From plant genetics to environment of selection: exploring the drivers of fungal communities in the roots and rhizosphere of Brassica napus

Abstract

PurposeOur aim was to characterize the fungal root and rhizosphere microbiomes of genetically diverse Brassica napus lines in a temporally-intensive, multi-site field study to assess the relative contributions of plant genetics, growth stage and environmental conditions to microbiome composition and to identify fungi that were associated with yield performance. MethodsSixteen B. napus lines were grown across three sites in the Canadian Prairies. Sixteen lines were sampled weekly for ten weeks at one site in 2016, as well as a subset of eight lines at the same site in 2017; the sixteen lines were sampled three times at three sites in 2017. The root and rhizosphere fungal microbiomes were assessed using amplicon sequencing of the fungal ITS region with the Illumina MiSeq. ResultsOverall, B. napus line was associated with only 2% of the variation in community structure. Constrained to within a single site-year, this association increased to between 4 and 16% and to between 25 and 37% in a single week within individual sites. The fungal core microbiome consisted of 38 ASVs; Olpidium, Fusicola, Fusarium, Gibberella, Mortierella, and Cutaneotrichosporon were the most abundant taxa with varied abundance during different B. napus growth stages. Thirteen ASVs across three growth stages were highly associated with B. napus yield. ConclusionOur results point to the potential to exploit the B. napus microbiome for improving plant performance by targeting the core taxa identified here as well as those that lead to greater fitness under more specific conditions.