Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing

Abstract

In this study, three different methods (fruiting body collection, mycelial isolation, and 454 sequencing) were implemented to determine the diversity of wood-inhabiting basidiomycetes from dead Manchurian fir (Abies holophylla). The three methods recovered similar species richness (26 species from fruiting bodies, 32 species from mycelia, and 32 species from 454 sequencing), but Fisher's alpha, Shannon-Wiener, Simpson's diversity indices of fungal communities indicated fruiting body collection and mycelial isolation displayed higher diversity compared with 454 sequencing. In total, 75 wood-inhabiting basidiomycetes were detected. The most frequently observed species were Heterobasidion orientale (fruiting body collection), Bjerkandera adusta (mycelial isolation), and Trichaptum fusco-violaceum (454 sequencing). Only two species, Hymenochaete yasudae and Hypochnicium karstenii, were detected by all three methods. This result indicated that Manchurian fir harbors a diverse basidiomycetous fungal community and for complete estimation of fungal diversity, multiple methods should be used. Further studies are required to understand their ecology in the context of forest ecosystems.

Wood‐rotting basidiomycetes are a minor component of fungal communities associated with Acacia hybrid trees grown for sawlogs in South Vietnam

“…The low overlap between fungi detected by isolation and those detected by environmental sequencing has been observed previously in wood (Jang et al, 2016) and other substrates (Arnold, Henk, Eells, Lutzoni, & Vilgalys, 2007). We detected 35 wood decay species, 12 by isolation, 24 from direct DNA extracts and only one by both methods.…”

Wood‐rotting basidiomycetes associated with declining native trees in timber‐harvesting compartments of the Garden Route National Park of South Africa

“…Jang et al (2015) noted, for example that basidiomycetes detection based on fruiting body collection could be hampered by the ephemeral character of basidiocarps of some species, which due to high water content persist for a short period compared to those of perennial species and thus may not be present at the time of sampling. Another constraint related to this approach may also be the selective medium used for fungal isolation, because, even though benomyl is effective in inhibiting the growth of a large range of fungi other than basidiomycetes, some basidiomycetous species may be sensitive to it and their growth can be inhibited (Jang et al 2015). For macro-fungi revealed by mycelium isolated from infected woody tissues, Taylor (2002) indicated that the number of species of a particular sample is based on the size of the sample, the abundance of species in the sample and the distribution of these species in the substrate where the sample was originally collected.…”

USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS

“…Nine studies have already specifically investigated the mycobiomes of decaying wood using targeted, ampliconbased metagenomics, five in palearctic boreal forests in northern Europe (Ovaskainen et al 2010, Kubartova et al 2012, Ovaskainen et al 2013, Runnel et al 2015 and four in palearctic temperate forests in Europe and Asia (Van der Wal et al 2015, Hoppe et al 2015, Jang et al 2015, Yamashita et al 2015. With the exception of Yamashita et al (2015), which used the V9 region of 18S rDNA, all the other works used the complete ITS (Ovaskainen et al 2010, Kubartova et al 2012, Ovaskainen et al 2013, Hoppe et al 2015, Otosson et al 2015 or the ITS2 (Jang et al 2015, Runnel et al 2015, Van der Wal et al 2015 as the targeted region.…”

“…With the exception of Yamashita et al (2015), which used the V9 region of 18S rDNA, all the other works used the complete ITS (Ovaskainen et al 2010, Kubartova et al 2012, Ovaskainen et al 2013, Hoppe et al 2015, Otosson et al 2015 or the ITS2 (Jang et al 2015, Runnel et al 2015, Van der Wal et al 2015 as the targeted region. Furthermore, all the analyses of these studies were mainly focused on Basidiomycota, limiting a fully global comparison with our study.…”

“…To date, studies specifically investigating the mycobiomes of decaying wood using targeted, amplicon-based metagenomics are few, and all of these studies were conducted strictly in palearctic boreal and temperate forests (Ovaskainen et al 2010, Kubartova et al 2012, Ovaskainen et al 2013, Van der Wal et al 2015, Hoppe et al 2015, Jang et al 2015, Runnel et al 2015, Yamashita et al 2015. Thus, as far as we know, there has not been a similar metabarcoding study in tropical, and more specifically, neotropical forests.…”