Disruption of Traditional Grazing and Fire Regimes Shape the Fungal Endophyte Assemblages of the Tall-Grass Brachypodium rupestre

Abstract

The plant microbiome is likely to play a key role in the resilience of communities to the global climate change. This research analyses the culturable fungal mycobiota of Brachypodium rupestre across a sharp gradient of disturbance caused by an intense, anthropogenic fire regime. This factor has dramatic consequences for the community composition and diversity of high-altitude grasslands in the Pyrenees. Plants were sampled at six sites, and the fungal assemblages of shoots, rhizomes, and roots were characterized by culture-dependent techniques. Compared to other co-occurring grasses, B. rupestre hosted a poorer mycobiome which consisted of many rare species and a few core species that differed between aerial and belowground tissues. Recurrent burnings did not affect the diversity of the endophyte assemblages, but the percentages of infection of two core species -Omnidemptus graminis and Lachnum sp. -increased significantly. The patterns observed might be explained by (1) the capacity to survive in belowground tissues during winter and rapidly spread to the shoots when the grass starts its spring growth (O. graminis), and (2) the location in belowground tissues and its resistance to stress (Lachnum sp.). Future work should address whether the enhanced taxa have a role in the expansive success of B. rupestre in these anthropized environments.

Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes

“…Root tissues display the most diverse and rich fungal assemblages, and the endophytic community in plants collected in more disrupted, LD grasslands had the highest diversity and richness. Similar patterns have been reported in previous research in the area, conducted with a much greater sampling effort and using the culturing method [39], that analyzed the fungal assemblages in terms of the ecological mechanisms favored by the different disturbance regimes.…”

“…In similar studies comparing both methods, the metabarcoding identified ×5.2 and ×4.3 times more OTUs in roots of Elymus repens and Deschampsia flexuosa respectively than the culturing technique [ 62 , 63 ]. A parallel study using 240 plants of B. rupestre recognized 45 fungal endophytic taxa using the culturing method [ 39 ], in contrast to the 88 taxa sequenced using metabarcoding from 10 plants in the current survey. In this parallel study, the singletons isolated accounted for 48.9% of the taxa identified via culturing methods and 28.4% of the taxa identified via metabarcoding (with OTUs clustered with a 97% of similarity threshold).…”

“…Despite the restricted sampling effort, the two methodologies produced consistent results and detected the same trends in endophytic richness and diversity among tissues (roots > rhizomes > shoot) and grassland types (low-diversity > high-diversity). Comparatively, the metabarcoding method allowed the identification of a much larger number of taxa than the culturing method and revealed differences in richness and diversity that were not apparent with the culturing method (even when a larger number of samples was collected [ 39 ]).…”

“…To date, the research in the Brachypodium genus has focused on the systemic fungi of the Clavicipitaceae family hosted by B. sylvaticum [ 34 , 35 ], B. phoenicoides [ 36 , 37 ] and B. pinnatum [ 38 ]. Only a previous study of our research team has characterized the systemic and non-systemic mycobiome of Brachypodium rupestre under a gradient of grazing and fire disturbances using culturable techniques [ 39 ].…”