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Moubset O, Filloux D, Fontes H, Julian C, Fernandez E, Galzi S, Blondin L, Chehida SB, Lett JM, Mesléard F, Kraberger S, Custer JM, Salywon A, Makings E, Marais A, Chiroleu F, Lefeuvre P, Martin DP, Candresse T, Varsani A, Ravigné V, Roumagnac P. Virome release of an invasive exotic plant species in southern France. Virus Evol 2024; 10:veae025. [PMID: 38566975 PMCID: PMC10986800 DOI: 10.1093/ve/veae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.
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Affiliation(s)
- Oumaima Moubset
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Hugo Fontes
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Charlotte Julian
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Serge Galzi
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Laurence Blondin
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | | | | | - François Mesléard
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Salywon
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA
| | - Elizabeth Makings
- Vascular Plant Herbarium, School of Life Sciences, Arizona State University, 734 West Alameda Drive, Tempe Tempe, AZ 85282, USA
| | - Armelle Marais
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | | | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Cape Town 7925, South Africa
| | - Thierry Candresse
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7700, South Africa
| | - Virginie Ravigné
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
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2
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Harman RR, Kim TN. Differentiating spillover: an examination of cross-habitat movement in ecology spillover in ecology. Proc Biol Sci 2024; 291:20232707. [PMID: 38351801 PMCID: PMC10865012 DOI: 10.1098/rspb.2023.2707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Organisms that immigrate into a recipient habitat generate a movement pattern that affects local population dynamics and the environment. Spillover is the pattern of unidirectional movement from a donor habitat to a different, adjacent recipient habitat. However, ecological definitions are often generalized to include any cross-habitat movement, which limits within- and cross-discipline collaboration. To assess spillover nomenclature, we reviewed 337 studies within the agriculture, disease, fisheries and habitat fragmentation disciplines. Each study's definition of spillover and the methods used were analysed. We identified four descriptors (movement, habitat type and arrangement, and effect) used that differentiate spillover from other cross-habitat movement patterns (dispersal, foray loops and edge movement). Studies often define spillover as movement (45%) but rarely measure it as such (4%), particularly in disease and habitat fragmentation disciplines. Consequently, 98% of studies could not distinguish linear from returning movement out of a donor habitat, which can overestimate movement distance. Overall, few studies (12%) included methods that matched their own definition, revealing a distinct mismatch. Because theory shows that long-term impacts of the different movement patterns can vary, differentiating spillover from other movement patterns is necessary for effective long-term and inter-disciplinary management of organisms that use heterogeneous landscapes.
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Affiliation(s)
- Rachel R. Harman
- Department of Entomology, Kansas State University, 123 W. Waters Hall, Manhattan, KS 66506, USA
| | - Tania N. Kim
- Department of Entomology, Kansas State University, 123 W. Waters Hall, Manhattan, KS 66506, USA
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3
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Blackwood PE, Jonasen KL, Hoenig BD, Heil BN, Searle CL. Epidemics in native species influence the outcome of a species invasion. Oecologia 2024; 204:327-337. [PMID: 37620681 DOI: 10.1007/s00442-023-05444-4] [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: 09/28/2022] [Accepted: 08/08/2023] [Indexed: 08/26/2023]
Abstract
Invasive species can have large effects on native communities. When native and invasive species share parasites, an epidemic in a native species could facilitate or inhibit the invasion. We sought to understand how the incidence and timing of epidemics in native species caused by a generalist parasite influenced the success and impact of an invasive species. We focused on North American native and invasive species of zooplankton (Daphnia dentifera and Daphnia lumholtzi, respectively), that can both become infected with a fungal parasite (Metschnikowia bicuspidata). In a laboratory microcosm experiment, we exposed the native species to varying parasite inocula (none, low, high) and two invasive species introduction times (before or during an epidemic in the native species). We found that the invasive species density in treatments with the parasite was higher compared to uninfected treatments, though only the early invasion, low-parasite and uninfected treatments exhibited significant pairwise differences. However, invasive resting eggs were only found in the uninfected treatments. The density of the native species was lowest with a combination of the parasite present, and the invasive species introduced during the epidemic. Native infection prevalence in these treatments (late invasion, parasite present) was also higher than prevalence in treatments where the invasive species was introduced before the epidemic. Therefore, the timing of an invasion relative to an epidemic can affect both the native and invasive species. Our results suggest that the occurrence and timing of epidemics in native species can influence the impacts of a species invasion.
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Affiliation(s)
- Paradyse E Blackwood
- Department of Biological Sciences, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47907, USA.
| | - Kacie L Jonasen
- Department of Biological Sciences, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47907, USA
| | - Brandon D Hoenig
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Pymatuning Laboratory of Ecology, Linesville, PA, 16424, USA
| | - Brittany N Heil
- Department of Biological Sciences, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47907, USA
- Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN, 47907, USA
| | - Catherine L Searle
- Department of Biological Sciences, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47907, USA
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Fetters AM, Ashman TL. The pollen virome: A review of pollen-associated viruses and consequences for plants and their interactions with pollinators. AMERICAN JOURNAL OF BOTANY 2023:e16144. [PMID: 36924316 DOI: 10.1002/ajb2.16144] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 06/18/2023]
Abstract
The movement of pollen grains from anthers to stigmas, often by insect pollinator vectors, is essential for plant reproduction. However, pollen is also a unique vehicle for viral spread. Pollen-associated plant viruses reside on the outside or inside of pollen grains, infect susceptible individuals through vertical or horizontal infection pathways, and can decrease plant fitness. These viruses are transferred with pollen between plants by pollinator vectors as they forage for floral resources; thus, pollen-associated viral spread is mediated by floral and pollen grain phenotypes and pollinator traits, much like pollination. Most of what is currently known about pollen-associated viruses was discovered through infection and transmission experiments in controlled settings, usually involving one virus and one plant species of agricultural or horticultural interest. In this review, we first provide an updated, comprehensive list of the recognized pollen-associated viruses. Then, we summarize virus, plant, pollinator vector, and landscape traits that can affect pollen-associated virus transmission, infection, and distribution. Next, we highlight the consequences of plant-pollinator-virus interactions that emerge in complex communities of co-flowering plants and pollinator vectors, such as pollen-associated virus spread between plant species and viral jumps from plant to pollinator hosts. We conclude by emphasizing the need for collaborative research that bridges pollen biology, virology, and pollination biology.
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Affiliation(s)
- Andrea M Fetters
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
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Dobelmann J, Felden A, Lester PJ. An invasive ant increases deformed wing virus loads in honey bees. Biol Lett 2023; 19:20220416. [PMID: 36651030 PMCID: PMC9845979 DOI: 10.1098/rsbl.2022.0416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The majority of invasive species are best known for their effects as predators. However, many introduced predators may also be substantial reservoirs for pathogens. Honey bee-associated viruses are found in various arthropod species including invasive ants. We examined how the globally invasive Argentine ant (Linepithema humile), which can reach high densities and infest beehives, is associated with pathogen dynamics in honey bees. Viral loads of deformed wing virus (DWV), which has been linked to millions of beehive deaths around the globe, and black queen cell virus significantly increased in bees when invasive ants were present. Microsporidian and trypanosomatid infections, which are more bee-specific, were not affected by ant invasion. The bee virome in autumn revealed that DWV was the predominant virus with the highest infection levels and that no ant-associated viruses were infecting bees. Viral spillback from ants could increase infections in bees. In addition, ant attacks could pose a significant stressor to bee colonies that may affect virus susceptibility. These viral dynamics are a hidden effect of ant pests, which could have a significant impact on disease emergence in this economically important pollinator. Our study highlights a perhaps overlooked effect of species invasions: changes in pathogen dynamics.
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Affiliation(s)
- Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand,Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm 89081, Germany
| | - Antoine Felden
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Philip J. Lester
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
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6
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The dynamics of disease mediated invasions by hosts with immune reproductive tradeoff. Sci Rep 2022; 12:4108. [PMID: 35260702 PMCID: PMC8904827 DOI: 10.1038/s41598-022-07962-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/25/2022] [Indexed: 01/01/2023] Open
Abstract
The modern world involves both increasingly frequent introduction of novel invasive animals into new habitat ranges and novel epidemic-causing pathogens into new host populations. Both of these phenomena have been well studied. Less well explored, however, is how the success of species invasions may themselves be affected by the pathogens they bring with them. In this paper, we construct a simple, modified Susceptible-Infected-Recovered model for a vector-borne pathogen affecting two annually reproducing hosts. We consider an invasion scenario in which a susceptible native host species is invaded by a disease-resistant species carrying a vector-borne infection. We assume the presence of abundant, but previously disease-free, competent vectors. We find that the success of invasion is critically sensitive to the infectivity of the pathogen. The more the pathogen is able to spread, the more fit the invasive host is in competition with the more vulnerable native species; the pathogen acts as a ‘wingman pathogen,’ enhancing the probability of invader establishment. While not surprising, we provide a quantitative predictive framework for the long-term outcomes from these important coupled dynamics in a world in which compound invasions of hosts and pathogens are increasingly likely.
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Fetters AM, Cantalupo PG, Wei N, Robles MTS, Stanley A, Stephens JD, Pipas JM, Ashman TL. The pollen virome of wild plants and its association with variation in floral traits and land use. Nat Commun 2022; 13:523. [PMID: 35082293 PMCID: PMC8791949 DOI: 10.1038/s41467-022-28143-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/03/2022] [Indexed: 12/18/2022] Open
Abstract
Pollen is a unique vehicle for viral spread. Pollen-associated viruses hitchhike on or within pollen grains and are transported to other plants by pollinators. They are deposited on flowers and have a direct pathway into the plant and next generation via seeds. To discover the diversity of pollen-associated viruses and identify contributing landscape and floral features, we perform a species-level metagenomic survey of pollen from wild, visually asymptomatic plants, located in one of four regions in the United States of America varying in land use. We identify many known and novel pollen-associated viruses, half belonging to the Bromoviridae, Partitiviridae, and Secoviridae viral families, but many families are represented. Across the regions, species harbor more viruses when surrounded by less natural and more human-modified environments than the reverse, but we note that other region-level differences may also covary with this. When examining the novel connection between virus richness and floral traits, we find that species with multiple, bilaterally symmetric flowers and smaller, spikier pollen harbored more viruses than those with opposite traits. The association of viral diversity with floral traits highlights the need to incorporate plant-pollinator interactions as a driver of pollen-associated virus transport into the study of plant-viral interactions.
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Affiliation(s)
- Andrea M Fetters
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA.
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA.
| | - Paul G Cantalupo
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Boulevard, Pittsburgh, PA, 15206, USA
| | - Na Wei
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
- The Holden Arboretum, 9500 Sperry Road, Kirtland, OH, 44094, USA
| | - Maria Teresa Sáenz Robles
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Amber Stanley
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Jessica D Stephens
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
- Department of Biology, Westfield State University, 577 Western Avenue, Westfield, MA, 01086, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA.
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Bai CM, Rosani U, Zhang X, Xin LS, Bortoletto E, Wegner KM, Wang CM. Viral Decoys: The Only Two Herpesviruses Infecting Invertebrates Evolved Different Transcriptional Strategies to Deflect Post-Transcriptional Editing. Viruses 2021; 13:v13101971. [PMID: 34696401 PMCID: PMC8537636 DOI: 10.3390/v13101971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
The highly versatile group of Herpesviruses cause disease in a wide range of hosts. In invertebrates, only two herpesviruses are known: the malacoherpesviruses HaHV-1 and OsHV-1 infecting gastropods and bivalves, respectively. To understand viral transcript architecture and diversity we first reconstructed full-length viral genomes of HaHV-1 infecting Haliotis diversicolor supertexta and OsHV-1 infecting Scapharca broughtonii by DNA-seq. We then used RNA-seq over the time-course of experimental infections to establish viral transcriptional dynamics, followed by PacBio long-read sequencing of full-length transcripts to untangle viral transcript architectures at two selected time points. Despite similarities in genome structure, in the number of genes and in the diverse transcriptomic architectures, we measured a ten-fold higher transcript variability in HaHV-1, with more extended antisense gene transcription. Transcriptional dynamics also appeared different, both in timing and expression trends. Both viruses were heavily affected by post-transcriptional modifications performed by ADAR1 affecting sense-antisense gene pairs forming dsRNAs. However, OsHV-1 concentrated these modifications in a few genomic hotspots, whereas HaHV-1 diluted ADAR1 impact by elongated and polycistronic transcripts distributed over its whole genome. These transcriptional strategies might thus provide alternative potential roles for sense-antisense transcription in viral transcriptomes to evade the host's immune response in different virus-host combinations.
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Affiliation(s)
- Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Umberto Rosani
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Warden Sea Station, 25992 List auf Sylt, Germany; (U.R.); (K.M.W.)
- Department of Biology, University of Padova, 35121 Padova, Italy;
| | - Xiang Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- College of Fisheries, Tianjin Agricultural University, Tianjin 300380, China
| | - Lu-Sheng Xin
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | | | - K. Mathias Wegner
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Warden Sea Station, 25992 List auf Sylt, Germany; (U.R.); (K.M.W.)
| | - Chong-Ming Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence:
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Blossey B, Nuzzo V, Dávalos A, Mayer M, Dunbar R, Landis DA, Evans JA, Minter B. Residence time determines invasiveness and performance of garlic mustard (Alliaria petiolata) in North America. Ecol Lett 2021; 24:327-336. [PMID: 33295700 PMCID: PMC7839695 DOI: 10.1111/ele.13649] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 11/28/2022]
Abstract
While biological invasions have the potential for large negative impacts on local communities and ecological interactions, increasing evidence suggests that species once considered major problems can decline over time. Declines often appear driven by natural enemies, diseases or evolutionary adaptations that selectively reduce populations of naturalised species and their impacts. Using permanent long-term monitoring locations, we document declines of Alliaria petiolata (garlic mustard) in eastern North America with distinct local and regional dynamics as a function of patch residence time. Projected site-specific population growth rates initially indicated expanding populations, but projected population growth rates significantly decreased over time and at the majority of sites fell below 1, indicating declining populations. Negative soil feedback provides a potential mechanism for the reported disappearance of ecological dominance of A. petiolata in eastern North America.
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Affiliation(s)
- Bernd Blossey
- Department of Natural ResourcesFernow HallCornell UniversityIthacaNY14853USA
| | - Victoria Nuzzo
- Natural Area Consultants1 West Hill School RoadRichfordNY13835USA
| | - Andrea Dávalos
- Biological Sciences DepartmentSUNY CortlandCortlandNY13045USA
| | - Mark Mayer
- New Jersey Department of AgricultureDivision of Plant IndustryPO Box 330TrentonNJ08625USA
| | - Richard Dunbar
- Division of Nature PreservesIndiana Department of Natural Resources1040 E 700 N Columbia CityIN46725‐8948USA
| | - Douglas A. Landis
- Department of EntomologyMichigan State UniversityEast LansingMI48824USA
| | - Jeffrey A. Evans
- Department of EntomologyMichigan State UniversityEast LansingMI48824USA
- Farmscape Analytics16 Merrimack StConcordNH03301USA
| | - Bill Minter
- Institute for Ecological RegenerationGoshen College1700 South Main StreetGoshenIN46526USA
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10
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Disease Pandemics and Major Epidemics Arising from New Encounters between Indigenous Viruses and Introduced Crops. Viruses 2020; 12:v12121388. [PMID: 33291635 PMCID: PMC7761969 DOI: 10.3390/v12121388] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/13/2023] Open
Abstract
Virus disease pandemics and epidemics that occur in the world’s staple food crops pose a major threat to global food security, especially in developing countries with tropical or subtropical climates. Moreover, this threat is escalating rapidly due to increasing difficulties in controlling virus diseases as climate change accelerates and the need to feed the burgeoning global population escalates. One of the main causes of these pandemics and epidemics is the introduction to a new continent of food crops domesticated elsewhere, and their subsequent invasion by damaging virus diseases they never encountered before. This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops. This spillover requires new encounters at the managed and natural vegetation interface. The principal virus disease pandemic examples described are two (cassava mosaic, cassava brown streak) that threaten food security in sub-Saharan Africa (SSA), and one (tomato yellow leaf curl) doing so globally. A further example describes a virus disease pandemic threatening a major plantation crop producing a vital food export for West Africa (cacao swollen shoot). Also described are two examples of major virus disease epidemics that threaten SSA’s food security (rice yellow mottle, groundnut rosette). In addition, brief accounts are provided of two major maize virus disease epidemics (maize streak in SSA, maize rough dwarf in Mediterranean and Middle Eastern regions), a major rice disease epidemic (rice hoja blanca in the Americas), and damaging tomato tospovirus and begomovirus disease epidemics of tomato that impair food security in different world regions. For each pandemic or major epidemic, the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution, are explained. Finally, clarification is provided over what needs to be done globally to achieve effective management of severe virus disease pandemics and epidemics initiated by spillover events.
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12
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Dobelmann J, Felden A, Lester PJ. Genetic Strain Diversity of Multi-Host RNA Viruses that Infect a Wide Range of Pollinators and Associates is Shaped by Geographic Origins. Viruses 2020; 12:E358. [PMID: 32213950 PMCID: PMC7150836 DOI: 10.3390/v12030358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 01/29/2023] Open
Abstract
Emerging viruses have caused concerns about pollinator population declines, as multi-host RNA viruses may pose a health threat to pollinators and associated arthropods. In order to understand the ecology and impact these viruses have, we studied their host range and determined to what extent host and spatial variation affect strain diversity. Firstly, we used RT-PCR to screen pollinators and associates, including honey bees (Apis mellifera) and invasive Argentine ants (Linepithema humile), for virus presence and replication. We tested for the black queen cell virus (BQCV), deformed wing virus (DWV), and Kashmir bee virus (KBV) that were initially detected in bees, and the two recently discovered Linepithema humile bunya-like virus 1 (LhuBLV1) and Moku virus (MKV). DWV, KBV, and MKV were detected and replicated in a wide range of hosts and commonly co-infected hymenopterans. Secondly, we placed KBV and DWV in a global phylogeny with sequences from various countries and hosts to determine the association of geographic origin and host with shared ancestry. Both phylogenies showed strong geographic rather than host-specific clustering, suggesting frequent inter-species virus transmission. Transmission routes between hosts are largely unknown. Nonetheless, avoiding the introduction of non-native species and diseased pollinators appears important to limit spill overs and disease emergence.
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Affiliation(s)
- Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; (A.F.); (P.J.L.)
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13
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Bloch CP, Curry KD, Fisher-Reid MC, Surasinghe TD. Population Decline of the Invasive Asian Shore Crab (Hemigrapsus sanguineus) and Dynamics of Associated Intertidal Invertebrates on Cape Cod, Massachusetts. Northeast Nat (Steuben) 2019. [DOI: 10.1656/045.026.0408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Christopher P. Bloch
- Department of Biological Sciences, Bridgewater State University, Bridgewater, MA 02325
| | - Kevin D. Curry
- Department of Biological Sciences, Bridgewater State University, Bridgewater, MA 02325
| | | | - Thilina D. Surasinghe
- Department of Biological Sciences, Bridgewater State University, Bridgewater, MA 02325
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14
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Lefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A. Evolution and ecology of plant viruses. Nat Rev Microbiol 2019; 17:632-644. [PMID: 31312033 DOI: 10.1038/s41579-019-0232-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2019] [Indexed: 02/07/2023]
Abstract
The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.
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Affiliation(s)
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Paterna, València, Spain.,The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Philippe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA. .,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
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15
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Abstract
Viral diseases provide a major challenge to twenty-first century agriculture worldwide. Climate change and human population pressures are driving rapid alterations in agricultural practices and cropping systems that favor destructive viral disease outbreaks. Such outbreaks are strikingly apparent in subsistence agriculture in food-insecure regions. Agricultural globalization and international trade are spreading viruses and their vectors to new geographical regions with unexpected consequences for food production and natural ecosystems. Due to the varying epidemiological characteristics of diverent viral pathosystems, there is no one-size-fits-all approach toward mitigating negative viral disease impacts on diverse agroecological production systems. Advances in scientific understanding of virus pathosystems, rapid technological innovation, innovative communication strategies, and global scientific networks provide opportunities to build epidemiologic intelligence of virus threats to crop production and global food security. A paradigm shift toward deploying integrated, smart, and eco-friendly strategies is required to advance virus disease management in diverse agricultural cropping systems.
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Affiliation(s)
- Roger A C Jones
- Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia; .,Department of Primary Industries and Regional Development, South Perth, Western Australia 6151, Australia
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350, USA;
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16
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Broadley HJ, Kula RR, Boettner GH, Andersen JC, Griffin BP, Elkinton JS. Recruitment of native parasitic wasps to populations of the invasive winter moth in the northeastern United States. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02019-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Wang RL, Zhu-Salzman K, Elzaki MEA, Huang QQ, Chen S, Ma ZH, Liu SW, Zhang JE. Mikania Micrantha Wilt Virus Alters Insect Vector's Host Preference to Enhance Its Own Spread. Viruses 2019; 11:E336. [PMID: 30970658 PMCID: PMC6521231 DOI: 10.3390/v11040336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 01/29/2023] Open
Abstract
As an invasive weed, Mikaniamicrantha Kunth has caused serious damage to natural forest ecosystems in South China in recent years. Mikania micrantha wilt virus (MMWV), an isolate of the Gentian mosaic virus (GeMV), is transmitted by Myzuspersicae (Sulzer) in a non-persistent manner and can effectively inhibit the growth of M. micrantha. To explore the MMWV-M. micrantha-M. persicae interaction and its impact on the invasion of M. micrantha, volatile compounds (VOCs) emitted from healthy, mock-inoculated, and MMWV-infected plants were collected, and effects on host preference of the apterous and alate aphids were assessed with Y-shaped olfactometers. Gas chromatography-mass spectrometry (GC-MS) analysis indicated that MMWV infection changed the VOC profiles, rendering plants more attractive to aphids. Clip-cages were used to document the population growth rate of M.persicae fed on healthy, mock-inoculated, or MMWV-infected plants. Compared to those reared on healthy plants, the population growth of M. persicae drastically decreased on the MMWV-infected plants. Plant host choice tests based on visual and contact cues were also conducted using alate M.persicae. Interestingly, the initial attractiveness of MMWV-infected plants diminished, and more alate M. persicae moved to healthy plants. Taken together, MMWV appeared to be able to manipulate its plant host to first attract insect vectors to infected plants but then repel viruliferous vectors to promote its own dispersal. Its potential application for invasive weed management is discussed.
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Affiliation(s)
- Rui-Long Wang
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Keyan Zhu-Salzman
- Departments of Entomology, Texas A&M University, College Station, TX 77843, USA.
| | | | - Qiao-Qiao Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shi Chen
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China.
| | - Zhi-Hui Ma
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Shi-Wei Liu
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Jia-En Zhang
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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18
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Lu-Irving P, Harenčár JG, Sounart H, Welles SR, Swope SM, Baltrus DA, Dlugosch KM. Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria. mSphere 2019; 4:e00088-19. [PMID: 30842267 PMCID: PMC6403453 DOI: 10.1128/msphere.00088-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 11/29/2022] Open
Abstract
Invasive species could benefit from being introduced to locations with more favorable species interactions, including the loss of enemies, the gain of mutualists, or the simplification of complex interaction networks. Microbiomes are an important source of species interactions with strong fitness effects on multicellular organisms, and these interactions are known to vary across regions. The highly invasive plant yellow starthistle (Centaurea solstitialis) has been shown to experience more favorable microbial interactions in its invasions of the Americas, but the microbiome that must contribute to this variation in interactions is unknown. We sequenced amplicons of 16S rRNA genes to characterize bacterial community compositions in the phyllosphere, ectorhizosphere, and endorhizosphere of yellow starthistle plants from seven invading populations in California, USA, and eight native populations in Europe. We tested for the differentiation of microbiomes by geography, plant compartment, and plant genotype. Bacterial communities differed significantly between native and invading plants within plant compartments, with consistently lower diversity in the microbiome of invading plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbiome differences between ranges. Our results reveal that these invading plants are experiencing either a simplified microbial environment or simplified microbial interactions as a result of the dominance of a few taxa within their microbiome. Our findings highlight several alternative hypotheses for the sources of variation that we observe in invader microbiomes and the potential for altered bacterial interactions to facilitate invasion success.IMPORTANCE Previous studies have found that introduced plants commonly experience more favorable microbial interactions in their non-native range, suggesting that changes to the microbiome could be an important contributor to invasion success. Little is known about microbiome variation across native and invading populations, however, and the potential sources of more favorable interactions are undescribed. Here, we report one of the first microbiome comparisons of plants from multiple native and invading populations, in the noxious weed yellow starthistle. We identify clear differences in composition and diversity of microbiome bacteria. Our findings raise new questions about the sources of these differences, and we outline the next generation of research that will be required to connect microbiome variation to its potential role in plant invasions.
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Affiliation(s)
- Patricia Lu-Irving
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Evolutionary Ecology, Royal Botanic Gardens Sydney, Sydney, New South Wales, Australia
| | - Julia G Harenčár
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
| | - Hailey Sounart
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Department of Biology, Mills College, Oakland, California, USA
| | - Shana R Welles
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Sarah M Swope
- Department of Biology, Mills College, Oakland, California, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, USA
| | - Katrina M Dlugosch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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19
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Rosani U, Shapiro M, Venier P, Allam B. A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data. Viruses 2019; 11:v11030205. [PMID: 30832203 PMCID: PMC6466128 DOI: 10.3390/v11030205] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 02/08/2023] Open
Abstract
Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padua, 35121 Padua, Italy.
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Paola Venier
- Department of Biology, University of Padua, 35121 Padua, Italy.
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
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20
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Jones RAC. Plant and Insect Viruses in Managed and Natural Environments: Novel and Neglected Transmission Pathways. Adv Virus Res 2018; 101:149-187. [PMID: 29908589 DOI: 10.1016/bs.aivir.2018.02.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The capacity to spread by diverse transmission pathways enhances a virus' ability to spread effectively and survive when circumstances change. This review aims to improve understanding of how plant and insect viruses spread through natural and managed environments by drawing attention to 12 novel or neglected virus transmission pathways whose contribution is underestimated. For plant viruses, the pathways reviewed are vertical and horizontal transmission via pollen, and horizontal transmission by parasitic plants, natural root grafts, wind-mediated contact, chewing insects, and contaminated water or soil. For insect viruses, they are transmission by plants serving as passive "vectors," arthropod vectors, and contamination of pollen and nectar. Based on current understanding of the spatiotemporal dynamics of virus spread, the likely roles of each pathway in creating new primary infection foci, enlarging previously existing infection foci, and promoting generalized virus spread are estimated. All pathways except transmission via parasitic plants, root grafts, and wind-mediated contact transmission are likely to produce new primary infection foci. All 12 pathways have the capability to enlarge existing infection foci, but only to a limited extent when spread occurs via virus-contaminated soil or vertical pollen transmission. All pathways except those via parasitic plant, root graft, contaminated soil, and vertical pollen transmission likely contribute to generalized virus spread, but to different extents. For worst-case scenarios, where mixed populations of host species occur under optimal virus spread conditions, the risk that host species jumps or virus emergence events will arise is estimated to be "high" for all four insect virus pathways considered, and, "very high" or "moderate" for plant viruses transmitted by parasitic plant and root graft pathways, respectively. To establish full understanding of virus spread and thereby optimize effective virus disease management, it is important to examine all transmission pathways potentially involved, regardless of whether the virus' ecology is already presumed to be well understood or otherwise.
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Affiliation(s)
- Roger A C Jones
- Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, Australia; Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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21
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Kamar O, Sun SC, Lin CH, Chung WY, Lee MS, Liao YC, Kolpashchikov DM, Chuang MC. A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids. Chem Commun (Camb) 2017; 53:10592-10595. [PMID: 28900642 PMCID: PMC5645154 DOI: 10.1039/c7cc05576e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Highly selective probes hybridize only to fully complementary DNA or RNA sequences and, therefore, often fail to recognize mutated viral genomes. Here we designed a probe that possesses two seemingly incompatible properties: it tolerates some point mutations in genome, while it remains selective towards others. An OR deoxyribozyme logic gate was designed to fluorescently report the sequences of enterovirus 71 (EV71) covering ∼90% of all known EV71 strains. Importantly, sequences of closely related coxsackieviruses that differed by single nucleotides were reliably differentiated in 7 out of 8 cases.
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Affiliation(s)
- Ola Kamar
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA.
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22
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Darling JA, Galil BS, Carvalho GR, Rius M, Viard F, Piraino S. Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems. MARINE POLICY 2017; 85:56-64. [PMID: 29681680 PMCID: PMC5909192 DOI: 10.1016/j.marpol.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The European Union's Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain "Good Environmental Status" for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, United States Environmental
Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711,
USA
- Corresponding author.
(J.A. Darling)
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Israel National Center for
Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Marc Rius
- Ocean and Earth Science, National Oceanography Centre, University of
Southampton, UK
- Centre for Ecological Genomics and Wildlife Conservation, University
of Johannesburg, South Africa
| | - Frédérique Viard
- Sorbonne Université, Université Paris 06, CNRS, UMR
7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff,
France
| | - Stefano Piraino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali,
Università del Salento, Lecce, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare
(CoNISMa), Roma, Italy
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