454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

Abstract

Summary Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). Here, we assessed the fungal diversity in six different forest soils using tag‐encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer‐1 (ITS‐1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS‐1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. This study validates the effectiveness of high‐throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

“…The bacterial and fungal community composition at the phylum (Table 6) and genus levels (Tables S1 & S2) in rhizosphere soils of P. notoginseng generally corresponded with previous studies carried out in agricultural or other soil types for bacteria by deep 16S rRNA pyrosequencing (Acosta-Martinez et al 2008;Roesch et al 2007), and for fungi by ITS sequencing (Buee et al 2009). Furthermore, the main bacterial and fungal phyla found in roots were in general accordance with those in rhizosphere soils.…”

Fungal Communities Respond to Long-Term CO 2 Elevation by Community Reassembly

“…The grassland soil ecosystem in the BioCON experimental site in Minnesota was dominated by Ascomycota (81% at aCO 2 and 77% at eCO 2 ) and Basidiomycota (11% at aCO 2 and 14% at eCO 2 ). Compared to the reports by previous studies (31,(58)(59)(60)(61), fungal community composition in soil varied greatly across different types of soil ecosystems. Such variations in fungal community composition between different studies might be caused by different coverage of different primer sets or phylogenetic markers (such as ITS versus 28S) (62), but more likely caused by plant species, soil, and/or climate differences (58).…”

Host Identity Impacts Rhizosphere Fungal Communities Associated with Three Alpine Plant Species

“…A growing body of evidence indicates that many of these effects depend on fungal identity [4,5]; however, only a small fraction of the estimated 1.5 million fungal species has been characterized [6]. This is particularly true for soil microbial communities where diversity is thought to be especially high [7,8], yet technical issues hamper species isolation and identification. The lack of information regarding soil fungi poses a problem in terms of fully understanding the importance of fungal diversity and predicting how changes in the fungal community will impact ecosystem processes [9].…”