Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples

Abstract

Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimenbased collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized.

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

“…The abundance of Ascomycota was much higher than in previous reports (O'Brien et al 2005). By further analysis at the genus level, 51 abundant genera (more than 1 % of total sequences) were found in rhizosphere soils and 27 in roots (Tables S1 & S2), but the genera Fusarium and Cylindrocarpon, which were considered to be the main pathogens causing root-rot of P. notoginseng (Mao et al 2014), showed no significant difference between diseased and healthy plants both in rhizosphere soils and in roots.…”

Community structure of endophytic fungi of four mangrove species in Southern China

“…A value of 97% ITS identity was used as a DNA barcoding criterion (O’Brien et al 2005). Sequence-based identifications were made by searching with Blastn in the UNITE+INSD database of fungal nucleotide sequences (Abarenkov et al 2010; Tedersoo et al 2014)…”

Secondary metabolite chemistry of the marine-derived fungus Massarina sp., strain CNT-016

“…The uncultured ascomycete relative of this Massarina sp., strain CNT-016, was the only one identified from a terrestrial soil habitat (O'Brien et al, 2005); the other strains in this clade were isolated from plant material (Aptroot, 1998) collected from locations including Europe, North America, Asia and Papua New Guinea. No secondary metabolites are known from species in the Massarina clade 1 except for the study reported here.…”