- -

The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: Català et al 2015 ...
Tamaño: 444.7Kb
Formato: PDF
Descripción: Versión editorial
Abrir
dc.contributor.author Català, Santiago es_ES
dc.contributor.author Pérez Sierra, Ana María es_ES
dc.contributor.author Abad Campos, Paloma es_ES
dc.date.accessioned 2016-06-02T12:29:14Z
dc.date.available 2016-06-02T12:29:14Z
dc.date.issued 2015-03-16
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10251/65124
dc.description.abstract [EN] Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems. es_ES
dc.description.sponsorship This project has been supported by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (EUPHRESCO-CEP: "Current and Emerging Phytophthoras: Research Supporting Risk Assessment And Risk Management"). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. en_EN
dc.language Inglés es_ES
dc.publisher Public Library of Science es_ES
dc.relation.ispartof PLoS ONE es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Phytophthora detection es_ES
dc.subject Forest pathogens es_ES
dc.subject.classification PRODUCCION VEGETAL es_ES
dc.title The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1371/journal.pone.0119311
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/266505/EU/EUROPEAN PHYTOSANITARY RESEARCH COORDINATION II/
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Agroforestal Mediterráneo - Institut Agroforestal Mediterrani es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ecosistemas Agroforestales - Departament d'Ecosistemes Agroforestals es_ES
dc.description.bibliographicCitation Català, S.; Pérez Sierra, AM.; Abad Campos, P. (2015). The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain. PLoS ONE. 10(3):1-14. doi:10.1371/journal.pone.0119311 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://dx.doi.org/10.1371/journal.pone.0119311 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 14 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 10 es_ES
dc.description.issue 3 es_ES
dc.relation.senia 310259 es_ES
dc.identifier.pmid 25775250 en_EN
dc.identifier.pmcid PMC4361056
dc.description.references REICHARD, S. H., & WHITE, P. (2001). Horticulture as a Pathway of Invasive Plant Introductions in the United States. BioScience, 51(2), 103. doi:10.1641/0006-3568(2001)051[0103:haapoi]2.0.co;2 es_ES
dc.description.references Brasier, C. M. (2008). The biosecurity threat to the UK and global environment from international trade in plants. Plant Pathology, 57(5), 792-808. doi:10.1111/j.1365-3059.2008.01886.x es_ES
dc.description.references TABERLET, P., COISSAC, E., HAJIBABAEI, M., & RIESEBERG, L. H. (2012). Environmental DNA. Molecular Ecology, 21(8), 1789-1793. doi:10.1111/j.1365-294x.2012.05542.x es_ES
dc.description.references Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., … Herndl, G. J. (2006). Microbial diversity in the deep sea and the underexplored «rare biosphere». Proceedings of the National Academy of Sciences, 103(32), 12115-12120. doi:10.1073/pnas.0605127103 es_ES
dc.description.references Roesch, L. F. W., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., … Triplett, E. W. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal, 1(4), 283-290. doi:10.1038/ismej.2007.53 es_ES
dc.description.references Acosta-Martínez, V., Dowd, S., Sun, Y., & Allen, V. (2008). Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology and Biochemistry, 40(11), 2762-2770. doi:10.1016/j.soilbio.2008.07.022 es_ES
dc.description.references Jumpponen, A., & Jones, K. L. (2009). Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere. New Phytologist, 184(2), 438-448. doi:10.1111/j.1469-8137.2009.02990.x es_ES
dc.description.references Nilsson, R. H., Ryberg, M., Abarenkov, K., Sjökvist, E., & Kristiansson, E. (2009). The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters, 296(1), 97-101. doi:10.1111/j.1574-6968.2009.01618.x es_ES
dc.description.references Coince, A., Caël, O., Bach, C., Lengellé, J., Cruaud, C., Gavory, F., … Buée, M. (2013). Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. Fungal Ecology, 6(3), 223-235. doi:10.1016/j.funeco.2013.01.002 es_ES
dc.description.references Vannini, A., Bruni, N., Tomassini, A., Franceschini, S., & Vettraino, A. M. (2013). Pyrosequencing of environmental soil samples reveals biodiversity of thePhytophthoraresident community in chestnut forests. FEMS Microbiology Ecology, 85(3), 433-442. doi:10.1111/1574-6941.12132 es_ES
dc.description.references Jerde, C. L., Mahon, A. R., Chadderton, W. L., & Lodge, D. M. (2011). «Sight-unseen» detection of rare aquatic species using environmental DNA. Conservation Letters, 4(2), 150-157. doi:10.1111/j.1755-263x.2010.00158.x es_ES
dc.description.references Monchy, S., Sanciu, G., Jobard, M., Rasconi, S., Gerphagnon, M., Chabé, M., … Sime-Ngando, T. (2011). Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environmental Microbiology, 13(6), 1433-1453. doi:10.1111/j.1462-2920.2011.02444.x es_ES
dc.description.references Jobard, M., Rasconi, S., Solinhac, L., Cauchie, H.-M., & Sime-Ngando, T. (2012). Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes. Environmental Microbiology, 14(9), 2480-2494. doi:10.1111/j.1462-2920.2012.02771.x es_ES
dc.description.references Livermore, J. A., & Mattes, T. E. (2013). Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets. Environmental Microbiology, 15(8), 2333-2341. doi:10.1111/1462-2920.12106 es_ES
dc.description.references NAKAYAMA, J., JIANG, J., WATANABE, K., CHEN, K., NINXIN, H., MATSUDA, K., … LEE, Y.-K. (2013). Up to Species-level Community Analysis of Human Gut Microbiota by 16S rRNA Amplicon Pyrosequencing. Bioscience of Microbiota, Food and Health, 32(2), 69-76. doi:10.12938/bmfh.32.69 es_ES
dc.description.references CREER, S., & SINNIGER, F. (2012). Cosmopolitanism of microbial eukaryotes in the global deep seas. Molecular Ecology, 21(5), 1033-1035. doi:10.1111/j.1365-294x.2012.05437.x es_ES
dc.description.references Davey, M. L., Heegaard, E., Halvorsen, R., Kauserud, H., & Ohlson, M. (2012). Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient. Molecular Ecology, 22(2), 368-383. doi:10.1111/mec.12122 es_ES
dc.description.references Weber, C. F., Vilgalys, R., & Kuske, C. R. (2013). Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon. Frontiers in Microbiology, 4. doi:10.3389/fmicb.2013.00078 es_ES
dc.description.references Bergmark, L., Poulsen, P. H. B., Al-Soud, W. A., Norman, A., Hansen, L. H., & Sørensen, S. J. (2012). Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing. FEMS Microbiology Letters, 333(1), 77-84. doi:10.1111/j.1574-6968.2012.02601.x es_ES
dc.description.references Li, L., Abu Al-Soud, W., Bergmark, L., Riber, L., Hansen, L. H., Magid, J., & Sørensen, S. J. (2013). Investigating the Diversity of Pseudomonas spp. in Soil Using Culture Dependent and Independent Techniques. Current Microbiology, 67(4), 423-430. doi:10.1007/s00284-013-0382-x es_ES
dc.description.references SCHENA, L., HUGHES, K. J. D., & COOKE, D. E. L. (2006). Detection and quantification ofPhytophthora ramorum,P. kernoviae,P. citricolaandP. quercinain symptomatic leaves by multiplex real-time PCR. Molecular Plant Pathology, 7(5), 365-379. doi:10.1111/j.1364-3703.2006.00345.x es_ES
dc.description.references Tooley, P. W., Martin, F. N., Carras, M. M., & Frederick, R. D. (2006). Real-Time Fluorescent Polymerase Chain Reaction Detection ofPhytophthora ramorumandPhytophthora pseudosyringaeUsing Mitochondrial Gene Regions. Phytopathology, 96(4), 336-345. doi:10.1094/phyto-96-0336 es_ES
dc.description.references Pavón, C. F., Babadoost, M., & Lambert, K. N. (2008). Quantification of Phytophthora capsici Oospores in Soil by Sieving-Centrifugation and Real-Time Polymerase Chain Reaction. Plant Disease, 92(1), 143-149. doi:10.1094/pdis-92-1-0143 es_ES
dc.description.references Than, D. J., Hughes, K. J. D., Boonhan, N., Tomlinson, J. A., Woodhall, J. W., & Bellgard, S. E. (2013). A TaqMan real-time PCR assay for the detection ofPhytophthora‘taxon Agathis’ in soil, pathogen of Kauri in New Zealand. Forest Pathology, 43(4), 324-330. doi:10.1111/efp.12034 es_ES
dc.description.references Chen, W., Djama, Z. R., Coffey, M. D., Martin, F. N., Bilodeau, G. J., Radmer, L., … Lévesque, C. A. (2013). Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species. Phytopathology, 103(1), 43-54. doi:10.1094/phyto-04-12-0092-r es_ES
dc.description.references Scibetta, S., Schena, L., Chimento, A., Cacciola, S. O., & Cooke, D. E. L. (2012). A molecular method to assess Phytophthora diversity in environmental samples. Journal of Microbiological Methods, 88(3), 356-368. doi:10.1016/j.mimet.2011.12.012 es_ES
dc.description.references Català S, Pérez-Sierra A, Berbegal M, Abad-Campos P. First approach into the knowledge of the <italic>Phytophthora</italic> species diversity in Mediterranean holm oak forests based on 454 parallel amplicon pyrosequencing of soil samples. <italic>Phytophthora</italic> in Forest and Natural Ecosystems 6<sup>th</sup> International IUFRO Working Party 7.02.09 Meeting, Córdoba, Spain, pp 34; 2012. es_ES
dc.description.references Català S, Pérez-Sierra A, Beltrán A, Abad-Campos P. Next Generation Sequencing shows <italic>Phytophthora</italic> species diversity in soil samples of Macaronesian laurel forests from the Canary Islands. <italic>Phytophthora</italic> in Forest and Natural Ecosystems 6<sup>th</sup> International IUFRO Working Party 7.02.09 Meeting, Córdoba, Spain, pp. 86; 2012. es_ES
dc.description.references Cooke, D. E. L., Drenth, A., Duncan, J. M., Wagels, G., & Brasier, C. M. (2000). A Molecular Phylogeny of Phytophthora and Related Oomycetes. Fungal Genetics and Biology, 30(1), 17-32. doi:10.1006/fgbi.2000.1202 es_ES
dc.description.references Andrews S. FastQC: a quality control tool for high throughput sequence data. Available: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ es_ES
dc.description.references Chou, H.-H., & Holmes, M. H. (2001). DNA sequence quality trimming and vector removal. Bioinformatics, 17(12), 1093-1104. doi:10.1093/bioinformatics/17.12.1093 es_ES
dc.description.references Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389 es_ES
dc.description.references Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. doi:10.1093/nar/gkh340 es_ES
dc.description.references Gouy, M., Guindon, S., & Gascuel, O. (2009). SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building. Molecular Biology and Evolution, 27(2), 221-224. doi:10.1093/molbev/msp259 es_ES
dc.description.references Park, J., Park, B., Veeraraghavan, N., Jung, K., Lee, Y.-H., Blair, J. E., … Kang, S. (2008). Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora. Plant Disease, 92(6), 966-972. doi:10.1094/pdis-92-6-0966 es_ES
dc.description.references Vettraino, A. M., Bonants, P., Tomassini, A., Bruni, N., & Vannini, A. (2012). Pyrosequencing as a tool for the detection ofPhytophthoraspecies: error rate and risk of false Molecular Operational Taxonomic Units. Letters in Applied Microbiology, 55(5), 390-396. doi:10.1111/j.1472-765x.2012.03310.x es_ES
dc.description.references Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95-110. doi:10.3767/003158509x442612 es_ES
dc.description.references Deagle, B. E., Eveson, J. P., & Jarman, S. N. (2006). Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces. Frontiers in Zoology, 3(1). doi:10.1186/1742-9994-3-11 es_ES
dc.description.references Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., & Miaud, C. (2011). Persistence of Environmental DNA in Freshwater Ecosystems. PLoS ONE, 6(8), e23398. doi:10.1371/journal.pone.0023398 es_ES
dc.description.references Guha Roy S, Grunwald NJ. The plant destroyer genus <italic>Phytophthora</italic> in the 21st century. In book: Review of Plant Pathology, Edition: Volume 6, Publisher: Scientific Publishers (India), Jodhpur, Editors: B.N.Chakraborty, B.B.L.Thakore, pp. In press; 2014. es_ES
dc.description.references Brasier, C. M., Cooke, D. E. L., Duncan, J. M., & Hansen, E. M. (2003). Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile. Mycological Research, 107(3), 277-290. doi:10.1017/s095375620300738x es_ES
dc.description.references Hüberli, D., Hardy, G. E. S. J., White, D., Williams, N., & Burgess, T. I. (2013). Fishing for Phytophthora from Western Australia’s waterways: a distribution and diversity survey. Australasian Plant Pathology, 42(3), 251-260. doi:10.1007/s13313-012-0195-6 es_ES
dc.description.references Jung, T., Stukely, M. J. C., Hardy, G. E. S. J., White, D., Paap, T., Dunstan, W. A., & Burgess, T. I. (2011). Multiple new <I>Phytophthora</I> species from ITS Clade 6 associated with natural ecosystems in Australia: evolutionary and ecological implications. Persoonia - Molecular Phylogeny and Evolution of Fungi, 26(1), 13-39. doi:10.3767/003158511x557577 es_ES
dc.description.references Brasier, C. M., Sanchez-Hernandez, E., & Kirk, S. A. (2003). Phytophthora inundata sp. nov., a part heterothallic pathogen of trees and shrubs in wet or flooded soils. Mycological Research, 107(4), 477-484. doi:10.1017/s0953756203007548 es_ES
dc.description.references Hansen, E. M., Reeser, P. W., & Sutton, W. (2012). PhytophthoraBeyond Agriculture. Annual Review of Phytopathology, 50(1), 359-378. doi:10.1146/annurev-phyto-081211-172946 es_ES
dc.description.references Reeser, P. W., Sutton, W., Hansen, E. M., Remigi, P., & Adams, G. C. (2011). Phytophthora species in forest streams in Oregon and Alaska. Mycologia, 103(1), 22-35. doi:10.3852/10-013 es_ES
dc.description.references Nechwatal, J., Bakonyi, J., Cacciola, S. O., Cooke, D. E. L., Jung, T., Nagy, Z. Á., … Brasier, C. M. (2012). The morphology, behaviour and molecular phylogeny ofPhytophthorataxon Salixsoil and its redesignation asPhytophthora lacustrissp. nov. Plant Pathology, 62(2), 355-369. doi:10.1111/j.1365-3059.2012.02638.x es_ES
dc.description.references Huai, W. -x., Tian, G., Hansen, E. M., Zhao, W. -x., Goheen, E. M., Grünwald, N. J., & Cheng, C. (2013). Identification ofPhytophthoraspecies baited and isolated from forest soil and streams in northwestern Yunnan province, China. Forest Pathology, 43(2), 87-103. doi:10.1111/efp.12015 es_ES
dc.description.references Oh, E., Gryzenhout, M., Wingfield, B. D., Wingfield, M. J., & Burgess, T. I. (2013). Surveys of soil and water reveal a goldmine of Phytophthora diversity in South African natural ecosystems. IMA Fungus, 4(1), 123-131. doi:10.5598/imafungus.2013.04.01.12 es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem