Assessment of soil fungal diversity in different alpine tundra habitats by means of pyrosequencing

Abstract

Studying fungal diversity is vital if we want to shed light on terrestrial ecosystem functioning. However, there is still poor understanding of fungal diversity and variation given that Fungi are highly diversified and that most of fungal species remain uncultured. In this study we explored diversity with 454 FLX sequencing technology by using the Internal Transcribed Spacer 1 (ITS1) as the fungal barcode marker in order to evaluate the effect of 11 environmental conditions on alpine soil fungal diversity, as well as the consistency of those results by taking into account rare or unidentified Molecular Operational Taxonomic Units (MOTUs). In total we obtained 205131 ITS1 reads corresponding to an estimated fungal gamma diversity of between 5100 and 12 000 MOTUs at a 98% similarity threshold when considering respectively only identified fungal and all MOTUs. Fungal beta-diversity patterns were significantly explained by the environmental conditions, and were very consistent for abundant/rare and fungal/unidentified MOTUs confirming the ecological significance of rare/unidentified MOTUs, and therefore the existence of a fungal rare biosphere. This study shows that a beta-diversity estimation based on pyrosequencing is robust enough to support ecological studies. Additionally, our results suggest that rare MOTUs harbour ecological Guillaume Lentendu and Lucie Zinger equally contributed to this paper.Electronic supplementary material The online version of this article (

Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions

“…After normalization for reads per sample, our genus-level diversity was higher than other 97 to 98% clusterbased estimates of species richness from a variety of environments determined by cloning and sequencing (8,37), ITS pyrosequencing (10,38,39), and 28S pyrosequencing but with 95% clustering (40). However, our results agreed with the ITS "species"-level OTU in recent studies from various Mediterranean land use categories (41) and neotropical rain forests (42) but were lower than that found in alpine tundra habitats (15). Such comparisons are difficult to interpret, as the classification resolution differs between the ITS and 28S genes.…”

“…After database filtering of unknown fungal species, their unclassified proportion dropped to 11% of the OTU by forcing assignment to a classified nearest neighbor. As such, taxonomic assignment is dependent on the composition of the reference database, which is further complicated by the high fungal species diversity in soil (10,15), estimated to be 7.12 ϫ 10 5 at the lower boundary (76).…”

“…With the exception of a few deep sequencing studies (7,10,15,16), most have not addressed the extent or composition of the unclassified members other than establishing them as nonfungal reads. The definition of unclassified reads is largely dependent on the classification method.…”

“…The abundance of fungal unclassified reads, even at higher subphylum or class levels (7), illustrates the dearth of sequences available from classified fungi. As such, the composition of any fungal database precludes the identification of the majority of sequences (15,17,18). As Lentendu et al (15) pointed out, the effect of the definition "unclassified" on fungal diversity estimates has been largely ignored.…”

The genus Hebeloma in the alpine belt of the Carpathians including two new species

“…In addition to these traditional studies European Arctic-alpine fungal communities have been studied by high throughput sequencing (e.g. Bjorbaekmo et al 2010, Fujiyoshi et al 2011, Lentendu et al 2011, Geml et al 2012, Botnen et al 2014. Also the Arctic region of Greenland has been relatively well studied mycologically (Borgen et al 2006).…”