The use of genus-specific amplicon pyrosequencing to assess phytophthora species diversity using eDNA from soil and water in Northern Spain

PloS One
Santiago CatalàPaloma Abad-Campos

Abstract

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 sequ...Continue Reading

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Citations

Mar 27, 2018·FEMS Microbiology Ecology·Ihsanul KhaliqTreena I Burgess
Mar 25, 2018·Applied and Environmental Microbiology·Jaime AguayoRenaud Ioos
May 29, 2016·Applied and Environmental Microbiology·Rio A StamlerJennifer J Randall
Jul 3, 2020·Microorganisms·Mohammed Y KhdiarTreena I Burgess
May 27, 2020·Environmental Microbiology·Jean LegeayMarc Buée

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Datasets Mentioned

BETA
SRP027499

Methods Mentioned

BETA
PCR
Genotyping
light scattering

Software Mentioned

MOTU
Python Fdn
Seaview
BLAST
Roche Newbler package
blastclust
FastQC
sfffile
Lucy
MUSCLE

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