RNA‐based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi‐trophic fungi

Abstract

Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.

Effects of rhizoma peanut cultivars (Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation

“…Reagents and reaction conditions for three PCR amplification steps were shown in Table . More details of PCR amplification are described by Chen, Liao, Arnold, Bonito, & Lutzoni (). Obtained PCR products were verified on 1% agarose gels and purified using AMPPure XP beads (Beckman Coulter) following the manufacturer's instructions.…”

Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium

“…Moreover, the “organonitrogen compound catabolic process” was detected as the most enriched GO term in the bottom layer of D. scoparium (Supporting Information Table S16). The overall increase of ammonium transporter activity in the bottom layer could be attributed to a high ammonium and low nitrate content beneath moss mats (Sedia and Ehrenfeld, ), high fungal activities in the lower layers (Davey et al ., ; Chen et al ., ), combined with a fungal preference for ammonium as an inorganic nitrogen source, and reduced competition with plants for the available ammonium at this location. MEPγ genes detected here represent one type of ammonium transporter genes, which have been reported across the fungal tree of life (McDonald et al ., ).…”

“…The overall higher abundance of fungal nutrient‐related transporters (Fig. and Table ) is characterized by higher fungal activities toward the bottom layer of D. scoparium (Chen et al ., ) and higher fungal biomass in the bottom layer of this moss (Davey et al ., , ). Most of the transporters significantly upregulated in the top layer were from fungi in the classes Leotiomycetes and Eurotiomycetes, which is in agreement with our previous finding that these two fungal classes have high activities (using nrRNA transcripts as a proxy) in the top layer of D. scoparium (Chen et al ., ).…”

“…These features make D. scoparium an ideal system to study the capacity of fungi to switch function or for a mycelium to have multiple functions simultaneously. Our previous study (Chen et al ., ) revealed that fungal communities were structured according to the senescence gradient of D. scoparium . We also found that some fungi were active (based on their nuclear ribosomal RNA [nrRNA] gene expression levels) (Chen et al ., ) throughout the three layers of the gametophytes.…”

“…Our previous study (Chen et al ., ) revealed that fungal communities were structured according to the senescence gradient of D. scoparium . We also found that some fungi were active (based on their nuclear ribosomal RNA [nrRNA] gene expression levels) (Chen et al ., ) throughout the three layers of the gametophytes. Here, we investigated the functions of these fungal communities and of the moss host D. scoparium across the same senescence gradient using messenger RNA (mRNA).…”