Site‐specific distribution of oak rhizosphere‐associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding

Abstract

The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and Phytophthora cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys, and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud‐F (Mycologia, 2000) and a reverse primer found using DegePrime (Applied and Environmental Microbiology, 2014). Factors reflecting topo‐edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and P. cinnamomi, both displaying strong site‐specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlight the importance to study oomycete communities in relation to such ecological patterns.

Different community compositions between obligate and facultative oomycete plant parasites in a landscape-scale metabarcoding survey

“…A study conducted only on peat bogs, using ad hoc primers, revealed nevertheless the occurrence of 34 phylotypes, most of which could not be assigned to known species (Singer et al 2016). Few plant-associated oomycetes were found in the roots of oaks (Sapp et al 2019), in that of Arabidopsis thaliana (Sapp et al 2018) and in various other plant roots along a glacier chronosequence (Dickie et al 2019). Their complex life cycle, including a stage with large, mycelium-like structures protected by cell walls, the occurrence of motile cells for dispersion and thick-walled resting stages (Beakes and Thines 2016), may explain their adaptability and dispersal potential.…”

Rhizosphere microbial communities associated to rose replant disease: links to plant growth and root metabolites

“…For oomycetes, the metabarcoding of a region of the mitochondrial cytochrome oxidase (cox-) subunit 2 was done 53 . In the first PCR, primers attached to Illumina overhang adapter sequences were used (Nex_Cox2hud-F: 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGCAAATGGGTTTTCAAGATCC-3′ and Nex_cox2_233D8r: 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGAATATTCATARS-TCCARTACC-3′).…”

First Investigation of Mediterranean Oak Tree Vitality With High-Resolution Worldview-3 Satellite Data: Comparing Ten Vegetation Indices and Three Machine Learning Classifiers

“…The dehesa covers an area of 500 ha with an altitude ranging between 350 m and 500 m above sea level. The territory is ideal for a study on tree vitality, as besides healthy areas, there are areas with a few diseased trees and severely affected areas (Sapp et al, 2019).…”