ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale

Abstract

As self-supporting and long-living symbiotic structures, lichens provide a habitat for many other organisms beside the traditionally considered lichen symbionts-the myco- and the photobionts. The lichen-inhabiting fungi either develop diagnostic phenotypes or occur asymptomatically. Because the degree of specificity towards the lichen host is poorly known, we studied the diversity of these fungi among neighbouring lichens on rocks in an alpine habitat. Using a sequencing metabarcoding approach, we show that lichen mycobiomes clearly reflect the overlap of multiple ecological sets of taxa, which differ in their trophic association with lichen thalli. The lack of specificity to the lichen mycobiome is further supported by the lack of community structure observed using clustering and ordination methods. The communities encountered across samples largely result from the subsampling of a shared species pool, in which we identify three major ecological components: (i) a generalist environmental pool, (ii) a lichenicolous/endolichenic pool and (iii) a pool of transient species. These taxa majorly belong to the fungal classes Dothideomycetes, Eurotiomycetes and Tremellomycetes with close relatives in adjacent ecological niches. We found no significant evidence that the phenotypically recognized lichenicolous fungi influence the occurrence of the other asymptomatic fungi in the host thalli. We claim that lichens work as suboptimal habitats or as a complex spore and mycelium bank, which modulate and allow the regeneration of local fungal communities. By performing an approach that minimizes ambiguities in the taxonomic assignments of fungi, we present how lichen mycobiomes are also suitable targets for improving bioinformatic analyses of fungal metabarcoding.

Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions

“…With the dominance of Ascomycota and Basidiomycota in LAF and Alphaproteobacteria in bacterial communities across diverse lichen species, lichen-associated microbial compositions are known to be largely influenced by various environmental factors Bates et al, 2011;Cardinale et al, 2012;Hodkinson et al, 2012;U'Ren et al, 2012;Beck et al, 2014;Park et al, 2015Park et al, , 2016Wang et al, 2016). For example, lichenassociated fungal communities varied according to the host species (Beck et al, 2014;Park et al, 2015;Fernández-Mendoza et al, 2017;Banchi et al, 2018), climate conditions (U'Ren et al, 2012), seasonal changes of environmental conditions (Beck et al, 2014), geographic location, and altitude (Wang et al, 2016). Bacterial compositions in lichens were influenced by host species (Bates et al, 2011), age and sun exposure (Cardinale et al, 2012), substrate type and growth form (Park et al, 2016), and photoautotrophic symbiont and geography (Hodkinson et al, 2012).…”

Fungal Diversity in Lichens: From Extremotolerance to Interactions with Algae

“…Lichens are, for their dominant part, developed and shaped from the structures of their lichenized fungal partner (mycobiont). The mycobiont DNA also represents the most abundant fraction of reads in the fungal high throughput sequencing approaches (e.g., [ 6 , 34 , 35 , 36 ]). However, largely varying abundances in the samples (as well as the nature of sequencing technologies) can lead to biased estimates of community richness and composition [ 37 ].…”

“…Metabarcoding studies (fungal community analyses) of lichen mycobiomes have previously relied on the 454 pyrosequencing platform and used specific primers to target the nuclear internal transcribe spacer region (ITS) [ 13 , 34 , 35 ]. The ITS locus has been proposed as the best performing fungal barcode [ 39 ] and ITS sequence data have proved suitable to delimit the molecular operational taxonomic units (MOTUs) in most studies, including the lichenized and non-lichenized fungi [ 13 , 34 , 35 , 40 , 41 ]. However, because of technical restrictions on the sequence lengths, either the ITS1 or ITS2 subregions were sequenced.…”

“…The authors identified 50 MOTUs comprising 28 Ascomycota, 11 Basidiomycota, 4 Zygomycota, 3 Chytridiomycota, and 4 unknown fungi. Fernández-Mendoza et al [ 35 ] focused on the lichen species of alpine habitats and recovered abundant MOTUs of Dothideomycetes and Eurotiomycetes, and also found 25 MOTUs of Tremellomycetes (Basidiomycota). That study also showed that lichenicolous fungi could occur symptomless in the thalli of their known hosts, and could also be present in other lichen species.…”

“…This spectrum of fungi indicated that generalists (either spores or mycelia), which grew fast in cultures, were mainly considered in secondary metabolite assays and that many slow-growing fungi, which were highly adapted to the lichen environment, had not been studied yet. This might have also explained why many specific lichenicolous basidiomycetes were not cultured yet, in particular Cyphobasidiales [ 16 , 35 , 88 ]. The common Tremellales with Fellomyces anamophs seemed to be isolated more easily from the lichens [ 89 ].…”