Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: the case of theLeptosphaeria maculans-Brassica napuspathosystem

Abstract

Oilseed rape residues are a crucial determinant of stem canker epidemiology, as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterise the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify micro-organisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterised by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify micro-organisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonisation of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial ASVs (amplicon sequence variants). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex was considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote micro-organisms with beneficial effects against residue-borne pathogens, and more broadly, to decipher the complex interactions between multi-species pathosystems and other microbial components in crop residues.

Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis

“…Microbiome studies revealed that pathogenic microbes highly impact microbial community structures [2]. In addition to microbiome communities, the proliferation of plant pathogens is influenced by microbial environmental conditions and host resistotypes [12,23,55]. Due to the availability of large numbers of samples, we could perform a downstream analysis implementing leaf symptoms for microbiome samples from wild tomatoes in Canta.…”

Effects of cultivar resistance and fungicide application on stem canker of oilseed rape (Brassica napus) and potential interseasonal transmission of Leptosphaeria spp. inoculum

“…However, in this study the pseudothecia produced on stubble were not distinguished as L. biglobosa or L. maculans. Recent work showed that L. biglobosa is a key species in microbial communities on oilseed rape stubble, whereas L. maculans plays a minor role (Kerdraon et al, 2020). Additionally, L. biglobosa is more competitive than L. maculans at the necrotrophic growth stage on stem stubble (West et al, 1999).…”

“…maculans promote colonization by L . biglobosa (Kerdraon et al, 2020). This suggests that use of cultivars with good resistance against L .…”

“…biglobosa is a key species in microbial communities on oilseed rape stubble, whereas L . maculans plays a minor role (Kerdraon et al, 2020). Additionally, L .…”

“…This is supported by previous work showing that more L. biglobosa ascospores than L. maculans ascospores were discharged from mature pseudothecia on the stems of cvs Roxet and Excel with the resistance gene Rlm7 in the 2010/2011, 2011/2012, and 2012/2013 cropping seasons (Sidique, 2015). A recent study showed that cultivars with resistance genes against L. maculans promote colonization by L. biglobosa (Kerdraon et al, 2020). This suggests that use of cultivars with good resistance against L. maculans may result in a shift in the ratio of L. maculans to L. biglobosa in the local Leptosphaeria spp.…”