Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes

Abstract

Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.

Drivers of grass endophyte communities in prairies of the Pacific Northwest, USA

“…While we sampled only 12 fewer individuals from D. californica , we found nearly 500 fewer OTUs than from F. roemeri communities. Interestingly, when we examined the higher-level taxonomy among these host species, there were few differences; the two host species had remarkably similar taxonomic composition at the phylum, class, and order levels, perhaps reflecting that both hosts were in the grass family, Poaceae; indeed at this higher taxonomy, our results were very similar to three other genera of grasses (Wemheuer et al 2019). However, the actual species in each of our host species were markedly different ( Fig.…”

“…DNA was stored at -20 °C until we constructed a metabarcode sequencing library of the internal transcribed spacer (ITS) region within the rRNA gene. Libraries were constructed as described in Thomas et al (2019), using a duel-indexed split In addition to our samples, we included a pure-water negative control and two positive mock community controls in order to address any downstream sequencing or bioinformatic inconsistencies. Our mock community was created in conjunction with a shared study, see Thomas et al (2019) for details.…”

“…Libraries were constructed as described in Thomas et al (2019), using a duel-indexed split In addition to our samples, we included a pure-water negative control and two positive mock community controls in order to address any downstream sequencing or bioinformatic inconsistencies. Our mock community was created in conjunction with a shared study, see Thomas et al (2019) for details. Taxonomic identities of the mock community are shown in supplementary materials ( Supplementary Table 2).…”

“…The bioinformatics pipeline was based on the USEARCH/UPARSE pipeline (Edgar 2013) and follows Thomas et al (2019). Reads were trimmed to remove low quality base calls and chimeric sequences, using a phred cutoff score of 34.…”

“…Traditionally, endophytic fungi have been described as those that live inside the host but cause no symptoms (Wilson 1995) but NGS and culturing studies frequently uncover many latent pathogens and saprotrophs from asymptomatic leaves. Here we use the term endophyte to describe all fungi living within asymptomatic plant leaves, that is, defined by habitat and regardless of their ecological role (Hardoim et al 2008, Porras-Alfaro and Bayman 2011, Wemheuer et al 2019). While grasses have been extensively studied from the perspective of clavicipitaceous endophyte fungal associations ('C-endophyte') (Rodriguez et al 2009), which are restricted to grasses and are sometimes mutualistic (Faeth 2002, Rodriguez et al 2009), relatively little is known about the non-clavicipitaceous ('NC-endophyte') diversity of native grass leaves from natural populations, but see (Higgins et al 2014) for a tropical example, and Nissinen et.…”