ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds

Abstract

In a recent study pyrosequencing of the ribosomal internal transcribed spacer-1 (ITS-1) has validated the effectiveness of such technology in the survey of soil fungal diversity. Here we compare the two ITS regions, ITS-1 and ITS-2, of the fungal populations occurring in Tuber melanosporum/Quercus pubescens truffle grounds and sampled in two areas, one devoid of vegetation (''burned'', brulé in French) where T. melanosporum fruiting bodies are usually collected, and outside the brulé. TS1F/ITS2 and ITS3/ITS4 were used respectively for the amplification of the ITS-1 and ITS-2 regions. Two amplicon libraries were built, one for inside and the other for outside. A set of 15.788 reads was obtained. After the removal of low quality sequences, 3568 and 3156 sequences were obtained from inside the brulé with the ITS-1 and ITS-2 primers respectively. The sequences obtained from outside the brulé were 4490 with the ITS-1 primers and 2432 with the ITS-2 primers. Most of the sequences obtained for both ITS fragments could be attributed to fungal organisms.The pair of primers, ITS1-F/ITS2, was more selective, producing fewer non-fungal sequences (1% inside, 3% outside), in addition to a higher number of sequences, than the pair ITS3/ITS4 (6% inside, 11% outside). Although differences are present in the taxa percentages between ITS-1 and ITS-2, both reveal that Ascomycota were the dominant fungal phylum and that their number decreased moving from inside the brulé to outside, while the number of Basidiomycota increased. Taken together, both the short ITS-1 and ITS-2 reads obtained by the high throughput 454 sequencing provide adequate information for taxon assignment and are suitable to correlate the dynamics of the fungal populations to specific environments.

High Fungal Diversity and Dominance by Ascomycota in Dam Reservoir Soils of Arid Climates

“…Previous studies have indicated the dominance of Ascomycota in truffle grounds (Mello et al, 2011) and in the rhizosphere of Xinjiang Jujube (Liu et al, 2015). Zygomycota was the second dominant phylum, which has also been reported as sub-dominant species in the Negev desert (Bates et al, 2010).…”

454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome

“…Indeed, patterns observed at a given level of taxonomic discrimination might not be found at lower or higher levels [5,7,14]. Studies on the diversity of soil fungal communities carried out so far by means of NGS have either focused on a phylogenetically restricted set of taxa (e.g., arbuscular mycorrhizal fungi [31][32][33][34]) or have been performed on a restricted (local or regional) spatial scale (e.g., [21,[35][36][37][38][39][40][41][42][43][44]). To bridge the gap between local and wide-scale assessments, additional studies are required, encompassing greater spatial sampling across multiple soil biomes.…”

Assessing the Genetic Diversity of <i>Alternaria Bataticola</i> in South Africa using Molecular Markers

“…The isolates from Mohlaba cross and Dan village appeared as independents. The size of the ITS2 region and the G-C content of A. bataticola corresponds to those reported in other studies [13,41]. Clustering patterns produced with the RAPD data ( Fig.…”