associated with contaminated food product recalls and litigations. Bacteriophages (phages) are an attractive additional weapon in the ongoing search for preventative measures to improve food safety and public health. However, like all other antimicrobial interventions that are being employed in food production systems, phages are not a panacea to all food safety challenges. Therefore, while phage-based biocontrol can be promising in combating foodborne pathogens, their antibacterial spectrum is generally narrower than most antibiotics. The emergence of phage-insensitive single-cell variants and the formulation of effective cocktails are some of the challenges faced by phage-based biocontrol methods. This review examines phage-based applications at critical control points in food production systems with an emphasis on when and where they can be successfully applied at production and processing levels. Shortcomings associated with phage-based control measures are outlined together with strategies that can be applied to improve phage utility for current and future applications in food safety.
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Affiliation(s)
- Emmanuel W Bumunang
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Dongyan Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Claudia Narvaez-Bravo
- Food and Human Nutritional Sciences, Faculty of Agricultural & Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Trevor Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
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15
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Dunstan RA, Bamert RS, Tan KS, Imbulgoda U, Barlow CK, Taiaroa G, Pickard DJ, Schittenhelm RB, Dougan G, Short FL, Lithgow T. Epitopes in the capsular polysaccharide and the porin OmpK36 receptors are required for bacteriophage infection of Klebsiella pneumoniae. Cell Rep 2023; 42:112551. [PMID: 37224021 DOI: 10.1016/j.celrep.2023.112551] [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: 08/30/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
To kill bacteria, bacteriophages (phages) must first bind to a receptor, triggering the release of the phage DNA into the bacterial cell. Many bacteria secrete polysaccharides that had been thought to shield bacterial cells from phage attack. We use a comprehensive genetic screen to distinguish that the capsule is not a shield but is instead a primary receptor enabling phage predation. Screening of a transposon library to select phage-resistant Klebsiella shows that the first receptor-binding event docks to saccharide epitopes in the capsule. We discover a second step of receptor binding, dictated by specific epitopes in an outer membrane protein. This additional and necessary event precedes phage DNA release to establish a productive infection. That such discrete epitopes dictate two essential binding events for phages has profound implications for understanding the evolution of phage resistance and what dictates host range, two issues critically important to translating knowledge of phage biology into phage therapies.
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Affiliation(s)
- Rhys A Dunstan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Rebecca S Bamert
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Kher Shing Tan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Uvini Imbulgoda
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Christopher K Barlow
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Clayton, VIC, Australia
| | - Derek J Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesca L Short
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
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16
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Bhatt P, Engel BA, Reuhs M, Simsek H. Cyanophage technology in removal of cyanobacteria mediated harmful algal blooms: A novel and eco-friendly method. CHEMOSPHERE 2023; 315:137769. [PMID: 36623591 DOI: 10.1016/j.chemosphere.2023.137769] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Cyanophages are highly abundant specific viruses that infect cyanobacterial cells. In recent years, the cyanophages and cyanobacteria interactions drew attention to environmental restoration due to their discovery in marine and freshwater systems. Cyanobacterial harmful algal blooms (cyanoHABs) are increasing throughout the world and contaminating aquatic ecosystems. The blooms cause severe environmental problems including unpleasant odors and cyanotoxin production. Cyanotoxins have been reported to be lethal agents for living beings and can harm animals, people, aquatic species, recreational activities, and drinking water reservoirs. Biological remediation of cyanoHABs in aquatic systems is a sustainable and eco-friendly approach to increasing surface water quality. Therefore, this study compiles the fragmented information with the solution of removal of cyanoHABs using cyanophage therapy techniques. To date, scant information exists in terms of bloom formation, cyanophage occurrence, and mode of action to remediate cyanoHABs. Overall, this study illustrates cyanobacterial toxin production and its impacts on the environment, the mechanisms involved in the cyanophage-cyanobacteria interaction, and the application of cyanophages for the removal of toxic cyanobacterial blooms.
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Affiliation(s)
- Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Bernard A Engel
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Mikael Reuhs
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Halis Simsek
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA.
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17
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Shaer Tamar E, Kishony R. Multistep diversification in spatiotemporal bacterial-phage coevolution. Nat Commun 2022; 13:7971. [PMID: 36577749 PMCID: PMC9797572 DOI: 10.1038/s41467-022-35351-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/29/2022] [Indexed: 12/29/2022] Open
Abstract
The evolutionary arms race between phages and bacteria, where bacteria evolve resistance to phages and phages retaliate with resistance-countering mutations, is a major driving force of molecular innovation and genetic diversification. Yet attempting to reproduce such ongoing retaliation dynamics in the lab has been challenging; laboratory coevolution experiments of phage and bacteria are typically performed in well-mixed environments and often lead to rapid stagnation with little genetic variability. Here, co-culturing motile E. coli with the lytic bacteriophage T7 on swimming plates, we observe complex spatiotemporal dynamics with multiple genetically diversifying adaptive cycles. Systematically quantifying over 10,000 resistance-infectivity phenotypes between evolved bacteria and phage isolates, we observe diversification into multiple coexisting ecotypes showing a complex interaction network with both host-range expansion and host-switch tradeoffs. Whole-genome sequencing of these evolved phage and bacterial isolates revealed a rich set of adaptive mutations in multiple genetic pathways including in genes not previously linked with phage-bacteria interactions. Synthetically reconstructing these new mutations, we discover phage-general and phage-specific resistance phenotypes as well as a strong synergy with the more classically known phage-resistance mutations. These results highlight the importance of spatial structure and migration for driving phage-bacteria coevolution, providing a concrete system for revealing new molecular mechanisms across diverse phage-bacterial systems.
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Affiliation(s)
- Einat Shaer Tamar
- grid.6451.60000000121102151Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Roy Kishony
- grid.6451.60000000121102151Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel ,grid.6451.60000000121102151Faculty of Computer Science, Technion–Israel Institute of Technology, Haifa, Israel ,grid.6451.60000000121102151Faculty of Biomedical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
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18
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Borin JM, Lee JJ, Gerbino KR, Meyer JR. Comparison of bacterial suppression by phage cocktails, dual-receptor generalists, and coevolutionarily trained phages. Evol Appl 2022; 16:152-162. [PMID: 36699129 PMCID: PMC9850009 DOI: 10.1111/eva.13518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
The evolution and spread of antibiotic-resistant bacteria have renewed interest in phage therapy, the use of bacterial viruses (phages) to combat bacterial infections. The delivery of phages in cocktails where constituent phages target different modalities (e.g., receptors) may improve treatment outcomes by making it more difficult for bacteria to evolve resistance. However, the multipartite nature of cocktails may lead to unintended evolutionary and ecological outcomes. Here, we compare a 2-phage cocktail with a largely unconsidered group of phages: generalists that can infect through multiple, independent receptors. We find that λ phage generalists and cocktails that target the same receptors (LamB and OmpF) suppress Escherichia coli similarly for ~2 days. Yet, a "trained" generalist phage, which previously adapted to its host via 28 days of coevolution, demonstrated superior suppression. To understand why the trained generalist was more effective, we measured the resistance of bacteria against each of our phages. We find that, when bacteria were assailed by two phages in the cocktail, they evolved mutations in manXYZ, a host inner-membrane transporter that λ uses to move its DNA across the periplasmic space and into the cell for infection. This provided cross-resistance against the cocktail and untrained generalist. However, these mutations were ineffective at blocking the trained generalist because, through coevolutionary training, it evolved to bypass manXYZ resistance. The trained generalist's past experiences in training make it exceedingly difficult for bacteria to evolve resistance, further demonstrating the utility of coevolutionary phage training for improving the therapeutic properties of phages.
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Affiliation(s)
- Joshua M. Borin
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Justin J. Lee
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Krista R. Gerbino
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Justin R. Meyer
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
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19
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Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
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20
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Strobel HM, Stuart EC, Meyer JR. A Trait-Based Approach to Predicting Viral Host-Range Evolvability. Annu Rev Virol 2022; 9:139-156. [PMID: 36173699 DOI: 10.1146/annurev-virology-091919-092003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predicting the evolution of virus host range has proven to be extremely difficult, in part because of the sheer diversity of viruses, each with unique biology and ecological interactions. We have not solved this problem, but to make the problem more tractable, we narrowed our focus to three traits intrinsic to all viruses that may play a role in host-range evolvability: mutation rate, recombination rate, and phenotypic heterogeneity. Although each trait should increase evolvability, they cannot do so unbounded because fitness trade-offs limit the ability of all three traits to maximize evolvability. By examining these constraints, we can begin to identify groups of viruses with suites of traits that make them especially concerning, as well as ecological and environmental conditions that might push evolution toward accelerating host-range expansion.
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Affiliation(s)
- Hannah M Strobel
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth C Stuart
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Justin R Meyer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
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21
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Wang Z, Cai X, Jiang X, Xia Q, Li L, Lu B. Sympatric genetic divergence between early- and late-season weedy rice populations. THE NEW PHYTOLOGIST 2022; 235:2066-2080. [PMID: 35637631 PMCID: PMC9544748 DOI: 10.1111/nph.18288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Sympatric genetic divergence is the most appealing and controversial pattern in the theory of ecological speciation. Examples that support sympatric genetic divergence in plant species are extremely rare. Solid evidence of sympatric genetic divergence will provide deep insights for revealing the underlying mechanisms of ecological speciation. We analysed the total genomic DNA sequences of 120 weedy rice (WR; Oryza sativa f. spontanea) plants, representing three WR population pairs separately from three early- and late-season rice fields, in comparison with those of the co-occurring rice cultivars and other rice materials. We detected substantial genetic divergence within the pairs of the sympatric early- and late-season WR populations, although genetic divergence was unevenly distributed across the genomes. Restricted gene flow was determined between the sympatric WR populations, resulting in their distinct genetic structures. We also detected relatively low genetic diversity that was likely to be associated with stronger selection in early-season WR populations. Our findings provide strong evidence for sympatric genetic divergence between the WR populations in the same fields but in different seasons. We conclude that temporal isolation plays an important role in creating genetic divergence between sympatric populations/species in plants.
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Affiliation(s)
- Zhi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xingxing Cai
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xiao‐Qi Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Qi‐Yu Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsInstitute of Tropical Bioscience and Biotechnology, CATASHaikou571101China
| | - Lin‐Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
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22
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Gupta A, Zaman L, Strobel HM, Gallie J, Burmeister AR, Kerr B, Tamar ES, Kishony R, Meyer JR. Host-parasite coevolution promotes innovation through deformations in fitness landscapes. eLife 2022; 11:e76162. [PMID: 35793223 PMCID: PMC9259030 DOI: 10.7554/elife.76162] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/20/2022] [Indexed: 01/14/2023] Open
Abstract
During the struggle for survival, populations occasionally evolve new functions that give them access to untapped ecological opportunities. Theory suggests that coevolution between species can promote the evolution of such innovations by deforming fitness landscapes in ways that open new adaptive pathways. We directly tested this idea by using high-throughput gene editing-phenotyping technology (MAGE-Seq) to measure the fitness landscape of a virus, bacteriophage λ, as it coevolved with its host, the bacterium Escherichia coli. An analysis of the empirical fitness landscape revealed mutation-by-mutation-by-host-genotype interactions that demonstrate coevolution modified the contours of λ's landscape. Computer simulations of λ's evolution on a static versus shifting fitness landscape showed that the changes in contours increased λ's chances of evolving the ability to use a new host receptor. By coupling sequencing and pairwise competition experiments, we demonstrated that the first mutation λ evolved en route to the innovation would only evolve in the presence of the ancestral host, whereas later steps in λ's evolution required the shift to a resistant host. When time-shift replays of the coevolution experiment were run where host evolution was artificially accelerated, λ did not innovate to use the new receptor. This study provides direct evidence for the role of coevolution in driving evolutionary novelty and provides a quantitative framework for predicting evolution in coevolving ecological communities.
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Affiliation(s)
- Animesh Gupta
- Department of Physics, University of California San DiegoLa JollaUnited States
| | - Luis Zaman
- Department of Ecology and Evolutionary Biology, University of MichiganAnn ArborUnited States
| | - Hannah M Strobel
- Department of Ecology, Behavior and Evolution, University of California San DiegoLa JollaUnited States
| | - Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale UniversityNew HavenUnited States
| | - Benjamin Kerr
- Department of Biology, University of WashingtonSeattleUnited States
| | - Einat S Tamar
- Department of Biology, Technion – Israel Institute of TechnologyHaifaIsrael
| | - Roy Kishony
- Department of Biology, Technion – Israel Institute of TechnologyHaifaIsrael
| | - Justin R Meyer
- Department of Ecology, Behavior and Evolution, University of California San DiegoLa JollaUnited States
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23
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Strobel HM, Horwitz EK, Meyer JR. Viral protein instability enhances host-range evolvability. PLoS Genet 2022; 18:e1010030. [PMID: 35176040 PMCID: PMC8890733 DOI: 10.1371/journal.pgen.1010030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/02/2022] [Accepted: 01/11/2022] [Indexed: 12/29/2022] Open
Abstract
Viruses are highly evolvable, but what traits endow this property? The high mutation rates of viruses certainly play a role, but factors that act above the genetic code, like protein thermostability, are also expected to contribute. We studied how the thermostability of a model virus, bacteriophage λ, affects its ability to evolve to use a new receptor, a key evolutionary transition that can cause host-range evolution. Using directed evolution and synthetic biology techniques we generated a library of host-recognition protein variants with altered stabilities and then tested their capacity to evolve to use a new receptor. Variants fell within three stability classes: stable, unstable, and catastrophically unstable. The most evolvable were the two unstable variants, whereas seven of eight stable variants were significantly less evolvable, and the two catastrophically unstable variants could not grow. The slowly evolving stable variants were delayed because they required an additional destabilizing mutation. These results are particularly noteworthy because they contradict a widely supported contention that thermostabilizing mutations enhance evolvability of proteins by increasing mutational robustness. Our work suggests that the relationship between thermostability and evolvability is more complex than previously thought, provides evidence for a new molecular model of host-range expansion evolution, and identifies instability as a potential predictor of viral host-range evolution.
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Affiliation(s)
- Hannah M. Strobel
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Elijah K. Horwitz
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Justin R. Meyer
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
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24
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Gupta A, Peng S, Leung CY, Borin JM, Medina S, Weitz JS, Meyer JR. Leapfrog dynamics in phage‐bacteria coevolution revealed by joint analysis of cross‐infection phenotypes and whole genome sequencing. Ecol Lett 2022; 25:876-888. [PMID: 35092147 PMCID: PMC10167754 DOI: 10.1111/ele.13965] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/21/2021] [Accepted: 11/10/2021] [Indexed: 01/21/2023]
Abstract
Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), both players are predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. By coupling phenotypic and genomic analyses of coevolving populations of bacteriophage λ and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet genomic analyses revealed fluctuating selection dynamics. Rather than coevolution unfolding along a single trajectory, cryptic genetic variation emerges and is maintained at low frequency for generations until it eventually supplants dominant lineages. These observations suggest a hybrid 'leapfrog' dynamic, revealing weaknesses in the predictive power of standard coevolutionary models. The findings shed light on the mechanisms that structure coevolving ecological networks and reveal the limits of using phenotypic or genomic data alone to differentiate coevolutionary dynamics.
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Affiliation(s)
- Animesh Gupta
- Department of Physics University of California San Diego La Jolla California USA
| | - Shengyun Peng
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
| | - Chung Yin Leung
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
| | - Joshua M. Borin
- Division of Biological Science University of California San Diego La Jolla California USA
| | - Sarah J. Medina
- Division of Biological Science University of California San Diego La Jolla California USA
| | - Joshua S. Weitz
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
- School of Physics Georgia Institute of Technology Atlanta Georgia USA
| | - Justin R. Meyer
- Division of Biological Science University of California San Diego La Jolla California USA
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25
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Bakerlee CW, Phillips AM, Nguyen Ba AN, Desai MM. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations. eLife 2021; 10:e70918. [PMID: 34596043 PMCID: PMC8579951 DOI: 10.7554/elife.70918] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in each of three environments, and then assayed their fitness in multiple environments over 1000 generations of evolution. We find that replicate populations evolved in the same condition share common patterns of pleiotropic effects across other environments, which emerge within the first several hundred generations of evolution. However, we also find dynamic and environment-specific variability within these trends: variability in pleiotropic effects tends to increase over time, with the extent of variability depending on the evolution environment. These results suggest shifting and overlapping contributions of chance and contingency to the pleiotropic effects of adaptation, which could influence evolutionary trajectories in complex environments that fluctuate across space and time.
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Affiliation(s)
- Christopher W Bakerlee
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angela M Phillips
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard University, CambridgeCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard University, CambridgeCambridgeUnited States
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26
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San Roman M, Wagner A. Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling. Mol Ecol 2021; 30:5874-5887. [PMID: 34478597 PMCID: PMC9293205 DOI: 10.1111/mec.16161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities are hugely diverse, but we do not yet understand how species invasions and extinctions drive and limit their diversity. On the one hand, the ecological limits hypothesis posits that diversity is primarily limited by environmental resources. On the other hand, the diversity‐begets‐diversity hypothesis posits that such limits can be easily lifted when new ecological niches are created by biotic interactions. To find out which hypothesis better explains the assembly of microbial communities, we used metabolic modelling. We represent each microbial species by a metabolic network that harbours thousands of biochemical reactions. Together, these reactions determine which carbon and energy sources a species can use, and which metabolic by‐products—potential nutrients for other species—it can excrete in a given environment. We assemble communities by modelling thousands of species invasions in a chemostat‐like environment. We find that early during the assembly process, diversity begets diversity. By‐product excretion transforms a simple environment into one that can sustain dozens of species. During later assembly stages, the creation of new niches slows down, existing niches become filled, successful invasions become rare, and species diversity plateaus. Thus, ecological limitations dominate the late assembly process. We conclude that each hypothesis captures a different stage of the assembly process. Species interactions can raise a community's diversity ceiling dramatically, but only within limits imposed by the environment.
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Affiliation(s)
- Magdalena San Roman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM, USA.,Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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27
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Crespo-Bellido A, Hoyer JS, Dubey D, Jeannot RB, Duffy S. Interspecies Recombination Has Driven the Macroevolution of Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0054121. [PMID: 34106000 PMCID: PMC8354330 DOI: 10.1128/jvi.00541-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Begomoviruses (family Geminiviridae, genus Begomovirus) significantly hamper crop production and threaten food security around the world. The frequent emergence of new begomovirus genotypes is facilitated by high mutation frequencies and the propensity to recombine and reassort. Homologous recombination has been especially implicated in the emergence of novel cassava mosaic begomovirus (CMB) genotypes, which cause cassava mosaic disease (CMD). Cassava (Manihot esculenta) is a staple food crop throughout Africa and an important industrial crop in Asia, two continents where production is severely constrained by CMD. The CMD species complex is comprised of 11 bipartite begomovirus species with ample distribution throughout Africa and the Indian subcontinent. While recombination is regarded as a frequent occurrence for CMBs, a revised, systematic assessment of recombination and its impact on CMB phylogeny is currently lacking. We assembled data sets of all publicly available, full-length DNA-A (n = 880) and DNA-B (n = 369) nucleotide sequences from the 11 recognized CMB species. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the CMB sequences. Six out of the 11 species descended from unique interspecies recombination events. Estimates of recombination and mutation rates revealed that all species experience mutation more frequently than recombination, but measures of population divergence indicate that recombination is largely responsible for the genetic differences between species. Our results support that recombination has significantly impacted the CMB phylogeny and has driven speciation in the CMD species complex. IMPORTANCE Cassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange. Here, we present a systematic analysis of the contribution of genetic exchange to cassava mosaic virus species-level diversity. Most of these species emerged as a result of genetic exchange. This is the first study to report the significant impact of genetic exchange on speciation in a group of viruses.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Divya Dubey
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ronica B. Jeannot
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
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28
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Chevallereau A, Pons BJ, van Houte S, Westra ER. Interactions between bacterial and phage communities in natural environments. Nat Rev Microbiol 2021; 20:49-62. [PMID: 34373631 DOI: 10.1038/s41579-021-00602-y] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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Affiliation(s)
- Anne Chevallereau
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK. .,Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.
| | - Benoît J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.
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29
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Bier E, Nizet V. Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance. Trends Genet 2021; 37:745-757. [PMID: 33745750 DOI: 10.1016/j.tig.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.
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Affiliation(s)
- Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA.
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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30
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Chaikeeratisak V, Birkholz EA, Pogliano J. The Phage Nucleus and PhuZ Spindle: Defining Features of the Subcellular Organization and Speciation of Nucleus-Forming Jumbo Phages. Front Microbiol 2021; 12:641317. [PMID: 34326818 PMCID: PMC8314001 DOI: 10.3389/fmicb.2021.641317] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/16/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages and their bacterial hosts are ancient organisms that have been co-evolving for billions of years. Some jumbo phages, those with a genome size larger than 200 kilobases, have recently been discovered to establish complex subcellular organization during replication. Here, we review our current understanding of jumbo phages that form a nucleus-like structure, or “Phage Nucleus,” during replication. The phage nucleus is made of a proteinaceous shell that surrounds replicating phage DNA and imparts a unique subcellular organization that is temporally and spatially controlled within bacterial host cells by a phage-encoded tubulin (PhuZ)-based spindle. This subcellular architecture serves as a replication factory for jumbo Pseudomonas phages and provides a selective advantage when these replicate in some host strains. Throughout the lytic cycle, the phage nucleus compartmentalizes proteins according to function and protects the phage genome from host defense mechanisms. Early during infection, the PhuZ spindle positions the newly formed phage nucleus at midcell and, later in the infection cycle, the spindle rotates the nucleus while delivering capsids and distributing them uniformly on the nuclear surface, where they dock for DNA packaging. During the co-infection of two different nucleus-forming jumbo phages in a bacterial cell, the phage nucleus establishes Subcellular Genetic Isolation that limits the potential for viral genetic exchange by physically separating co-infection genomes, and the PhuZ spindle causes Virogenesis Incompatibility, whereby interacting components from two diverging phages negatively affect phage reproduction. Thus, the phage nucleus and PhuZ spindle are defining cell biological structures that serve roles in both the life cycle of nucleus-forming jumbo phages and phage speciation.
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Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Erica A Birkholz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
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31
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Borin JM, Avrani S, Barrick JE, Petrie KL, Meyer JR. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proc Natl Acad Sci U S A 2021; 118:e2104592118. [PMID: 34083444 PMCID: PMC8201913 DOI: 10.1073/pnas.2104592118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The evolution of antibiotic-resistant bacteria threatens to become the leading cause of worldwide mortality. This crisis has renewed interest in the practice of phage therapy. Yet, bacteria's capacity to evolve resistance may debilitate this therapy as well. To combat the evolution of phage resistance and improve treatment outcomes, many suggest leveraging phages' ability to counter resistance by evolving phages on target hosts before using them in therapy (phage training). We found that in vitro, λtrn, a phage trained for 28 d, suppressed bacteria ∼1,000-fold for three to eight times longer than its untrained ancestor. Prolonged suppression was due to a delay in the evolution of resistance caused by several factors. Mutations that confer resistance to λtrn are ∼100× less common, and while the target bacterium can evolve complete resistance to the untrained phage in a single step, multiple mutations are required to evolve complete resistance to λtrn. Mutations that confer resistance to λtrn are more costly than mutations for untrained phage resistance. Furthermore, when resistance does evolve, λtrn is better able to suppress these forms of resistance. One way that λtrn improved was through recombination with a gene in a defunct prophage in the host genome, which doubled phage fitness. This transfer of information from the host genome is an unexpected but highly efficient mode of training phage. Lastly, we found that many other independently trained λ phages were able to suppress bacterial populations, supporting the important role training could play during phage therapeutic development.
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Affiliation(s)
- Joshua M Borin
- Division of Biological Sciences, University of California San Diego, San Diego, CA 92093
| | - Sarit Avrani
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, 3498838 Haifa, Israel
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Katherine L Petrie
- Division of Biological Sciences, University of California San Diego, San Diego, CA 92093
- Earth-Life Science Institute, Tokyo Institute of Technology, 145-0061 Tokyo, Japan
| | - Justin R Meyer
- Division of Biological Sciences, University of California San Diego, San Diego, CA 92093;
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32
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Baquero F, Coque TM, Galán JC, Martinez JL. The Origin of Niches and Species in the Bacterial World. Front Microbiol 2021; 12:657986. [PMID: 33815348 PMCID: PMC8010147 DOI: 10.3389/fmicb.2021.657986] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, "species" are biological units of individuation. Niches do not exist without individual organisms, and every organism has a niche. We use "niche" in the Hutchinsonian sense as an abstraction of a multidimensional environmental space characterized by a variety of conditions, both biotic and abiotic, whose quantitative ranges determine the positive or negative growth rates of the microbial individual, typically a species, but also parts of the communities of species contained in this space. Microbial organisms ("species") constantly diversify, and such diversification (radiation) depends on the possibility of opening up unexploited or insufficiently exploited niches. Niche exploitation frequently implies "niche construction," as the colonized niche evolves with time, giving rise to new potential subniches, thereby influencing the selection of a series of new variants in the progeny. The evolution of niches and organisms is the result of reciprocal interacting processes that form a single unified process. Centrifugal microbial diversification expands the limits of the species' niches while a centripetal or cohesive process occurs simultaneously, mediated by horizontal gene transfers and recombinatorial events, condensing all of the information recovered during the diversifying specialization into "novel organisms" (possible future species), thereby creating a more complex niche, where the selfishness of the new organism(s) establishes a "homeostatic power" limiting the niche's variation. Once the niche's full carrying capacity has been reached, reproductive isolation occurs, as no foreign organisms can outcompete the established population/community, thereby facilitating speciation. In the case of individualization-speciation of the microbiota, its contribution to the animal' gut structure is a type of "niche construction," the result of crosstalk between the niche (host) and microorganism(s). Lastly, there is a parallelism between the hierarchy of niches and that of microbial individuals. The increasing anthropogenic effects on the biosphere (such as globalization) might reduce the diversity of niches and bacterial individuals, with the potential emergence of highly transmissible multispecialists (which are eventually deleterious) resulting from the homogenization of the microbiosphere, a possibility that should be explored and prevented.
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Affiliation(s)
- Fernando Baquero
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Teresa M Coque
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Juan Carlos Galán
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
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33
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Hashemi Shahraki A, Mirsaeidi M. Phage Therapy for Mycobacterium Abscessus and Strategies to Improve Outcomes. Microorganisms 2021; 9:microorganisms9030596. [PMID: 33799414 PMCID: PMC7999966 DOI: 10.3390/microorganisms9030596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Members of Mycobacterium abscessus complex are known for causing severe, chronic infections. Members of M. abscessus are a new "antibiotic nightmare" as one of the most resistant organisms to chemotherapeutic agents. Treatment of these infections is challenging due to the either intrinsic or acquired resistance of the M. abscessus complex to the available antibiotics. Recently, successful phage therapy with a cocktail of three phages (one natural lytic phage and two engineered phages) every 12 h for at least 32 weeks has been reported against a severe case of the disseminated M. abscessus subsp. massiliense infection, which underlines the high value of phages against drug-resistant superbugs. This report also highlighted the limitations of phage therapy, such as the absence of lytic phages with a broad host-range against all strains and subspecies of the M. abscessus complex and also the risk of phage resistant bacteria over treatment. Cutting-edge genomic technologies have facilitated the development of engineered phages for therapeutic purposes by introducing new desirable properties, changing host-range and arming the phages with additional killing genes. Here, we review the available literature and suggest new potential solutions based on the progress in phage engineering that can help to overcome the present limitations of M. abscessus treatment.
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34
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Viral speciation through subcellular genetic isolation and virogenesis incompatibility. Nat Commun 2021; 12:342. [PMID: 33436625 PMCID: PMC7804931 DOI: 10.1038/s41467-020-20575-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding how biological species arise is critical for understanding the evolution of life on Earth. Bioinformatic analyses have recently revealed that viruses, like multicellular life, form reproductively isolated biological species. Viruses are known to share high rates of genetic exchange, so how do they evolve genetic isolation? Here, we evaluate two related bacteriophages and describe three factors that limit genetic exchange between them: 1) A nucleus-like compartment that physically separates replicating phage genomes, thereby limiting inter-phage recombination during co-infection; 2) A tubulin-based spindle that orchestrates phage replication and forms nonfunctional hybrid polymers; and 3) A nuclear incompatibility factor that reduces phage fitness. Together, these traits maintain species differences through Subcellular Genetic Isolation where viral genomes are physically separated during co-infection, and Virogenesis Incompatibility in which the interaction of cross-species components interferes with viral production. Virus speciation cannot be fully explained by the evolution of different host specificities. Here, Chaikeeratisak et al. identify ways viruses can remain genetically isolated despite co-infecting the same cell, providing insight into how new virus species evolve.
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35
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Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci U S A 2020; 117:30554-30565. [PMID: 33199636 DOI: 10.1073/pnas.2015987117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Numerous studies of emerging species have identified genomic "islands" of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward "speciation genes" that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation.
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36
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Hill T, Unckless RL. Recurrent evolution of high virulence in isolated populations of a DNA virus. eLife 2020; 9:e58931. [PMID: 33112738 PMCID: PMC7685711 DOI: 10.7554/elife.58931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/28/2020] [Indexed: 12/30/2022] Open
Abstract
Hosts and viruses are constantly evolving in response to each other: as a host attempts to suppress a virus, the virus attempts to evade and suppress the host's immune system. Here, we describe the recurrent evolution of a virulent strain of a DNA virus, which infects multiple Drosophila species. Specifically, we identified two distinct viral types that differ 100-fold in viral titer in infected individuals, with similar differences observed in multiple species. Our analysis suggests that one of the viral types recurrently evolved at least four times in the past ~30,000 years, three times in Arizona and once in another geographically distinct species. This recurrent evolution may be facilitated by an effective mutation rate which increases as each prior mutation increases viral titer and effective population size. The higher titer viral type suppresses the host-immune system and an increased virulence compared to the low viral titer type.
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Affiliation(s)
- Tom Hill
- The Department of Molecular Biosciences, University of KansasLawrenceUnited States
| | - Robert L Unckless
- The Department of Molecular Biosciences, University of KansasLawrenceUnited States
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37
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Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L. The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages. Cell Host Microbe 2020; 28:390-401.e5. [DOI: 10.1016/j.chom.2020.06.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/30/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
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38
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Wang X, He Z, Shi S, Wu CI. Genes and speciation: is it time to abandon the biological species concept? Natl Sci Rev 2020; 7:1387-1397. [PMID: 34692166 PMCID: PMC8288927 DOI: 10.1093/nsr/nwz220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/31/2019] [Indexed: 01/04/2023] Open
Abstract
The biological species concept (BSC) is the cornerstone of neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, as gene flow during speciation is increasingly being reported in a substantial literature, it seems time to reassess the revered, but often doubted, BSC. Contrary to the common perception, BSC should expect substantial gene flow at the onset of speciation, not least because geographical isolation develops gradually. Although BSC does not stipulate how speciation begins, it does require a sustained period of isolation for speciation to complete its course. Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion. Importantly, recent genomic analyses cannot reject this more realistic version of BSC, although future analyses may still prove it wrong. The ultimate acceptance or rejection of BSC is not merely about a historical debate; rather, it is about the fundamental nature of species - are species (and, hence, divergent adaptations) driven by a relatively small number of genes, or by thousands of them? Many levels of biology, ranging from taxonomy to biodiversity, depend on this resolution.
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Affiliation(s)
- Xinfeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
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39
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Mangalea MR, Duerkop BA. Fitness Trade-Offs Resulting from Bacteriophage Resistance Potentiate Synergistic Antibacterial Strategies. Infect Immun 2020; 88:e00926-19. [PMID: 32094257 PMCID: PMC7309606 DOI: 10.1128/iai.00926-19] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacteria that cause life-threatening infections in humans are becoming increasingly difficult to treat. In some instances, this is due to intrinsic and acquired antibiotic resistance, indicating that new therapeutic approaches are needed to combat bacterial pathogens. There is renewed interest in utilizing viruses of bacteria known as bacteriophages (phages) as potential antibacterial therapeutics. However, critics suggest that similar to antibiotics, the development of phage-resistant bacteria will halt clinical phage therapy. Although the emergence of phage-resistant bacteria is likely inevitable, there is a growing body of literature showing that phage selective pressure promotes mutations in bacteria that allow them to subvert phage infection, but with a cost to their fitness. Such fitness trade-offs include reduced virulence, resensitization to antibiotics, and colonization defects. Resistance to phage nucleic acid entry, primarily via cell surface modifications, compromises bacterial fitness during antibiotic and host immune system pressure. In this minireview, we explore the mechanisms behind phage resistance in bacterial pathogens and the physiological consequences of acquiring phage resistance phenotypes. With this knowledge, it may be possible to use phages to alter bacterial populations, making them more tractable to current therapeutic strategies.
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Affiliation(s)
- Mihnea R Mangalea
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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40
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Sympatric speciation of wild emmer wheat driven by ecology and chromosomal rearrangements. Proc Natl Acad Sci U S A 2020; 117:5955-5963. [PMID: 32123089 DOI: 10.1073/pnas.1920415117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In plants, the mechanism for ecological sympatric speciation (SS) is little known. Here, after ruling out the possibility of secondary contact, we show that wild emmer wheat, at the microclimatically divergent microsite of "Evolution Canyon" (EC), Mt. Carmel, Israel, underwent triple SS. Initially, it split following a bottleneck of an ancestral population, and further diversified to three isolated populations driven by disruptive ecological selection. Remarkably, two postzygotically isolated populations (SFS1 and SFS2) sympatrically branched within an area less than 30 m at the tropical hot and dry savannoid south-facing slope (SFS). A series of homozygous chromosomal rearrangements in the SFS1 population caused hybrid sterility with the SFS2 population. We demonstrate that these two populations developed divergent adaptive mechanisms against severe abiotic stresses on the tropical SFS. The SFS2 population evolved very early flowering, while the SFS1 population alternatively evolved a direct tolerance to irradiance by improved ROS scavenging activity that potentially accounts for its evolutionary fate with unstable chromosome status. Moreover, a third prezygotically isolated sympatric population adapted on the abutting temperate, humid, cool, and forested north-facing slope (NFS), separated by 250 m from the SFS wild emmer wheat populations. The NFS population evolved multiple resistant loci to fungal diseases, including powdery mildew and stripe rust. Our study illustrates how plants sympatrically adapt and speciate under disruptive ecological selection of abiotic and biotic stresses.
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41
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A continuous evolution system for contracting the host range of bacteriophage T7. Sci Rep 2020; 10:307. [PMID: 31941920 PMCID: PMC6962156 DOI: 10.1038/s41598-019-57221-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage T7 is an intracellular parasite that recognizes its host via its tail and tail fiber proteins, known as receptor-binding proteins (RBPs). The RBPs attach to specific lipopolysaccharide (LPS) features on the host. Various studies have shown expansion of the phage’s host range via mutations in the genes encoding the RBPs, whereas only a few have shown contraction of its host range. Furthermore, most experimental systems have not monitored the alteration of host range in the presence of several hosts simultaneously. Here we show that T7 phage grown in the presence of five restrictive strains and one permissive host, each with a different LPS form, gradually avoids recognition of the restrictive strains. Remarkably, avoidance of the restrictive strains was repeated in different experiments using six different permissive hosts. The evolved phages carried mutations that changed their specificity, as determined by sequencing of the genes encoding the RBPs. This system demonstrates a major role for RBPs in narrowing the range of futile infections. The system can be harnessed for host-range contraction in applications such as detection or elimination of a specific bacterial serotype by bacteriophages.
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Gupta A, Soto AN, Medina SJ, Petrie KL, Meyer JR. Bacteriophage lambda overcomes a perturbation in its host-viral genetic network through mutualism and evolution of life history traits. Evolution 2020; 74:764-774. [PMID: 31891185 DOI: 10.1111/evo.13920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/19/2019] [Accepted: 12/26/2019] [Indexed: 11/27/2022]
Abstract
An important driver of evolution in viruses is natural selection to optimize the use of their hosts' genetic network. To learn how viruses respond to this pressure, we disrupted the genetic network of Escherichia coli to inhibit replication of its virus, bacteriophage lambda, and then observed how λ evolved to compensate. We deleted E. coli's dnaJ gene, which lambda uses to initiate DNA replication. Lambda partially restored its ability to reproduce with just two adaptive mutations associated with genes J and S. The location of the mutations was unexpected because they were not in genes that directly interact with DnaJ, rather they affected seemingly unrelated life history traits. A nonsynonymous J mutation increased lambda's adsorption rate and an S regulatory mutation delayed lysis timing. Lambda also recovered some of its reproductive potential through intracellular mutualism. This study offers two important lessons: first, viruses can rapidly adapt to disruptive changes in their host's genetic network. Second, organisms can employ mechanisms thought to operate at the population scale, such as evolution of life history traits and social interactions, in order to overcome hurdles at the molecular level. As life science research progresses and new fields become increasingly specialized, these results remind us of the importance of multiscale and interdisciplinary approaches to understand adaptation.
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Affiliation(s)
- Animesh Gupta
- Division of Physics, University of California San Diego, La Jolla, California
| | - Anechelle N Soto
- Division of Biological Science, University of California San Diego, La Jolla, California
| | - Sarah J Medina
- Division of Physics, University of California San Diego, La Jolla, California
| | - Katherine L Petrie
- Division of Physics, University of California San Diego, La Jolla, California.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Justin R Meyer
- Division of Physics, University of California San Diego, La Jolla, California
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43
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Vasconcelos P, Rueffler C. How Does Joint Evolution of Consumer Traits Affect Resource Specialization? Am Nat 2019; 195:331-348. [PMID: 32017627 DOI: 10.1086/706813] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Consumers regularly experience trade-offs in their ability to find, handle, and digest different resources. Evolutionary ecologists recognized the significance of this observation for the evolution and maintenance of biological diversity long ago and continue to elaborate on the conditions under which to expect one or several specialists, generalists, or combinations thereof. Existing theory based on a single evolving trait predicts that specialization requires strong trade-offs such that generalists perform relatively poorly, while weak trade-offs favor a single generalist. Here, we show that this simple dichotomy does not hold true under joint evolution of two or more foraging traits. In this case, the boundary between trade-offs resulting in resource specialists and resource generalists is shifted toward weaker trade-off curvatures. In particular, weak trade-offs can result in evolutionary branching, leading to the evolution of two coexisting resource specialists, while the evolution of a single resource generalist requires particularly weak trade-offs. These findings are explained by performance benefits due to epistatic trait interactions enjoyed by phenotypes that are specialized in more than one trait for the same resource.
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Card KJ, LaBar T, Gomez JB, Lenski RE. Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection. PLoS Biol 2019; 17:e3000397. [PMID: 31644535 PMCID: PMC6827916 DOI: 10.1371/journal.pbio.3000397] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/04/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022] Open
Abstract
Populations often encounter changed environments that remove selection for the maintenance of particular phenotypic traits. The resulting genetic decay of those traits under relaxed selection reduces an organism's fitness in its prior environment. However, whether and how such decay alters the subsequent evolvability of a population upon restoration of selection for a previously diminished trait is not well understood. We addressed this question using Escherichia coli strains from the long-term evolution experiment (LTEE) that independently evolved for multiple decades in the absence of antibiotics. We first confirmed that these derived strains are typically more sensitive to various antibiotics than their common ancestor. We then subjected the ancestral and derived strains to various concentrations of these drugs to examine their potential to evolve increased resistance. We found that evolvability was idiosyncratic with respect to initial genotype; that is, the derived strains did not generally compensate for their greater susceptibility by "catching up" to the resistance level of the ancestor. Instead, the capacity to evolve increased resistance was constrained in some backgrounds, implying that evolvability depended upon prior mutations in a historically contingent fashion. We further subjected a time series of clones from one LTEE population to tetracycline and determined that an evolutionary constraint arose early in that population, corroborating the role of contingency. In summary, relaxed selection not only can drive populations to increased antibiotic susceptibility, but it can also affect the subsequent evolvability of antibiotic resistance in an unpredictable manner. This conclusion has potential implications for public health, and it underscores the need to consider the genetic context of pathogens when designing drug-treatment strategies.
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Affiliation(s)
- Kyle J. Card
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - Thomas LaBar
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jasper B. Gomez
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Biomedical Laboratory Diagnostics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Richard E. Lenski
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
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45
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Dissecting Trait Variation across Species Barriers. Trends Ecol Evol 2019; 34:1131-1136. [PMID: 31443904 DOI: 10.1016/j.tree.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022]
Abstract
Dissecting the basis of naturally occurring trait variation is one of the central goals of modern genetics. For eukaryotes, classic methods for this purpose rely on screens of recombinants from matings between distinct parents. These tools cannot be used in studies of species that cannot mate to form recombinant progeny in the first place. However, new approaches are coming online to shuffle the genomes of otherwise incompatible species. With them, geneticists can elucidate how evolution built a new trait, even if it happened millions of years ago, in a lineage that is now reproductively cutoff from its closest relatives.
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McDonald MJ. Microbial Experimental Evolution - a proving ground for evolutionary theory and a tool for discovery. EMBO Rep 2019; 20:e46992. [PMID: 31338963 PMCID: PMC6680118 DOI: 10.15252/embr.201846992] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/23/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life sciences, microbial experimental evolution has become a tool, deployed as part of the suite of techniques available to the molecular biologist. Here, I provide a review of the general findings of microbial experimental evolution, especially those relevant to molecular microbiologists that are new to the field. I also relate these results to design considerations for an evolution experiment and suggest future directions for those working at the intersection of experimental evolution and molecular biology.
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Forsdyke DR. Success of alignment-free oligonucleotide (k-mer) analysis confirms relative importance of genomes not genes in speciation and phylogeny. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many 21st century practitioners. A path from the 19th century recognition of the informational basis of heredity to the modern era can be discerned. Crick’s DNA ‘unpairing postulate’ predicted that recombinational pairing of homologous DNAs during meiosis would be mediated by short k-mers in the loops of stem-loop structures extruded from classical duplex helices. The complementary ‘kissing’ duplex loops – like tRNA anticodon–codon k-mer duplexes – would seed a more extensive pairing that would then extend until limited by lack of homology or other factors. Indeed, this became the principle behind alignment-based methods that assessed similarity by degree of DNA–DNA reassociation in vitro. These are now seen as less sensitive than alignment-free methods that are closely consistent, both theoretically and mechanistically, with chromosomal anti-recombination models for the initiation of divergence into new species. The analytical power of k-mer differences supports the theses that evolutionary advance sometimes serves the needs of nucleic acids (genomes) rather than proteins (genes), and that such differences can play a role in early speciation events.
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Affiliation(s)
- Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
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48
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Villa SM, Altuna JC, Ruff JS, Beach AB, Mulvey LI, Poole EJ, Campbell HE, Johnson KP, Shapiro MD, Bush SE, Clayton DH. Rapid experimental evolution of reproductive isolation from a single natural population. Proc Natl Acad Sci U S A 2019; 116:13440-13445. [PMID: 31182608 PMCID: PMC6613143 DOI: 10.1073/pnas.1901247116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ecological speciation occurs when local adaptation generates reproductive isolation as a by-product of natural selection. Although ecological speciation is a fundamental source of diversification, the mechanistic link between natural selection and reproductive isolation remains poorly understood, especially in natural populations. Here, we show that experimental evolution of parasite body size over 4 y (approximately 60 generations) leads to reproductive isolation in natural populations of feather lice on birds. When lice are transferred to pigeons of different sizes, they rapidly evolve differences in body size that are correlated with host size. These differences in size trigger mechanical mating isolation between lice that are locally adapted to the different sized hosts. Size differences among lice also influence the outcome of competition between males for access to females. Thus, body size directly mediates reproductive isolation through its influence on both intersexual compatibility and intrasexual competition. Our results confirm that divergent natural selection acting on a single phenotypic trait can cause reproductive isolation to emerge from a single natural population in real time.
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Affiliation(s)
- Scott M Villa
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112;
| | - Juan C Altuna
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - James S Ruff
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Andrew B Beach
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Lane I Mulvey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Erik J Poole
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Heidi E Campbell
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
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49
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Saxenhofer M, Schmidt S, Ulrich RG, Heckel G. Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus. PLoS Biol 2019; 17:e3000142. [PMID: 30785873 PMCID: PMC6382107 DOI: 10.1371/journal.pbio.3000142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5' region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| | - Sabrina Schmidt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
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50
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Maxwell CS. Hypothesis: a Plastically Produced Phenotype Predicts Host Specialization and Can Precede Subsequent Mutations in Bacteriophage. mBio 2018; 9:e00765-18. [PMID: 30425142 PMCID: PMC6234872 DOI: 10.1128/mbio.00765-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/04/2018] [Indexed: 01/24/2023] Open
Abstract
The role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host range in the presence of R-M systems. The model makes two main predictions. The first prediction is that the offspring of the first phage to gain a new methylation pattern by infecting a new host make up a disproportionate fraction of the subsequent specialist population, indicating that the plastically produced phenotype is highly predictive of evolutionary outcome. The second prediction is that the first phage to gain this pattern is not always genetically distinct from other phages in the population. Taken together, these results suggest that plasticity could play a causal role on par with mutation during the evolution of phage host range. This uniquely tractable system could enable the first direct test of "plasticity first" evolution.
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Affiliation(s)
- Colin S Maxwell
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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