Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs

Abstract

An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to identify the composition of fungal communities associated with different strawberry organs (leaves, flowers, immature and mature fruits), grown on a farm using management practices that entailed the routine use of various chemical pesticides. ITS2 sequences clustered into 316 OTUs and Ascomycota was the dominant phyla (95.6%) followed by Basidiomycota (3.9%). Strawberry plants supported a high diversity of microbial organisms, but two genera, Botrytis and Cladosporium, were the most abundant, representing 70–99% of the relative abundance (RA) of all detected sequences. According to alpha and beta diversity analyses, strawberry organs displayed significantly different fungal communities with leaves having the most diverse fungal community, followed by flowers, and fruit. The interruption of chemical treatments for one month resulted in a significant modification in the structure of the fungal community of leaves and flowers while immature and mature fruit were not significantly affected. Several plant pathogens of other plant species, that would not be intuitively expected to be present on strawberry plants such as Erysiphe, were detected, while some common strawberry pathogens, such as Rhizoctonia, were less evident or absent.

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes

“…) and olive fruits (Abdelfattah et al . ). Ten fungal genera dominated the orange surfaces including some important groups such as Davidiella , Cryptococcus , Penicillium , Epicoccum and Sporobolomyces .…”

“…; Abdelfattah et al . ). Among the many culture‐independent techniques, pyrosequencing is a recently developed next‐generation sequencing technology that has been used to characterize microbial communities in numerous environments including the rhizosphere (Peiffer et al .…”

“…; Abdelfattah et al . ) and recently roof‐harvested rain water (Chidamba and Korsten ). We are not aware of such studies conducted to date to describe the impact of commercial postharvest treatments including fungicide drenching and degreening on the community structure of the citrus carpoplane.…”

Changes of Scots Pine Phyllosphere and Soil Fungal Communities during Outbreaks of Defoliating Insects

“…[30,31]). The phyllosphere of Norway spruce (Picea abies L.) stands following a spruce bud scale outbreak (Physokermes piceae S.) in Lithuania showed also high abundances of plant pathogenic fungi (Rhizosphaera kalkhoffii, Exobasidium bisporum, Phialophora sessilis) [30].…”

“…The effects of outbreaks of single pests either on phyllosphere or soil microbial communities have been studied already (e.g., [21,24,[27][28][29][30][31][32][33][34][35]), but these data did not simultaneously compare the effect of pest outbreaks on phyllosphere and soil microbial communities and did not differentiate between the effects of different pest insects in the same forest ecosystem. Here, we analyzed the effect of outbreaks of two defoliating insects, nun moth or pine tree lappet, in Scots pine stands in eastern Germany on the bacterial and fungal community structure in the soil and the phyllosphere using DGGE.…”