Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

Abstract

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 16 000-32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000-32 000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one-third of the OTUs are presumed plant-associates (pathogens, saprotrophs and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.

Alder and the Golden Fleece: high diversity of Frankia and ectomycorrhizal fungi revealed from Alnus glutinosa subsp. barbata roots close to a Tertiary and glacial refugium

“…Now, Beringia has been pinpointed as a hotspot for high-latitude fungi (Geml et al, 2010; Bellemain et al, 2013), and could have been a glacial refugium for the fungi. In Europe, the Perigord truffle Tuber melanosporum , also an EM species, has more genetically diverse populations in southern-Italy (Rubini et al, 2005) and Spain (García-Cunchillos et al, 2014).…”

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

“…Because we used short markers, clustering sequences at a high level of similarity, as is usually performed with this type of data 47 , was not suitable because a single difference in the nucleotide sequence often indicated different species. The obiclean program 48 was developed to detect artifactual sequences that contained amplification and/or sequencing errors. For each PCR product, the program creates networks that connect sequences with one indel or substitution difference.…”

ITS2 metabarcoding analysis complements lichen mycobiome diversity data

“…For this reason, only one of the two spacers, either ITS1 or ITS2, has been sequenced so far. Even though diversity studies using these new technologies have become more and more common in the last years (Bellemain et al 2013; Abdelfattah et al 2015; Miller et al 2016), it is still debated whether ITS1 or ITS2 has the best taxonomic resolution.…”