Open AccessPyrosequencing of environmental soil samples reveals biodiversity of the P hytophthora resident community in chestnut forests
Author(s) -
Vannini Andrea,
Bruni Natalia,
Tomassini Alessia,
Franceschini Selma,
Vettraino Anna Maria
Publication year - 2013
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/1574-6941.12132
Subject(s) - pyrosequencing , biology , phytophthora , biodiversity , ecology , phytophthora cinnamomi , taxon , soil water , microbial ecology , botany , gene , biochemistry , genetics , bacteria
Pyrosequencing analysis was performed on soils from Italian chestnut groves to evaluate the diversity of the resident P hytophthora community. Sequences analysed with a custom database discriminated 15 pathogenic P hytophthoras including species common to chestnut soils, while a total of nine species were detected with baiting. The two sites studied differed in P hytophthora diversity and the presence of specific taxa responded to specific ecological traits of the sites. Furthermore, some species not previously recorded were represented by a discrete number of reads; among these species, P hytophthora ramorum was detected at both sites. Pyrosequencing was demonstrated to be a very sensitive technique to describe the P hytophthora community in soil and was able to detect species not easy to be isolated from soil with standard baiting techniques. In particular, pyrosequencing is an highly efficient tool for investigating the colonization of new environments by alien species, and for ecological and adaptive studies coupled with biological detection methods. This study represents the first application of pyrosequencing for describing P hytophthoras in environmental soil samples.