Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (F_ST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.

Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.

The Qaidam Basin is the highest and one of the largest and driest deserts on Earth. It is considered a mars analog area in China. In contrast to numerous studies concerning its geology, geophysical, and chemistry, relatively few studies have reported microbial diversity and distribution in this area. Here, we investigated culturable yeast diversity in the northeast Qaidam Basin. A total of 194 yeast strains were isolated, and 12 genera and 21 species were identified, among which 19 were basidiomycetous yeasts. Naganishia albida, N. adeliensis, and Filobasidium magnum were the three most dominant species and were distributed in thirteen samples from eight locations. Five new species (Filobasidium chaidanensis, Kondoa globosum, Symmetrospora salmoneus, Teunia nitrariae, and Vishniacozyma pseudodimennae) were found and described based on ITS and D1D2 gene loci together with phenotypic characteristics and physiochemical analysis. Representative strains from each species were chosen for the salt-tolerant test, in which species showed different responses to different levels of NaCl concentrations. Further, the strain from soil can adapt well to the higher salt stress compared to those from plants or lichens. Our study represents the first report of the yeast diversity in the Qaidam Basin, including five new species, and also provides further information on the halotolerance of yeasts from the saline environment in mars analog.

Lichen-associated fungal species have already been investigated in almost all the main growth forms of lichens, however whether or not they are homogeneous and constant within each lichen species are still inconclusive. Moreover, the related ecological factors to affect and structure the fungal composition have been poorly studied. In order to answer these questions, we took Hypogymnia hypotrypa as a model to study the relationship between the lichen-associated fungal composition and two ecological factors, i.e. site and altitude, using the method of IlluminaMiSeq sequencing. Four different sites and two levels of altitude were included in this study, and the effects of site and altitude on fungal community composition were assessed at three levels, i.e. OTU, class and phylum. The results showed that a total of 50 operational taxonomic units (OTUs) were identified and distributed in 4 phyla, 13 classes and 20 orders. The lichen-associated fungal composition within H. hypotrypa were significantly affected by both site and altitude at OTU and class levels, while at the phylum level, it was only affected by altitude. While the lichen associated fungal communities were reported to be similar with endophytic fungi of the moss, our results indicated the opposite results in some degree. But whether there exist specific OTUs within this lichen species corresponding to different sites and altitudes is still open. More lichen species and ecological factors would be taken into the integrated analyses to address these knowledge gaps in the near future.

We employed a molecular phylogenetic approach using five markers (ITS, nuSSU, nuLSU, TEF1-α, and RPB2) to assess potential cryptic speciation in foliicolous members of Strigula s.lat. (Strigulaceae), including the recently segregated genera Phylloporis, Puiggariella, Raciborskiella, Racoplaca, and Serusiauxiella, from tropical areas in Asia, with selected materials from the Neotropics as reference. On the basis of combined molecular and phenotypic datasets, two new species of Racoplaca and 10 new species of Strigula s.str. are described: Racoplaca macrospora sp. nov., R. maculatoides sp. nov., Strigula guangdongensis sp. nov., S. intermedia sp. nov., S. laevis sp. nov., S. microcarpa sp. nov., S. pseudoantillarum sp. nov., S. pseudosubtilissima sp. nov., S. pycnoradians sp. nov., S. sinoconcreta sp. nov., S. stenoloba sp. nov., and S. subtilissimoides sp. nov. In addition, we propose the new combination Phylloporis palmae comb. nov. (≡ =Manaustrum palmae) and we validate the earlier combination Racoplaca melanobapha comb. nov. (≡ Verrucaria melanobapha; Strigula melanobapha). Our data clearly indicate a considerable degree of cryptic diversification in foliicolous representatives of Strigula s.lat., particularly in the presumably widespread taxa Strigula antillarum, S. concreta, S. nitidula, and S. smaragdula. Given that these phylogenetic revisions are thus far limited to few regions, we predict that our findings only represent the proverbial tip of the iceberg in this group of lichenized fungi.

Three yeast strains belonging to the ascomycetous yeast genus Pichia were isolated from two soil samples from Yunnan and Guizhou provinces and a marine water sample from Liaoning province, PR China. Phylogenetic analyses based on the sequences of the D1/D2 domains of the large subunit(LSU) rRNA gene and the internal transcribed spacer (ITS) region indicate that these three strains, together with 12 additional strains isolated from various substrates collected in different regions or countries of the world, represent a novel species of the genus Pichia, for which the name Pichia kurtzmaniana sp. nov. (holotype: strain CGMCC 2.7213) is proposed. The novel species differs from its close relatives Candida californica by eight (1.5 %) and 26 (11.1 %) mismatches in the D1/D2 domains and the ITS region, respectively; and from Pichia chibodasensis by 11 (2.1 %) and 20 (8.7 %) mismatches in the D1/D2 domains and the ITS region, respectively. In addition, eight Candida species which belong to the Pichia clade are transferred to the genus Pichia, resulting in the proposal of the following new combinations: Pichia cabralensis comb. nov., Pichia californica comb. nov., Pichia ethanolica comb. nov., Pichia inconspicua comb. nov., Pichia phayaonensis comb. nov., Pichia pseudolambica comb. nov., Pichia rugopelliculosa comb. nov., and Pichia thaimueangensis comb. nov.