Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing

Abstract

SummaryOrchid mycorrhizal (OrM) symbionts play a key role in the growth of orchids, but the temporal variation and habitat partitioning of these fungi in roots and soil remain unclear.Temporal changes in root and rhizosphere fungal communities of Cypripedium calceolus, Neottia ovata and Orchis militaris were studied in meadow and forest habitats over the vegetation period by using 454 pyrosequencing of the full internal transcribed spacer (ITS) region.The community of typical OrM symbionts differed by plant species and habitats. The root fungal community of N. ovata changed significantly in time, but this was not observed in C. calceolus and O. militaris. The rhizosphere community included a low proportion of OrM symbionts that exhibited a slight temporal turnover in meadow habitats but not in forests. Habitat differences in OrM and all fungal associates are largely attributable to the greater proportion of ectomycorrhizal fungi in forests.Temporal changes in OrM fungal communities in roots of certain species indicate selection of suitable fungal species by plants. It remains to be elucidated whether these shifts depend on functional differences inside roots, seasonality, climate or succession.

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

“…With technological advances in read length and quality, we advocate the use of full ITS region due to a better choice of forward primers and the presence of critical differences in either ITS1 or ITS2 in many pairs of closely related species (Blaalid et al 2013;Kõljalg et al 2013). Our in silico and in vivo results indicate that combining amplicons of ITS1Fngs and ITS1ngs forward primers effectively accounts for biases arising from primer mismatches and the occurrence of introns (Oja et al 2015). In addition, the D1 and potentially D2 regions of LSU perform well in higher-level taxonomic assignment of fungi (see also Begerow et al 2010).…”

“…The ITS4 and LR0R primer families possess two mismatches to Archaeorhizomycetes and one mismatch to most Chaetothyriales, the latter of which was accounted for by a degenerate position in the ITS4ngs and LR0Rngs primers. Both primers are ill-suited for amplification of a large proportion of Tulasnellaceae and Microsporidia due to multiple central mismatches (Taylor and McCormick 2008;Oja et al 2015). The LF402 and LF402F primers discriminate among most non-fungal groups and cover most of the fungal kingdom, except for a number of taxa within Cantharellus, Tulasnellaceae, Ustilaginaceae, Candida, and some early diverging lineages.…”

New species of Tulasnella associated with terrestrial orchids in Australia

“…Indeed, numerous molecular OTUs have been designated amongst Tulasnella associated with orchids (e.g. Smith et al 2010, Jacquemyn et al 2011, 2012, Pandey M et al 2013, Cruz et al 2014, Oja et al 2015) or liverworts (Kottke et al 2003, Bidartondo & Duckett 2010), without formally naming the species. Formal naming of the species is preferred and essential to prevent confusion of taxonomic units discovered in separate studies (Hibbett & Taylor 2013).…”

Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza

“…Further evidence for local environmental conditions affecting orchid mycorrhizal communities comes from comparisons of mycorrhizal communities across different habitats within a single orchid species. For example, it was recently shown that individuals from grassland populations of Neottia ovata associated with significantly different fungal communities than individuals from forest populations14. Similarly, pronounced differences in mycorrhizal communities were reported between dune slack and forest populations of Epipactis species.…”