Revisiting the phylogeny and taxonomy of the genus Sidera (Hymenochaetales, Basidiomycota) with particular emphasis on S.vulgaris

The genus Sidera (Hymenochaetales, Basidiomycota) comprises white-rot, mono- or dimitic fungi with poroid or hydnoid hymenophore. It has a worldwide distribution albeit with fewer species present in the Southern Hemisphere. Although recent studies revealed the existence of several new Sidera species, there are still taxonomic inconsistencies and obscure phylogenetic relationships amongst certain taxa of the genus. In this work, a large number of Sidera collections were used to obtain an updated phylogeny, based on ITS and 28S rDNA sequences by including new material from Mediterranean Europe. The monophyly of the genus was strongly supported and all species with poroid hymenophore formed a highly-supported lineage with two major subclades. In total, 23 putative species were recognised. Amongst those, five are considered to possibly represent entities new to science, but further work is required since they are represented by single specimens or environmental sequences. Examined collections originally named S.lenis from southern Europe were grouped within S.vulgaris. Similarly, several collections under various names were hereby identified as S.vulgaris, including those of the recently described species S.tibetica. Furthermore, a critical discussion (based on morphoanatomical findings) is made on the key features that could be used to distinguish S.lenis from S.vulgaris.

Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics

The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.

Mallocybe heimii ectomycorrhizae with Cistus creticus and Pinus halepensis in Mediterranean littoral sand dunes - assessment of phylogenetic relationships to M. arenaria and M. agardhii

Ectomycorrhizal symbiosis appears extensively in the Northern Hemisphere, where Mediterranean ecosystems constitute an important ecological area of considerable biodiversity value. Littoral sand dunes are among high-risk habitats, and ectomycorrhizal lifestyle contributes significantly to supporting life in such regions. Mallocybe heimii (Bon) Matheny & Esteve-Rav. (Inocybaceae, Basidiomycota) and the very similar M. arenaria (Bon) Matheny & Esteve-Rav. grow in poor, usually sandy soils, in association with angiosperms or gymnosperms. Basidiomata originally identified under these names were collected from littoral sand dunes of Greece, and their morpho-anatomical characteristics were examined in conjunction with material derived from other European regions. Sequences from basidiomata and root tips corresponding to the nuclear rDNA internal transcribed spacer region (ITS) and large subunit (LSU) were obtained and analyzed. Phylogenetic results demonstrated that material identified as M. heimii or M. arenaria form a single well-supported group, while M. agardhii (N. Lund) Matheny & Esteve-Rav. is confirmed to be distinct from M. arenaria (the latter was initially described as a variety of the former, i.e., I. agardhii var. arenaria Bon). A detailed tree of the genus Mallocybe was generated on the basis of concatenated ITS and LSU sequences, and relationships of selected taxa are discussed in the light of morphological and sequence data. In addition, the first morphotype descriptions of M. heimii ectomycorrhizae with Cistus creticus L. and Pinus halepensis Miller are hereby provided. Both morphotypes exhibited the typical characteristics of Inocybe/Mallocybe ectomycorrhizae; however, differences were noted, the most significant being the presence of clamps on mantle hyphae and the type of anastomoses.

A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa

Ganoderma P. Karst. is a cosmopolitan genus of white-rot fungi which comprises species with highly-prized pharmaceutical properties, valuable biotechnological applications and of significant phytopathological interest. However, the status of the taxonomy within the genus is still highly controversial and ambiguous despite the progress made through molecular approaches. A metadata analysis of 3908 nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences obtained from GenBank/ENA/DDBJ and UNITE was performed by targeting sequences annotated as Ganoderma, but also sequences from environmental samples and from material examined for the first time. Ganoderma taxa segregated into five main lineages (Clades A to E). Clade A corresponds to the core of laccate species and includes G. shanxiense and three major well-supported clusters: Cluster A.1 ('G. lucidum sensu lato') consists of taxa from Eurasia and North America, Cluster A.2 of material with worldwide occurrence including G. resinaceum and Cluster A.3 is composed of species originating from all continents except Europe and comprises G. lingzhi. Clade B includes G. applanatum and allied species with a Holarctic distribution. Clade C comprises taxa from Asia and Africa only. Clade D consists of laccate taxa with tropical/subtropical occurrence, while clade E harbours the highest number of non-laccate species with a cosmopolitan distribution. The 92 Ganoderma-associated names, initially used for sequences labelling, correspond to at least 80 taxa. Amongst them, 21 constitute putatively new phylospecies after our application of criteria relevant to the robustness/support of the terminal clades, intra- and interspecific genetic divergence and available biogeographic data. Moreover, several other groups or individual sequences seem to represent distinct taxonomic entities and merit further investigation. A particularly large number of the public sequences was revealed to be insufficiently and/or incorrectly identified, for example, 87% and 78% of entries labelled as G. australe and G. lucidum, respectively. In general, ITS demonstrated high efficacy in resolving relationships amongst most of the Ganoderma taxa; however, it was not equally useful at elucidating species barriers across the entire genus and such cases are outlined. Furthermore, we draw conclusions on biogeography by evaluating species occurrence on a global scale in conjunction with phylogenetic structure/patterns. The sequence variability assessed in ITS spacers could be further exploited for diagnostic purposes.

Multiple evolutionary origins of sequestrate species in the agaricoid genus Chlorophyllum

Chlorophyllum accommodates lamellate agaricoid species as well as sequestrate angiocarpic taxa, which do not form a monophyletic lineage within the genus. To clarify phylogenetic affinities and delimit species boundaries among sequestrate representatives of the genus, we analyzed historical and contemporary material from a broad geographic range, encompassing North America, southern Africa, eastern Asia, the Greek and Iberian peninsulas, and the Mediterranean islands of Cyprus and Lesvos. Six sequestrate lineages of Chlorophyllum were identified, which appear to have evolved in at least three independent gasteromycetation events. Multigene analysis of the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of the nuc 28S rDNA (28S), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-α (tef1) genes revealed the presence of a previously undescribed species, introduced here as Chlorophyllum levantinum, sp. nov. Its sister species C. lusitanicum, previously known only from Spain, is shown to have a wider distribution throughout the Mediterranean basin. A South African collection of Secotium gueinzii, a poorly known taxon described in 1840 and seldom appearing in literature since, was also shown to nest within Chlorophyllum. An epitype for this rare species is designated, Secotium becomes a priority synonym of Chlorophyllum, and nomenclatural implications are discussed. The phylogenetic placement of C. arizonicum is confirmed after successful sequencing of the century-old holotype and an undescribed sister lineage of this species detected. Emended descriptions of sections Chlorophyllum, Endoptychorum, and Sphaerospororum are provided to reflect current results, along with updated descriptions and extensive imagery for all known sequestrate taxa of Chlorophyllum.

Accumulation of heavy metals by wild edible mushrooms with respect to soil substrates in the Athens metropolitan area (Greece)

Six wild edible mushroom species, Agaricus bisporus, A. bitorquis, A. gennadii, Coprinus comatus, Psathyrella candolleana and Volvopluteus gloiocephalus, were collected from the Greater Athens area (Greece), together with their soil substrates (two depth-layers) for studying bioaccumulation of heavy metals in a densely populated urban environment. Total and bioavailable Cr, Cu, Fe, Mn, Ni, Pb and Zn concentrations in soils were assessed along with their respective concentrations in mushrooms, and were evaluated in conjunction with soil properties, including K, P and Na content, CaCO₃ equivalent percentage, mechanical composition, pH and organic matter. In particular, Cu, Pb, Zn and Ni displayed a high variability in their total and bioavailable concentrations measured in the upper soil layer. Relatively high Pb and Ni contents were measured in mushrooms, while Cu, Zn, Fe and Mn concentrations varied considerably. No significant correlations were detected between total concentrations of heavy metals in soils and mushrooms, whereas bioavailable fractions for several metals were significantly correlated with their respective content in A. bisporus, C. comatus, P. candolleana and V. gloiocephalus. K, Na and P concentrations in soils were associated to the content of several metals in fruit-bodies. The effect of soil texture on metals accumulation by mushrooms was species-dependent since high correlations were found for V. gloiocephalus and C. comatus only. Interactions between metals content in fruit-bodies seem to be species-specific except for Ni vs. Fe and Mn vs. Fe, which are positively correlated in all cases. Overaccumulation of metals in fruit-bodies was established only in respect to the bioavailable fractions of Cu, Mn, Zn and Ni in soil. The levels of toxicity for Pb were exceeded in mushrooms of five species, whereas the rest of the heavy metals (with the exception of Cu) were detected at lower contents than their recommended dietary allowances or tolerable upper intake levels.

Tuberpulchrosporum sp. nov., a black truffle of the Aestivum clade (Tuberaceae, Pezizales) from the Balkan peninsula

Knowledge on the diversity of hypogeous sequestrate ascomycetes is still limited in the Balkan Peninsula. A new species of truffle, Tuberpulchrosporum, is described from Greece and Bulgaria. Specimens were collected from habitats dominated by various oak species (i.e. Quercusilex, Q.coccifera, Q.robur) and other angiosperms. They are morphologically characterised by subglobose, ovoid to irregularly lobed, yellowish-brown to dark brown ascomata, usually with a shallow basal cavity and surface with fissures and small, dense, almost flat, trihedral to polyhedral warts. Ascospores are ellipsoid to subfusiform, uniquely ornamented, crested to incompletely reticulate and are produced in (1-)2-8-spored asci. Hair-like, hyaline to light yellow hyphae protrude from the peridium surface. According to the outcome of ITS rDNA sequence analysis, this species forms a distinct well-supported group in the Aestivum clade, with T.panniferum being the closest phylogenetic taxon.

Pleurotus opuntiae revisited - An insight to the phylogeny of dimitic Pleurotus species with emphasis on the P. djamor complex

The name Pleurotus opuntiae is indiscriminately used for describing mushrooms with white to off-white to white-grey pilei with short or absent stipe and dimitic hyphal system, which grow on plants of the genera Opuntia, Yucca, Agave, Phytolacca etc. However, the outcome of the present study evidences that this name should be reserved for specimens deriving from the Mediterranean area only; an epitype originating from Italy on Opuntia ficus-indica is designated. Pertinent material was sequenced by using the internal transcribed spacer region (ITS) and found to be phylogenetically related to P. djamor from Kenya and Nigeria, while members of the P. djamor complex from other continents were clearly more distant. Results were further corroborated by examining the large subunit of nuclear ribosomal DNA (LSU) and the second subunit of RNA polymerase II (RPB2). The P. djamor complex shows high intraspecific polymorphism evidenced by sequence divergence and genetic distance values, presents a cosmopolitan distribution and also comprises material initially identified as P. flabellatus, P. opuntiae, P. ostreatoroseus, P. parsonsiae and P. salmoneostramineus. An ITS tree including representative specimens from all major Pleurotus species is provided for the first time and ambiguous taxa are discussed in the context of new findings.

A reappraisal of the Pleurotus eryngii complex - new species and taxonomic combinations based on the application of a polyphasic approach, and an identification key to Pleurotus taxa associated with Apiaceae plants

The Pleurotus eryngii species-complex comprises choice edible mushrooms growing on roots and lower stem residues of Apiaceae (umbellifers) plants. Material deriving from extensive sampling was studied by mating compatibility, morphological and ecological criteria, and through analysis of ITS1-5.8S-ITS2 and IGS1 rRNA sequences. Results revealed that P. eryngii sensu stricto forms a diverse and widely distributed aggregate composed of varieties elaeoselini, eryngii, ferulae, thapsiae, and tingitanus. Pleurotuseryngii subsp. tuoliensis comb. nov. is a phylogenetically sister group to the former growing only on various Ferula species in Asia. The existence of Pleurotusnebrodensis outside of Sicily (i.e., in Greece) is reported for the first time on the basis of molecular data, while P. nebrodensis subsp. fossulatus comb. nov. is a related Asiatic taxon associated with the same plant (Prangos ferulacea). Last, Pleurotusferulaginis sp. nov. grows on Ferulago campestris in northeast Italy, Slovenia and Hungary; it occupies a distinct phylogenetic position accompanied with significant differences in spore size and mating incompatibility versus other Pleurotus populations. Coevolution with umbellifers and host/substrate specificity seem to play key roles in speciation processes within this fungal group. An identification key to the nine Pleurotus taxa growing in association with Apiaceae plants is provided.