Soymilk stability increase using polyphenols microcapsules.

Functional beverages have aroused a great interest to the food industry. Among the functional ingredients, there is a growing demand for antioxidant incorporation into foods, which implies a challenge to preserve their bioactivity. The health benefits provided by soymilk can be improved by the addition with microcapsules of polyphenols from peanut skin and this procedure is an alternative to protect these natural and bioactive compounds from environmental factors. The aim of this work was to determine the chemical, antioxidant, microbiological and sensory changes during storage of the product. Soymilk samples were prepared without any addition (C); with peanut skin extract (BEA); and with microcapsules with polyphenols (MCBEA) and stored at 4 °C for 30 days. Results showed that the addition of polyphenols (free or microencapsulated) improved the chemical, microbiological and sensory stability of soymilk. The BEA and MCBEA had lower values of hydroperoxides, hexanal, bacterial growth, oxidised flavour, and sweet taste than C. The BEA exhibited higher phenol content (819.72 mg gallic acid equivalents/L), antioxidant activity (64.66% DPPH inhibition) and colour intensity than MCBEA. The study suggested that polyphenol microencapsulation is a procedure that can protect these sensitive compounds and control their release into this food matrix.

Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa.

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

The relation of fibrosis stage with nutritional deficiencies and bioelectrical impedance analysis of body composition in patients with chronic hepatitis C.

UNLABELLED:  Background. Nutritional deficiencies may aggravate the course of chronic hepatitis C (CHC). Our aim has been to perform a comprehensive analysis of body composition and nutritional deficiencies in CHC patients in non-cirrhotic and compensated cirrhotic stages to correlate the detected deficiencies with the fibrosis stage. MATERIAL AND METHODS: Body multifrequency bioimpedance analysis (BIA) and a wide and simultaneous analytical profile were prospectively performed in 74 CHC patients (36 male) with known METAVIR fibrosis stage established with liver biopsy or transient elastography. Results were analyzed to identify deviations from the normal range and variations according to the fibrosis stage. RESULTS: Body fat compartment was greater in women. Body composition did not change among the 4 stages of liver fibrosis. Low levels (< 30 µg/L) of vitamin D were detected in 74.3% of patients irrespective of the fibrosis stage. Most analytical results remained into the normal range with the exceptions of thrombocytopenia and vitamin A deficiency, that were limited to the stage 4 of fibrosis, and low Zn and LDL-cholesterol values, that were frequently found in patients with advanced (F3 and F4) fibrosis stage. CONCLUSION: Body composition and most biochemical parameters, including cyanocobalamin, folic acid and vitamin E, are well preserved in compensated patients with CHC, with the exception of generalized vitamin D insufficiency and of deficiencies of vitamin A and zinc that are restricted to the more advanced, although still compensated, stages of the disease.

Molecular and morphological analyses confirm Rhizopogon verii as a widely distributed ectomycorrhizal false truffle in Europe, and its presence in South America.

The genus Rhizopogon includes species with hypogeous or subepigeus habit, forming ectomycorrhizae with naturally occurring or planted pines (Pinaceae). Species of the genus Rhizopogon can be distinguished easily from the other hypogeous basidiomycetes by their lacunose gleba without columella and their smooth elliptical spores; however, the limit between species is not always easy to establish. Rhizopogon luteolus, the type species of the genus, has been considered one of the species that are more abundant in Europe, as well as it has been cited in pine plantation of North and South America, different parts of Africa, Australia, and New Zealand. However, in this study, based on molecular analyses of the ITS nuclear ribosomal DNA (nrDNA) sequences (19 new sequences; 37 sequences from GenBank/UNITE, including those from type specimens), we prove that many GenBank sequences under R. luteolus were misidentified and correspond to Rhizopogon verii, a species described from Tunisia. Also, we confirm that basidiomes and ectomycorrhizae recently collected in Germany under Pinus sylvestris, as well as specimens from South of Brazil under Pinus taeda belong to R. verii. Thanks to the numerous ectomycorrhizal tips collected in Germany, a complete description of R. verii/P. sylvestris ectomycorrhiza is provided. Moreover, since in this paper the presence of R. verii in South America is here reported for the first time, a short description of basidiomes collected in Brazil, compared with collections located in different European herbaria, is included.

Combining morphological and phylogenetic analyses to unravel systematics in Geastrum sect. Schmidelia.

Systematics of the recently proposed Geastrum sect. Schmidelia are addressed through statistical analyses of quantitative morphological variables and phylogenetic reconstructions based on a multilocus approach. Emphasis is given to the taxonomic placement of G. schmidelii var. parvisporum. This variety is found to be not phylogenetically close to G. schmidelii var. schmidelii, the type species of G. sect. Schmidelia, and it therefore is excluded from this section, taxonomically raised to species rank (as G. parvisporum) and included as a member of G. sect. Hariotia. A second species in G. sect. Schmidelia is recognized and formally described as G. senoretiae. It is characterized by small basidiomata, non-hygrometric exoperidium, subsessile endoperidium and finely plicate, indistinctly delimited peristome, so far known only from Spain. Photographs and drawings are included, along with a comparison of morphologically close taxa. The presence of sclerified basidia in the mature gleba, previously not reported in the genus, is commented on.

Prevalence of Anisakiasis in Madrid (Spain) after 20 Years of Preventive Legislation.

Historical seroprevalence data for Anisakis in Spain vary greatly depending on the sampling region owing to different fish consumption habits. As a result of European Regulation (EC) No. 853/2004, the Royal Decree 1420/2006 on the prevention of parasitosis by Anisakis in fishery products supplied by establishments that serve food to final consumers or to communities came into force in Spain. In this study, a prevalence study of Anisakis in Madrid has been conducted to verify the prophylactic effects of the application of the law. Sera from 500 blood donors from the Fundación Jiménez Díaz University Hospital (Madrid/2021-2023) were collected, and the levels of anti-Anisakis IgG, IgA, and IgE were analyzed by ELISA, comparing them with those obtained with 110 donors from the Red Cross and the "Gómez Ulla" Central Defense Hospital (Madrid/2001-2002). The percentages of positivity in the 2021-2023 donor group were IgG (13.6%), IgA (13.6%), and IgE (2.2%), while in the 2001-2002 donors they were positive for IgG (15.45%), IgA (14.54%), and IgE (11.65%). A reduction of more than 80% was observed in the prevalence of anti-Anisakis IgE in the healthy population of Madrid, which confirmed the positive effect of RD1420/2006, which was later incorporated into RD1021/2022.

Towards a unified paradigm for sequence-based identification of fungi.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

Multilocus approach to species recognition in the Cladonia humilis complex (Cladoniaceae, Ascomycota).

PREMISE OF THE STUDY: The members of the Cladonia humilis complex are characterized by a well-developed primary thallus and broadly scyphose podetia. In the present study, this complex was phylogenetically analyzed to test the boundaries between the species and to determine the usefulness of the phenotypic characters to distinguish them. The species C. conista, C. cyathomorpha, C. hammeri, C. humilis, C. kurokawae, C. nashii, C. pulvinella, and C. subconistea were examined. METHODS: Four DNA loci were sequenced and analyzed to test the monophyly of the species. For the phylogenetic reconstructions, maximum parsimony, maximum likelihood, and Bayesian methods were employed. The genealogical sorting index was used to quantify the exclusive ancestry of the nonmonophyletic species on the tree. KEY RESULTS: The performed phylogenetic analyses showed that the C. humilis complex is not monophyletic. Cladonia nashii is not closely related to the remaining taxa within the complex. Seven monophyletic lineages were identified, most of which comprise specimens belonging to more than one chemotype. Cladonia hammeri and C. pulvinella are conspecific, and this taxon is not present in Europe. CONCLUSIONS: This study suggests that morphological characters and secondary metabolites have less taxonomical value than thought in the Cladonia humilis complex. Use of multilocus phylogeny is recommended to delimit species.

Real-time monitoring of biofilm growth identifies andrographolide as a potent antifungal compound eradicating Candida biofilms.

Candida species cause life-threatening infections with high morbidity and mortality rates and their resistance to conventional therapy is closely linked to biofilm formation. Thus, the development of new approaches to study Candida biofilms and the identification of novel therapeutic strategies could yield improved clinical outcomes. In the current study, we have set up an impedance-based in vitro system to study Candida spp. biofilms in real-time and to evaluate their sensitivity to two conventional antifungal groups used in clinical practice - azoles and echinocandins. Both fluconazole and voriconazole were unable to inhibit biofilm formation in most strains tested, while echinocandins showed biofilm inhibitory capacity at relatively low concentrations (starting from 0.625 mg/L). However, assays performed on 24 h Candida albicans and C. glabrata biofilms revealed that micafungin and caspofungin failed to eradicate mature biofilms at all tested concentrations, evidencing that once formed, Candida spp. biofilms are extremely difficult to eliminate using currently available antifungals. We then evaluated the antifungal and anti-biofilm effect of andrographolide, a natural compound isolated from the plant Andrographis paniculata with known antibiofilm activity on Gram-positive and Gram-negative bacteria. Optical density measures, impedance evaluation, CFU counts, and electron microscopy data showed that andrographolide strongly inhibits planktonic Candida spp. growth and halts Candida spp. biofilm formation in a dose-dependent manner in all tested strains. Moreover, andrographolide was capable of eliminating mature biofilms and viable cell numbers by up to 99.9% in the C. albicans and C. glabrata strains tested, suggesting its potential as a new approach to treat multi-resistant Candida spp. biofilm-related infections.

Two new species of Hydnum with ovoid basidiospores: H. ovoideisporum and H. vesterholtii.

Two new species of Hydnum, characterized by slender Hydnum rufescens-like basidiomes and ovoid to broadly ellipsoid basidiospores, are described from the Iberian Peninsula based on morphological and ITS molecular data. Hydnum ovoideisporum is distinguished by pilei with deep orange tones and strong preference for calcareous soil. It is widespread in the Iberian-Mediterranean area. Hydnum vesterholtii is characterized by its ocher to light ocher pileus, and nearly all the collections were made in the Pyrenees. Both ovoid-spored species are monophyletic well supported groups in the maximum parsimony and Bayesian ITS phylogenies, while the remainder of the samples assigned to H. rufescens s.l. and having globose basidiospores split into six well supported clades. The need to typify the name Hydnum rufescens is discussed, and a provisional key is given for the European taxa of Hydnum.

A new species of Hyphoderma (Meruliaceae, Polyporales) and its discrimination from closely related taxa.

Thirty-five corticioid collections from the Canary Islands and Azores Archipelago were examined morphologically and subjected to molecular phylogenetic analysis. These specimens, almost all collected on endemic and/or xerophilic vegetation, were similar in morphological and ecological characteristics to Hypochnicium prosopidis from the Sonoran Desert (Arizona, USA) and Hyphoderma amoenum. Thirty-seven new ITS nrDNA sequences from these specimens, including the nomenclatural type of the above-mentioned species, were obtained and aligned with homologous sequences from GenBank. These collections were distributed in two strongly supported monophyletic clades. However, similar patterns of morphological variability shared by specimens included in both clades and their differences with related species suggest that they should be described as a single new species. Therefore Hyphoderma macaronesicum is proposed. Studies will be required to test, in a more robust multilocus genealogical framework, whether these populations constitute two cryptic species or whether they are the same taxon. The position of Hypochnicium prosopidis in the resolved tree and its morphological characters suggest that it should be included in Hyphoderma and the new combination Hyphoderma prosopidis is proposed.

The diversity of Terfezia desert truffles: new species and a highly variable species complex with intrasporocarpic nrDNA ITS heterogeneity.

Desert truffles belonging to Terfezia are well known mycorrhizal members of the mycota of the Mediterranean region and the Middle East. We aimed to test (i) whether the morphological criteria of Terfezia species regularly collected in Spain enable their separation and (ii) whether the previously hypothesized edaphic/biotic specificity of one group could be confirmed by study of a larger number of specimens. The species T. arenaria and T. claveryi can be identified unambiguously by morphological characters. We consider T. leptoderma as a distinct species while several lineages of similar spiny spored Terfezia truffles with cellular peridium were detected that have no obvious anatomical differences. Several species treated generally as synonyms of T. olbiensis have been described in this group, and because they cannot be unambiguously assigned to separate lineages we propose to consider the group as the T. olbiensis species complex. A high level of intrasporocarpic variation of the nrDNA ITS was detected in the T. olbiensis species complex, especially in one of its lineages. We detected no exclusive specificity to either plant associates or soil, except in T. leptoderma, which was associated with Quercus spp. and cistaceous plants on acidic soils. Nevertheless the clades showed a tendency either to associate with Quercus/Helianthemum/Cistus or Pinus hosts. Specimens having distinct anatomical features, reticulate spores and cellular peridium formed a separate group in the molecular phylogenetic analyses of nrDNA ITS and LSU regions; for these specimens we propose a new species, Terfezia alsheikhii sp. nov.

Correction: Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.

[This corrects the article DOI: 10.1371/journal.pone.0237507.].

An Overview of 24 Years of Molecular Phylogenetic Studies in Phallales (Basidiomycota) With Notes on Systematics, Geographic Distribution, Lifestyle, and Edibility.

The order Phallales (Basidiomycota) is represented by gasteroid fungi with expanded and sequestrate basidiomata, known as stinkhorns and false truffles. In phalloids, the first DNA sequence was published in 1997, and after that, some studies aimed to resolve phylogenetic conflicts and propose new species based on DNA markers; however, the number of families and genera in the order still generates controversies among researchers. Thus, this work aims to provide an overview of Phallales diversity represented by selected DNA markers available in public databases. We retrieved Phallales sequences from DNA databases (GenBank and UNITE) of seven markers: ITS (internal transcribed spacer), nuc-LSU (nuclear large subunit rDNA), nuc-SSU (nuclear small subunit rDNA), mt-SSU (mitochondrial small subunit rDNA), ATP6 (ATPase subunit 6), RPB2 (nuclear protein-coding second largest subunit of RNA polymerase), and TEF1-α (translation elongation factor subunit 1α). To compose our final dataset, all ITS sequences retrieved were subjected to BLASTn searches to identify additional ITS sequences not classified as Phallales. Phylogenetic analyses based on Bayesian and maximum likelihood approaches using single and combined markers were conducted. All ITS sequences were clustered with a cutoff of 98% in order to maximize the number of species hypotheses. The geographic origin of sequences was retrieved, as well as additional information on species lifestyle and edibility. We obtained a total of 1,149 sequences, representing 664 individuals. Sequences of 41 individuals were unidentified at genus level and were assigned to five distinct families. We recognize seven families and 22 genera in Phallales, although the delimitation of some genera must be further revisited in order to recognize only monophyletic groups. Many inconsistencies in species identification are discussed, and the positioning of genera in each family is shown. The clustering revealed 118 species hypotheses, meaning that approximately 20% of all described species in Phallales have DNA sequences available. Information related to geographic distribution represents 462 individuals distributed in 46 countries on all continents, except Antarctica. Most genera are saprotrophic with only one putative ectomycorrhizal genus, and 2.1% of the legitimate specific names recognized in Phallales are confirmed edible species. Great progress in the molecular analyses of phalloids has already been made over these years, but it is still necessary to solve some taxonomic inconsistencies, mainly at genus level, and generate new data to expand knowledge of the group.

A re-evaluation of Hypochnicium (Polyporales) based on morphological and molecular characters.

Hypochnicium is a genus of corticioid, wood-inhabiting fungi in the Polyporales with a worldwide distribution. The genus has been characterized by the nature of the spores; they are thick-walled, smooth or ornamented, and cyanophilous. Nine new ITS nrDNA sequences from species of this genus were aligned with 32 sequences from GenBank, and phylogenetic analyses were performed. Six clades were determined within the genus; one contains taxa with smooth spores, and the other three with ornamented spores. Hypochnicium versatum must be included in Gloeohypochnicium, and the new combination Gloeohypochnicium versatum is proposed. Two new species, Hypochnicium michelii from Spain and Hypochnicium guineensis from Equatorial Guinea, are described.

Land use practices and ectomycorrhizal fungal communities from oak woodlands dominated by Quercus suber L. considering drought scenarios.

Oak woodlands in the Mediterranean basin have been traditionally converted into agro-silvo-pastoral systems and exemplified sustainable land use in Europe. In Portugal, in line with the trend of other European countries, profound changes in management options during the twentieth century have led to landscape simplification. Landscapes are dynamic and the knowledge of future management planning combining biological conservation and soil productivity is needed, especially under the actual scenarios of drought and increasing evidence of heavy oak mortality. We examined the ectomycorrhizal (ECM) fungal community associated with cork oak in managed oak woodlands (called montado) under different land use practices, during summer. ECM fungal richness and abundance were assessed in 15 stands established in nine montados located in the Alentejo region (southern Portugal), using morphotyping and ITS rDNA analysis. Parameters related to the montados landscape characteristics, land use history over the last 25 years, climatic and edaphic conditions were taken into account. Fifty-five ECM fungal taxa corresponding to the most abundant fungal symbionts were distinguished on cork oak roots. Cenococcum geophilum and the families Russulaceae and Thelephoraceae explained 56% of the whole ECM fungal community; other groups were represented among the community: Cortinariaceae, Boletaceae, Amanita, Genea, Pisolithus, Scleroderma, and Tuber. There were pronounced differences in ECM fungal community structure among the 15 montados stands: C. geophilum was the only species common to all stands, tomentelloid and russuloid species were detected in 87-93% of the stands, Cortinariaceae was detected in 60% of the stands, and the other groups were more unequally distributed. Ordination analysis revealed that ECM fungal richness was positively correlated with the silvo-pastoral exploitation regime and low mortality of cork oak, while ECM fungal abundance was positively correlated with extensive agro-silvo-pastoral exploitation under a traditional 9-year rotation cultivation system and recent soil tillage. The effects of land use on the ECM fungal community and its implications in different scenarios of landscape management options, oak mortality, and global warming are discussed.

Can NPK fertilizers enhance seedling growth and mycorrhizal status of Tuber melanosporum-inoculated Quercus ilex seedlings?

Although successful cultivation of the black truffle (Tuber melanosporum) has inspired the establishment of widespread truffle orchards in agricultural lands throughout the world, there are many unknowns involved in proper management of orchards during the 6-10 years prior to truffle production, and there are conflicting results reported for fertilizer treatments. Here, we systematically evaluate the combined effects of nitrogen, phosphorous, and potassium with different doses of each element, applied to either foliage or roots, on plant growth parameters and the mycorrhizal status of outplanted 3-year-old seedlings in five experimental Quercus ilex-T. melanosporum orchards. Fertilization did not significantly improve seedling aboveground growth, but the plants treated with the fertilizer 12-7-7 applied to the roots (HNr) displayed longer field-developed roots. Only the fertilizer with the highest dose of K (10-6-28) applied to the foliage (HKf) increased the probability of fine root tip colonization by T. melanosporum in field-developed roots. However, the plants treated with the same fertilizer applied to the soil (HKr) presented the highest probability for colonization by other competing mycorrhizal soil fungi. Potassium seems to have an important role in mycorrhizal development in these soils. Apart from T. melanosporum, we found 14 ectomycorrhizal morphotypes, from which seven were identified to species level, three to genus, two to family, and two remained unidentified by their morphological characteristics and DNA analyses.

Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.

DNA barcoding can identify biological species and provides an important tool in diverse applications, such as conserving species and identifying pathogens, among many others. If combined with statistical tests, DNA barcoding can focus taxonomic scrutiny onto anomalous species identifications based on morphological features. Accordingly, we put nonparametric tests into a taxonomic context to answer questions about our sequence dataset of the formal fungal barcode, the nuclear ribosomal internal transcribed spacer (ITS). For example, does DNA barcoding concur with annotated species identifications significantly better if expert taxonomists produced the annotations? Does species assignment improve significantly if sequences are restricted to lengths greater than 500 bp? Both questions require a figure of merit to measure of the accuracy of species identification, typically provided by the probability of correct identification (PCI). Many articles on DNA barcoding use variants of PCI to measure the accuracy of species identification, but do not provide the variants with names, and the absence of explicit names hinders the recognition that the different variants are not comparable from study to study. We provide four variant PCIs with a name and show that for fixed data they follow systematic inequalities. Despite custom, therefore, their comparison is at a minimum problematic. Some popular PCI variants are particularly vulnerable to errors in species annotation, insensitive to improvements in a barcoding pipeline, and unable to predict identification accuracy as a database grows, making them unsuitable for many purposes. Generally, the Fractional PCI has the best properties as a figure of merit for species identification. The fungal genus Ramaria provides unusual taxonomic difficulties. As a case study, it shows that a good taxonomic background can be combined with the pertinent summary statistics of molecular results to improve the identification of doubtful samples, linking both disciplines synergistically.

Linking morphological and molecular sources to disentangle the case of Xylodon australis.

The use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia-New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

Longistriata flava (Boletaceae, Basidiomycota) - a new monotypic sequestrate genus and species from Brazilian Atlantic Forest.

A new monotypic sequestrate genus, Longistriata is described based on collections from the Neotropical forest of Atlantic forest in Paraíba, Northeast Brazil - an area known for its high degree of endemism. The striking features of this new fungus are the hypogeous habit, the vivid yellow peridium in mature basidiomes, broadly ellipsoid basidiospores with a distinct wall that is ornamented with longitudinal striations and lageniform cystidia with rounded apices. Phylogenetic analysis, based on LSU and tef-1α regions, showed that the type species, Longistriata flava, is phylogenetically sister to the monotypic sequestrate African genus Mackintoshia in Boletaceae. Together these two species formed the earliest diverging lineage in the subfamily Zangioideae. Longistriata flava is found in nutrient-poor white sand habitats where plants in the genera Coccoloba (Polygonaceae) and Guapira (Nyctaginaceae) are the only potential ectomycorrhizal host symbionts.