Community structure and dynamics of ectomycorrhizal fungi in a dipterocarp forest fragment and plantation in Thailand

<p><b><i>Background</i></b>: Ectomycorrhizal (EcM) associations have been reported with trees of the plant family Dipterocarpaceae. We hypothesised that a dipterocarp forest fragment, with more host species, would yield a higher diversity of associated EcM fungal species than that of a <i>Dipterocarpus alatus</i> monoculture plantation.</p> <p><b><i>Aims</i></b>: To examine the above- and below-ground EcM community structure of a dry dipterocarp forest fragment and a <i>D. alatus</i> plantation in Thailand.</p> <p><b><i>Methods</i></b>: Sporocarps were collected and identified, and EcM root tips were collected in the dry and wet seasons and identified by terminal restriction fragment length polymorphism and internal transcribed spacer sequencing.</p> <p><b><i>Results</i></b>: Higher EcM fungal diversity was observed in the dry dipterocarp forest fragment than in the <i>D. alatus</i> plantation, with a larger number of species found in the wet seasons than the dry seasons. Sporocarp species richness was greater than root-tip EcM richness. Different dominant EcM taxa were observed in the above- and below-ground communities.</p> <p><b><i>Conclusions</i></b>: Our results suggest that host tree diversity may explain the greater EcM fungal diversity in the dry dipterocarp forest fragment than the <i>D. alatus</i> monoculture plantation. Seasonal dynamics also influences the composition of the EcM communities, with different dominant taxa and relative abundance in the dry and wet seasons. Further research would be of great help in providing useful information for management of dipterocarp forests as well as restoration of disturbed landscapes.</p

Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera

<div><p>Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera <em>Annulohypoxylon</em> and <em>Hypoxylon</em>, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of <em>Annulohypoxylon</em> and <em>Hypoxylon</em>. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many <em>Annulohypoxylon</em> and <em>Hypoxylon</em> species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in <em>Annulohypoxylon</em> and <em>Hypoxylon</em>, however. The URL <a href="http://tinyurl.com/spouge-barcode">http://tinyurl.com/spouge-barcode</a> contains computer programs and other supplementary material relevant to this article.</p> </div

Morphological characteristics of <i>Annulohypoxylon</i> and <i>Hypoxylon</i> species found in Thailand.

<p>Stromata (a–p); perithecial structure (q–s); ascospore shapes (t–z); perispore dehiscence (v, y, z). (a) <i>Annulohypoxylon stygium</i> SUT058, (b) <i>A. purpureonitens</i> H125, (c) <i>A. nitens</i> H154, (d) <i>A.</i> aff. <i>nitens</i> H099, (e) <i>Annulohypoxylon</i> sp. H213, (f) <i>Annulohypoxylon</i> sp. H255, (g) <i>Hypoxylon monticulosum</i> H188, (h) <i>H</i>. <i>lenormandii</i> H212, (i) <i>H. investiens</i> H259, (j) <i>H. perforatum</i> SUT218, (k) <i>H. duranii</i> H250, (l) <i>H. haematostroma</i> H114, (m) <i>H. crocopeplum</i> H119, (n) <i>H. pelliculosum</i> H227, (o) <i>H. diatrypeoides</i> H226, (p) <i>H. rubiginosum</i> SUT082, (q) <i>H. fendleri</i> SUT061, (r) <i>H. investiens</i> H259, (s) <i>H. haematostroma</i> H114, (t) <i>H. haematostroma</i> SUT293, (u) <i>A. stygium</i> SUT010, (v) <i>H. duranii</i> SUT284, (w) <i>H. investiens</i> SUT041, (x) <i>A. nitens</i> SUT249, (y) <i>H. monticulosum</i> SUT185 and (z) <i>A. nitens</i> SUT025.</p

PCIs for each of four alignment types and two types of sequence distance.

<p>The error bars indicate 95% confidence intervals, as calculated by the Wilson score interval <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054529#pone.0054529-Wilson1" target="_blank">[46]</a>. The four alignment types used (indicated by different colors at the bottom) were multiple sequence alignment (which imposes an implicit pairwise global alignment on each pair of sequences), and global, semi-global, and local pairwise alignment. The two types of sequence distance used for each alignment method were alignment distance and evolutionary distance. (In fact, for a fixed alignment type and dataset, all evolutionary distances produced the same PCI as p-distance.) The green bars give the value of the barcode gap PCI.</p