Por favor, use este identificador para citar o enlazar a este item:
http://hdl.handle.net/10261/223466
COMPARTIR / EXPORTAR:
SHARE CORE BASE | |
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE | |
Título: | Comparing high throughput sequencing and real time qPCR for characterizing entomopathogenic nematode biogeography |
Autor: | Dritsoulas, Alexandros; Campos-Herrera, Raquel CSIC ORCID ; Blanco-Pérez, Rubén CSIC ORCID ; Duncan, L. W. | Palabras clave: | Entomopathogenic nematodes Soil food webs qPCR Metabarcoding Species detection ITS1 |
Fecha de publicación: | jun-2020 | Editor: | Elsevier | Citación: | Soil Biology and Biochemistry 145: 107793 (2020) | Resumen: | Entomopathogenic nematodes (EPNs) are widely distributed in soils across all continents except Antarctica. Assessing the EPN community structure in an ecoregion can help reveal their biological control potential against important crop pests. Common methods for detecting EPNs in soil samples include baiting with sentinel insects, direct observation of extracted nematodes, or use of species-specific primer-probe combinations using qPCR. Less well studied is the use of high throughput sequencing (HTS), which has tremendous potential to characterize soil communities of EPNs and natural enemies of EPNs. Here, for the first time, we compared qPCR and HTS to characterize EPN food webs. The frequency and abundance of 10 EPN species and 13 organisms associated with EPNs from 50 orchard and natural area sites in two ecoregions of Portugal were evaluated using qPCR tools, and results were published in 2019. We applied an HTS approach to analyze frozen DNA samples from 36 sites in that study. Universal primers targeting ITS1 were used for nematode detection. All EPN species detected by qPCR were also detected by HTS. The EPN species and nearly all free-living nematodes detected by both processes were highly correlated (P < 0.01). Steinernema feltiae, the dominant EPN species, was detected by HTS in 55% more sites than by qPCR. HTS also detected more EPN species than did qPCR. Sample accuracy, measured by the fit of Taylor's Power Law to data from each method, was significantly better using HTS (r = 0.95, P < 0.01) than qPCR (r = 0.76, P < 0.01). The effect of biotic and abiotic variables on individual EPN species did not differ according to ANOVA and multiple regression analyses of both data sets while the drivers of EPN community structure did not differ when analyzing either data set with CCA. Our results combined with decreasing costs of metabarcoding, suggest that HTS may provide the most cost-effective and accurate means of assessing soil food webs of methods currently available. | Versión del editor: | http://dx.doi.org/10.1016/j.soilbio.2020.107793 | URI: | http://hdl.handle.net/10261/223466 | DOI: | 10.1016/j.soilbio.2020.107793 | ISSN: | 0038-0717 |
Aparece en las colecciones: | (ICVV) Artículos |
Ficheros en este ítem:
Fichero | Descripción | Tamaño | Formato | |
---|---|---|---|---|
Comparing High Throughput Sequencing.pdf | 810,71 kB | Adobe PDF | Visualizar/Abrir |
CORE Recommender
SCOPUSTM
Citations
12
checked on 28-mar-2024
WEB OF SCIENCETM
Citations
13
checked on 23-feb-2024
Page view(s)
138
checked on 28-mar-2024
Download(s)
119
checked on 28-mar-2024
Google ScholarTM
Check
Altmetric
Altmetric
NOTA: Los ítems de Digital.CSIC están protegidos por copyright, con todos los derechos reservados, a menos que se indique lo contrario.